Biology 10 Study Notes

Final Exam

2007-12-11T19:31:00.000-08:00

Biology 10 Fall 2007
Study questions 4.1

Lecture 20: Patterns of Inheritance and Lecture 21: Chromosomal inheritance

What is genetics?
Genetics: inheritance & how traits are passed from generation to generation

Who was Gregor Mendel?
Came up with the initial idea of genetics 1860's - the Principle of Segregation which described basic patterns of inheritance.

What did Mendel discover?
He studied genes for different types of trait (color) Genes have different forms, each person has two alleles for each trait, sex cells only have one gene/allele for traits so the alleles separate,

What were the strategies/approaches/ background he used that helped him to make his discoveries?

For a given single trait or gene, how many alleles does each cell of one individual usually have?
2

How many alleles for this trait would one gamete (a sperm cell or an egg cell) have?
1

Be able to state Mendel’s principle of segregation in simple terms.
According to the principle of segregation, for any particular trait, the pair of alleles of each parent separate and only one allele passes from each parent on to an offspring. Which allele in a parent's pair of alleles is inherited is a matter of chance. We now know that this segregation of alleles occurs during the process of sex cell formation

What does homozygous mean?
Same alleles for a gene - either both dominant or both recessive.

Heterozygous?
Different alleles for a trait - one dominant, one recessive

Dominant?
A type of phenotype

Recessive?

How do we represent alleles in writing? How are dominant alleles represented & how are recessive alleles represented?
BB, Bb, bb

What do homozygous dominant & homozygous recessive mean?
Homozygous dominant means that two dominant alleles were inherited for a trait (BB)
Homozygous recessive means that two recessive alleles were inherited for a trait. (bb)

What does genotype mean?
The exact genetic make up of an individual organism. Refers to the full hereditary information of an organism

What about phenotype?
The phenotype of an organism represents its actual physical properties, such as height, weight, hair color, and so on. It is the organism's physical properties that directly determine its chances of survival and reproductive output, while the inheritance of physical properties occurs only as a secondary consequence of the inheritance of genes. Therefore, to properly understand the theory of evolution via natural selection, one must understand the genotype-phenotype distinction.

What is the relationship between genotype and phenotype?
An organism's genotype is a major (the largest by far for morphology) influencing factor in the development of its phenotype, but it is not the only one. Even two organisms with identical genotypes normally differ in their phenotypes. One experiences this in everyday life with monozygous (i.e. identical) twins. Identical twins share the same genotype, since their genomes are identical; but they never have the same phenotype, although their phenotypes may be very similar. This is apparent in the fact that their mothers and close friends can always tell them apart, even though others might not be able to see the subtle differences. Further, identical twins can be distinguished by their fingerprints, which are never completely identical.

What is a Punnett square? What is it used for?
The Punnett square is a diagram designed by Reginald Punnett and used by biologists to determine the probability of an offspring having a particular genotype. It is made by comparing all the possible combinations of alleles from the mother with those from the father.

What do the letters along the top and side of the square represent?
The allele comginations of a trait of both the mother and the father. Father on top, mother on the side.

What do the paired letters within the squares represent?
The possible combinations of the parents alleles

For a simple F1 heterozygote vs. heterozygote cross (for example, Aa X Aa), what are the genotypic ratios and phenotypic ratios you expect to see in the offspring? (For example: How many AA vs how many Aa vs how many aa? Is this a genotypic or a phenotypic ratio?)
3 to 1 dominance - 1 homo dom, 2 hetero dom, 1 recess homo - This is genotypical

Be able to use the Punnett square to do any kind of simple cross and interpret the results.

What is a testcross and what is it used for? (If I gave you the results of a testcross, could you interpret these results?)
a procedure used especially in plant breeding whereby a plant's genetic constitution is inferred by examining the progeny resulting from crossing it with another individual of known genetic makeup
How do we represent a partially unknown genotype in writing?
A

What is the most common lethal genetic disease in the U.S.? Is this a recessive or a dominant genetic disorder? What are the symptoms of this disease?
Cystic Fibrosis - recessive
affects mainly the lungs and digestive system, causing progressive disability, and, for some, early death. Formerly known as cystic fibrosis of the pancreas, this entity has increasingly been labeled simply cystic fibrosis.[1] Average life expectancy is around 36.8 years, although improvements in treatments mean a baby born today could expect to live longer.[2]
Difficulty breathing and insufficient enzyme production in the pancreas are the most common symptoms. Thick mucus production, as well as a less competent immune system, results in frequent lung infections, which are treated, though not always cured, by oral and intravenous antibiotics and other medications. A multitude of other symptoms, including sinus infections, poor growth, diarrhea, and potential infertility (mostly in males, due to the condition Congenital bilateral absence of the vas deferens) result from the effects of CF on other parts of the body. Often, symptoms of CF appear in infancy and childhood; these include meconium ileus, failure to thrive, and recurrent lung infections.

What does it mean to say that someone is a carrier of a genetic disease?
It means that they carry a recessive allele for the disease and the potential to pass it on but do not have the disease itself.

What is sickle cell anemia? Is this a recessive or a dominant genetic disorder? What specific kind of change in a body/ a cell/ a molecule causes sickle cell anemia? What is the advantage of being a carrier of one sickle cell allele?
A genetically inherited disease that affects the protein polymers of the hemoglobin in red blood cell's cuasing them to take on elongated or jaggedly shaped cells rather than smoothly rounded cells. This results in abnormal clotting, vaso-occlusion (circulatory blockage) causing lack of oxygen, ischemia, and early mortality rates. It is a recessive disease but a heterozygous combination of the sickle cell alleles results in no manifestation of the disease but the potential to pass it on. As an advantage, heterozygous and homozygous alike are both immune to malaria.

Why are single-gene lethal disorders usually caused by recessive alleles rather than by dominant alleles?
Because of evolution/natural selection. Most species with this disease would die before they could reproduce so it is less common and have evolved into a recessive trait

What would be an example of an exception, and why is it possible for this lethal dominant allele to be passed from one generation to the next?
Huntington's disease - because they usually are in their mid - 3os before they get sick and have had children by that point.

As far as recessive disorders are concerned why are inbreeding or matings by close relatives generally not a good idea?
Because variation in traits would be limited and the likelihood of recessive combinations greater.

What is incomplete dominance?
Relationships described as incomplete or partial dominance are usually more accurately described as giving an intermediate or blended phenotype.

What genotype (homozygous dominant, heterozygous, homozygous recessive) would show the evidence of incomplete dominance?
heterozygous

What is an example in humans (from lecture or from lab) of incomplete dominance?

What are the four common blood types (= blood phenotypes) in humans?
AO
BO
ABO
O

How many different alleles are there for the blood type gene?
3 - ABO

How many alleles can one person have?
2

What are the possible genotype combinations (how many, what are they)?
AA, Ao, AB, BB, Bo, oo

What are the possible phenotype combinations (how many, what are they)?
A, B, AB, O

Which blood type is an example of co-dominance? (Note that co-dominance is a kind of incomplete dominance.)
AB

What is the cellular cause of the differences in blood types? (What occurs in/on cells that creates blood types? What makes A, B, AB and O blood types in/on cells?)
A chemical marker on the surface of the red blood cells called an antigen. They are different for A and B and absent in O. An AB type can receive either A, B or O type blood without ill effects, making them a universal recipient.

What happens if you give A type blood to a B type person? Why?
Antibodies reject the blood cells and cause abnormal clotting and death.

Which blood type is called the universal donor? Why?
O - because it has no antigens on its surface and can be accepted by any blood type.

Which blood type is called the universal recipient? Why?
AB - because it can take either A, B or O because it contains both A and B blood cells due to co-dominance, and O is a universal donor.

How can blood type information be useful in paternity testing?
It can only rule out the father in certain instances. For example - if a child is AB and the father a type O, it is impossible for him to have fathered the child. DNA testing is the only truly reliable source of paternity.

Be able to do a blood type Punnett square!

What is independent assortment?
Mendel's Second Law - the law of independent assortment; during gamete formation the segregation of the alleles of one allelic pair is independent of the segregation of the alleles of another allelic pair

How do chromosomes determine sex?
The chromosome X is carried only by females - XX. Men carry both XY. Therefore, whichever sperm inseminates the egg will determine the sex of the child.

What is a sex-linked trait or gene? (What chromosome are these genes usually found on?)
Traits (alleles) carried on the X or Y sex chromosome. They are usually found on the X but in rare instances, the Y

Can you give an example of a sex-linked trait?
Color blindness, hemophelia

What is the SRY gene, where is it found, and what does it determine?
It is a sex determining gene found on the Y chromosome

What is the pattern of inheritance seen for sex-linked genes? Why does it differ for males and females?
It is more common for males to inherit sex linked traits since they only need one x-linked trait to manifest the disease and women need 2 and sex linked genes are rare.

Be able to do a sex-linkage Punnett square.

How do we write the alleles for sex-linked traits? Can females have sex-linked traits? Why or why not?
BBx, AAy...rarely see above.

What is gene linkage? What is crossing over?
Genetic linkage occurs when particular genetic loci or alleles for genes are inherited jointly. Genetic loci on the same chromosome are physically connected and tend to segregate together during meiosis, and are thus genetically linked.

Chromosomal crossover (or crossing over) is the process by which two chromosomes, paired up during prophase 1 of meiosis, exchange some portion of their DNA. Crossing over is specifically initiated in pachytene, before the synaptonemal complex develops, and is not completed until near the end of prophase 1. Crossover usually occurs when matching regions on matching chromosomes break and then reconnect to the other chromosome. The result of this process is an exchange of genes, called genetic recombination.

What is nondisjunction? What type of birth defects can this lead to?
failure of chromosomal separation: a failure of paired chromosomes or sister chromatids to separate during cell division

Nondisjunction is the failure of homologous chromosome pairs to separate properly during meiosis or mitosis. The result of this error is a cell with an imbalance of chromosomes. When a chromosome is lost, it is called a monosomy, in which the daughter cell with the defect will have one or more chromosomes missing from one of its pairs. When a chromosome is gained, it is called a trisomy, in the case of a human gamete after nondisjunction in Meiosis II, it will have a set of 24 chromosomes instead of the usual 23.

Edward's Syndrome (trisomy 18),Down's Syndrome(trisomy 21), Turner's Syndrome(x), Klinefelter's syndrome (xxy),

What makes accidents during meiosis more likely?
The age of the mother.

How, in a general way, do changes in sex chromosome number affect humans, in comparison to changes in the number of other types of chromosomes?
Sex chromosome numbers do not result in retardation. Some physical symptoms are noted with Turner's syndrome but in most cases the difference is not notable.

Lecture 22: biotechnology (Chapter 16)
Why is it critical for biotechnology that DNA from all organisms is essentially the same kind of molecule?
Because it creates the possibility of creating recombinant DNA

What are some of the uses of biotechnology?
You can make virus or insect resistant organisms, delay ripening, BGH for milk production, transplant possibilities (pigs organs in humans), genetically leaner meats...(enzymes - detergents, foods, textiles...

What kinds of organisms do many of the enzymes used in biotech come from
From viruses

What is a virus? Are they alive? What are they made of?
submicroscopic parasitic particle of a nucleic acid surrounded by protein that can only replicate within a host cell. Viruses are not considered to be independent living organisms but some arguments exist that they are on the "edge of life".

How does a virus get itself replicated?
They use the machinery of the host cell to reproduce copies of themselves. They cannot replicate on their own because they are acellular.

What are some of the ways that virus DNA or RNA can get into a host cell?
Endocytosis (absorbed by mucous membranes or blood) from the external enviroment.

What happens to the host cell after many copies of the virus have been made?

How are simple RNA viruses like influenza different from complex RNA viruses (retroviruses)? What does a retrovirus do that is unusual?

What are restriction enzymes? What do they do & where do they come from? (Review: what kind of biological molecule are enzymes? What does the root –ase mean?)

In the separation of the two sides of a DNA double helix for the purpose of trying to find certain DNA, why are the molecules heated?

What happens as a result of this heating? (Review: What would happen to enzymes if you heated them?)
They would denature

What is gel electrophoresis and what does it do? Why do the small molecules move further in the gel than the large molecule?

What is a DNA fingerprint?

What is the purpose of PCR? What is the original source of the DNA polymerase that is used in PCR?

Lecture 23: Immune system
What is phagocytosis? What do cells do with bacteria that they take in?
Phagocytosis is cell eating

What is a pathogen?
An infectious or biological agent that causes disease or illness to its host.

What parts of the human body function as the first level of non-specific defenses against disease-causing agents, and how do these different defenses work? (What does each type do?)
Skin (barrier), mucous (capture, expel), cilia, (capture, expel), tears, saliva (flushing), urine, diarrhea (expel, flushing)

What is the general role of white blood cells in the body?
To protect the body from disease and infection

What does the word macrophages mean? What do natural killer cells do?
It means "big eaters"...they eat the damaged cells.

Natural killer cells detect irregular cells and puncture them and cause them to lyse.

Where are complement proteins found, and what do they do? Where do interferons come from, and what do they do?
Complement proteins are found in plasma and they enhance the immune system's response. When they encounter and antibody/antigen combination they change in form and signal other proteins to do the same - the enter the cell and kill it.

Interferons are complement proteins that inhibit the replications of affected cells.

What are some of the symptoms of the inflammatory response?
Redness, swelling, heat

Which symptoms are results of white blood cell activity?

What does histamine do?

Which symptom is a result of prostaglandin activity?

Why is fever a useful response?
Because heat can kill a virus or bacteria.

What are the advantages of having an immune system?

What does it mean to say that immunity is adaptive?
What type of molecules/ structures on B and T cells are used in the process of learning to recognize pathogens?
Where in or on the cell are these receptors found?

What is an antigen?

What is an antibody? (What is the type of antibody that is not called an antibody?)

What do antibodies do?

How many different antibody sequences can one person have? Why is it valuable to have many different types?

What happens after a B cell receptor binds to an antigen? What are clones? What actually kills the invading cells?
What is a memory cell? Are memory cells long-lived or short-lived?

What happens after a T cell receptor binds to an antigen? What do cytotoxic T cells do?
What types of cells do T cells attack? What do helper T cells do?

How do vaccinations (active immunization type) create resistance / immunity to disease?

What is the role of self-proteins on human cells?
Why is understanding self-proteins (such as MHC proteins) important for understanding some of the potential problems with organ donation?

What are some of the dysfunctions of the immune system?

Biology 10 Fall 2007
Study questions 4.2

Lecture 24: Human past and human future

What is gestation? How do gestation times in humans compare to those of other animals of similar size?

Why can the relative immaturity of humans at birth be seen as a compromise between the selection for increasing intelligence & the limitations on birth canal size? What is the relationship between human pairbonding & the relative immaturity of humans at birth?

What mammalian order do humans belong to? What event probably led to the adaptive radiation of the mammals?

How similar are we, genetically, to our closest non-human relatives, the chimpanzees?

What is a hominid? (You won’t need to know the term for the test, but you need to know that this group exists.)
What are some of the characteristics that separate hominids from the groups that are closely related to them?

Which apparently evolved first, upright posture or brain enlargement, in hominids?
What kind of evidence do we base this conclusion on?

Where does the fossil evidence suggested that Homo sapiens mostly evolved?
What kind of evidence has been used in establishing a common ancestry, from about 100,000 years ago, for all humans in our biosphere today?

What factors do scientists think have interacted to select for darkly pigmented skin in tropical regions? What factors have selected for lighter skin in northern/ less tropical parts of the world?

What is cultural evolution? How is it different from biological evolution?

What are some of the biological and ecological issues facing us in this new millenium?

What is biodiversity? How do human activities influence biodiversity and habitat availability?

How do introduced / non-native species affect the species normally found in a region?

Why (what are some of the reasons) does biodiversity matter?

Why is increasing human population potentially a concern, in terms of our effects on the planet and the other species on the planet?

What are biodiversity hot spots? Why are they so important?

2007-11-27T22:57:00.000-08:00

What is cell division?
It is the duplication of a cell into a parent and daughter cell

What are the purposes of cell division?
Reproduction and growth

How do sexual reproduction and asexual reproduction differ from one another? (How do the results of these two processes compare?)
Sexual reproduction requires 2 male and female organs and asexual reproduction can be done by oneself. Both result in the creation of new life.

What is a chromosome? Where did you get your original chromosomes? Where in the cell are they found?
A chromosome is the organized form of DNA in cells

How do chromosomes differ from chromatin?
Chromatin and protein make up a chromosome

What is chromatin? What is it for? What are chromatin & chromosomes made of? (Review: What kinds of biological macromolecules are these? Are they polymers? If so, what monomers are they made of?)
Nucleic acids and proteins

What are chromosomes for? When would you expect to see them? When would you not see them?

What are homologous chromosomes? How similar is one homolog to the other member of its pair?
Homologous chromosomes are either both dominant or both recessive and they are identical.

For a given pair of homologous chromosomes, where did you get each of them?
One from mom, one from dad.

How many chromosomes do humans usually have? How many pairs of chromosomes do humans usually have?
46 - 2 sets of 23

What are sister chromatids? When (during what phase of the cell cycle) are sister chromatids produced? How similar is one sister chromatid to the other sister chromatid that it is attached to?
Sister chromatids are identical copies of a chromosome. Compare sister chromatids to homologous chromosomes, which are the two different copies of the same chromosome that diploid organisms (like humans) inherit, one from each parent. In other words, sister chromatids contain the same genes and same alleles, and homologous chromosomes contain the same genes but two copies of alleles, each of which might or might not be the same as each other.

What are the stages of the cell cycle? (What is the cell cycle?)
Interphase, Prophase, Prometaphase, Metaphase, Anaphase, Telophase and Cytokinesis
IPPMATC - In pain, pup makes awful tiny cries

What occurs during the different stages?

Which stage are cells in most of the time?
Interphase - cell grows and collects nutrients needed for replication

What is the purpose of the S stage?
A full set of sister chromatids is created during the S subphase of interphase, when all the DNA in a cell is replicated. Identical chromosome pairs are separated into two different cells during mitosis, or cellular division.

How does mitosis differ from cytokinesis?
Mitosis is the prep process/duplication of dna, cytokinesis is the final stage where the duplicated material actual breaks apart

What are the basic functions of mitosis?
Duplication of the cellular material (dna, nuclei, expansion of cytoplasm, organelles.)

What are the 4 stages of mitosis? What happens in each?
prophase, metaphase, anaphase and telophase

What is the result or output of the mitotic division (& cytokinesis) of one cell?
1 identical daughter cell

How do the daughter cell/ cells produced by mitosis compare genetically to the original parent cell?
It is identical

How is the cell cycle controlled (in a general way)?

What kind of cell cycle malfunction causes cancers?
Mitosis

What is a tumor? How do chemotherapy & radiation work against cancer?
A tumor is a mass of cells caused by uncontrolled cellular division

Why aren’t non-cancerous body cells usually as badly affected by these treatments?
The tissues are affected but the treatments are targeted for areas of recognized uncontrolled growth.

What is meiosis?
Meiosis is cell division when it regards sexual reproduction

How does meiosis differ from mitosis?

What are gametes?

What is a zygote? What is the result or output of the meiotic division (& then cytokinesis) of one cell?

How do these daughter cells compare genetically to the original parent cell and to each other?

How many different possible gamete combinations could one human make?

What happens to homologous chromosomes during metaphase I of meiosis?

What happens to homologous chromosomes in anaphase I of meiosis?

What happens in crossing over?

What is nondisjunction? What is one possible consequence of nondisjunction?

Lecture 17: Cell cycle and cellular reproduction (Chapters 9 and 10)

2007-11-13T08:48:00.002-08:00

What is cell division? What are the purposes of cell division?
How do sexual reproduction and asexual reproduction differ from one another? (How do the results of these two processes compare?)
What is a chromosome? Where did you get your original chromosomes? Where in the cell are they found?
How do chromosomes differ from chromatin? What is chromatin? What is it for? What are chromatin & chromosomes made of? (Review: What kinds of biological macromolecules are these? Are they polymers? If so, what monomers are they made of?)
What are chromosomes for? When would you expect to see them? When would you not see them?
What are homologous chromosomes? How similar is one homolog to the other member of its pair? For a given pair of homologous chromosomes, where did you get each of them? How many chromosomes do humans usually have? How many pairs of chromosomes do humans usually have?
What are sister chromatids? When (during what phase of the cell cycle) are sister chromatids produced? How similar is one sister chromatid to the other sister chromatid that it is attached to?
What are the stages of the cell cycle? (What is the cell cycle?) What occurs during the different stages? Which stage are cells in most of the time? What is the purpose of the S stage? How does mitosis differ from cytokinesis? What are the basic functions of mitosis?
What are the 4 stages of mitosis? What happens in each? What is the result or output of the mitotic division (& cytokinesis) of one cell? How do the daughter cell/ cells produced by mitosis compare genetically to the original parent cell?
How is the cell cycle controlled (in a general way)? What kind of cell cycle malfunction causes cancers? What is a tumor? How do chemotherapy & radiation work against cancer? Why aren’t non-cancerous body cells usually as badly affected by these treatments?
What is meiosis? How does meiosis differ from mitosis? What are gametes? What is a zygote? What is the result or output of the meiotic division (& then cytokinesis) of one cell? How do these daughter cells compare genetically to the original parent cell and to each other?
How many different possible gamete combinations could one human make?
What happens to homologous chromosomes during metaphase I of meiosis? What happens to homologous chromosomes in anaphase I of meiosis?
What happens in crossing over?
What is nondisjunction? What is one possible consequence of nondisjunction?

Lecture 16: Respiratory systems (Organismal Respiration) (Chapter 37)

2007-11-13T08:48:00.001-08:00

What is the purpose of breathing?
To get oxygen into the body and CO2 out

Where does the oxygen that we breathe in go & what is it used for?
It is required for cellular respiration and the creation of ATP

Where does the carbon dioxide that we breathe out come from?
From the finalized process of cellular respiration

What are overall inputs and outputs of cellular respiration?
Glucose, oxygen - ATP and CO2

What is respiration?
Respiration is a gas exchange - O2 for CO2

What is gas exchange? What are the three stages of gas exchange? Where does each of these stages take place in humans?
Air in and out of lungs
Breathing-air in/out; Movement of gases into the blood stream; Cells take up O2 and release CO2

(What process is the oxygen used for? Where does the carbon dioxide come from?)
Cellular respiration - it is a waste product of cellular respiration

What is a respiratory surface? (What characteristic must respiratory surfaces have in order to function properly?)
A respiratory surface is where the gas exchange takes place - it must be moist

What do worms and amphibians use as their respiratory surfaces?
Their skin

What are the drawbacks of this solution?
They have to keep their skin moist

What do fish use as their respiratory surfaces?
Gills

What do terrestrial vertebrates such as lizards, birds and humans use as their respiratory surfaces?
Lungs

What is the major difference in location between our respiratory surfaces and those of fish? Why is this difference important?
Exterior versus interior. If our surfaces were on the outside we would need to keep them moist. Cuts down on water loss

What is the approximate area of the respiratory surface in an average human?

What are the parts of the human respiratory system? You should know all of these in order.
Nostrils or mouth, pharynx, larynx, adam's apple helps to stay open, trachea, bronchi, bronchioles, alveoli, capillaries

NMPLATBBAC - No man puts lust after the babes boobs are cupped

(What does the word root -ole seem to mean?)
opening or chamber

How many lungs does the average human have? In what part of the lung does gas exchange take place?
2. The alveoli

What are the alveoli?
Alveoli are small air sacs in the lungs

What are some of the ways in which smoking can affect the human respiratory system?
Alveoli are easily blocked or damaged by pollutants

What is vital capacity? What factors affect vital capacity?
Vital capacity is the maximum volume that we can inhale and exhale
Smoking, pollutants, disease

Explain how breathing can be both automatically and consciously controlled.
Breathing is controlled by centers in the brain. It is regulated by pH levels in the blood. CO2 causes pH levels to increase and it stimulates a contraction of the diaphragm to force a breath. However, we can consciously breathe, hold our breath etc.

Is it possible to hold your breath until you die? Why or why not?

Where are the centers of breath control? What are they called?
In the brain stem

What signal within the body do these centers respond to?
pH levels

What molecule is responsible for the transport of oxygen in the blood? (What type of biological molecule is this?)
Hemoglobin

In what kind of cell is this molecule found?
Red blood cell

Lecture 15: Circulation and Cardiovascular systems (Chapter 34)

2007-11-13T08:46:00.000-08:00

What is the purpose of a circulatory system?
Circulation: Transport of O2 & CO2 in the blood to & from all the body cells

What are capillaries?
Capillaries are small blood vessels, that allow blood to get to all the cells in the body.

How close is the average cell within your body to the nearest capillary?
About 1 cell wide

Why does this matter?
So that blood/O2 can get to cells or CO2 can get out via diffusion which is a slow process.

What are arteries?
Arteries are blood vessels that move blood away from the heart.

What are veins? (What would happen to a cancerous tumor if you were able to stop the growth of capillaries to that tumor? Why?)
Veins are blood vessels that take blood back to the heart and on to the lungs where C02 can be expelled. If capillaries surrounding a tumor could be blocked it would starve the tumor.

How many chambers does the human heart have?
4 - Left and right atria, Left and right ventricles

Do all animals have the same number of heart chambers? Why or why not? What are they called?
No - 2 for fish, 3 for amphibians - 3-4 for reptiles, and 4 for warm blooded mammals because it increases efficiency which is critical for warm blooded and more active animals.

Which chamber of the heart is the most heavily muscled – and why?
The left ventricle because it is pumping blood to all the body parts whereas the right is pumping blood only to the lungs which are located nearby.

What would happen to the heartbeat if a person ingested a poison that causes muscle paralysis? Why?
The heart would stop beating because it is a muscle.

What are the names of the four chambers of the human heart?
Left Ventricle, Right Ventricle, Left Atrium, Right Atrium

What are the blood vessels that go to and from the lungs called?
Pulmonary Artery and the Pulmonary Vein

What is the aorta and what is its function?
The aorta is the main artery that pumps blood from the heart to the entire body.

What do the valves in the heart prevent?
Valves in the heart prevent the blood from flowing back into the atria or ventricle.

What is a heart murmur?
A heart murmur occurs when one of the hearts valves are faulty and backflow of blood does occur.

What is the pacemaker and what is its function?
Pacemakers are implants that send small electrical charges to the heart to regulate its beating.

What causes/is a heart attack? (What are the coronary arteries? What is the function of coronary arteries?)
Coronary arteries carry blood away from the heart via the aorta. If they become blocked the pressure on the their walls will become severe and can result in a myocardial infarction.

What causes a stroke?
A blockage in an artery carrying blood/oxygen to the brain

What controls how severe a stroke is?
The area of the brain that is affected.

Why is high blood pressure dangerous?
Because it indicates an abnormal amount of pressure on the walls of the arteries

How does a high cholesterol diet increase the chance of high blood pressure?
Cholesterol can lead to a build up of plaque on the walls of the arteries which narrows the arteries resulting in the need to create more pressure on the vessel to force blood through.

Is low blood pressure a problem? Why or why not?
Yes, low blood pressure indicates that the heart is not beating as strongly as it should.
What is blood pressure?
Blood pressure is the measurement of the amount of pressure that blood puts on the walls of blood vessels.

What do the two numbers that are used to measure blood pressure indicate?
Systole indicates how much pressure is on the vessel when the heart is contracting
Diastole indicates how much pressure is on the vessel when the heart has relaxed

What would be an example of a normal blood pressure reading?
110/70

What are the different components of blood and what are their functions?
Red blood cells - carry oxygen to the body
White blood cells, platelets, plasma, proteins, ions, substances in transport

What do red blood cells do?
Red blood cells - carry oxygen to the body (hemoglobin binds to O2

What do white blood cells do?
Leukocytes-Considered part of immune system
made in bone marrow, may release proteins to fight infection, may help identify diseased cells, may engulf invader cells or diseased cells

Where are blood cells made?
In the bone marrow

What are some of the differences between red blood cells and white blood cells?

What is plasma & what is found in it?

What is a blood clot?
A blood clot is an accumulation of blood platelets (thrombus)

What components of the blood are important in forming blood clots?
Platelets & sticky stuff, plasma protein fibrinogen > fibrin

What kinds of defects in blood clotting systems are possible?
Hemophilia - a deficiency in the blood protein that causes clotting

What is leukemia? How is it treated?
Leukemia is uncontrolled replication of the wbc's. (cancer). They impair the creation of red blood cells in the marrow and cause clotting disorders.

What is the bone marrow and what is its function(s)?
Bone marrow is responsible for creating blood cells

(What are stem cells?)
Stem cells are primal cells that retain the ability to renew themselves through mitotic cell division and can differentiate into a diverse range of specialized cell types. Research in the stem cell field grew out of findings by Canadian scientists Ernest A. McCulloch and James E. Till in the 1960s.[1][2]
The two broad categories of mammalian stem cells are: embryonic stem cells, derived from blastocysts, and adult stem cells, which are found in adult tissues. In a developing embryo, stem cells can differentiate into all of the specialized embryonic tissues. In adult organisms, stem cells and progenitor cells act as a repair system for the body, replenishing specialized cells, but also maintain the normal turnover of regenerative organs, such as blood, skin or intestinal tissues.

What kind of cells do not have nuclei after they have differentiated (differentiated means become specialized/ finish developing)?
Red blood cells

Lecture 14: Nutrition and Digestion (Chapter 36)

2007-11-13T08:41:00.000-08:00

What are the basic reasons why animals such as humans need to eat?

Fuel for cellular respiration,
Fuel for cellular respiration
– E in bonds
Organic raw materials/ building blocks
– atoms & monomers
Essential nutrients (small)
– Prefab
– inorganic

What is the role of glucose?
Glucose is used by the body for energy in cellular respiration

What is the relationship between chemical energy and potential energy?

What is a kilocalorie?
Kilocalories are the measurement of of energy in food

What is BMR?
The basal metabolic rate is how many calories/or how much energy the body needs simply to exist

Why do animals need amino acids in their diet?
To build muscle and connective tissue

What are essential amino acids?
Essential amino acids are the building blocks of protein. There are 20 AAs, 8 of them are essential to the human diet (the body does not produce and must be obtained from an outside source.)

Why are some amino acids “inessential”?
Because some can be created by the body from other molecules or AAs.

What are complete and incomplete proteins?

Do humans eat (& digest) DNA? Why?
Yes, humans eat DNA. We need to consume nucleotides to build and repair RNA and DNA in cells.

What are vitamins for?
a vitamin is 'one of a group of organic substances, present in minute amounts in natural foodstuffs, that are essential to normal metabolism.' As defined, vitamins are present in very small quantities in most foods for people. Vitamins are also essential for life

What are water-soluble vitamins & how does your body get rid of excess water-soluble vitamins?
Water soluble vitamins C & B are absorbed in the body's bloodstream (water) and are not stored by the body but flushed away as waste material.

What are fat-soluble vitamins, and what happens to excess levels of fat-soluble vitamins? Why is this a problem?
Fat-soluble vitamins, A, D, E, and K are stored in the body's fat cells which can result in toxicity if more of the vitamin is consumed than the body can use.

What are essential minerals and what are some examples?
Essential minerals are inorganic materials that are a critical part of molecules and cellular reactions (ex: Fe)

What are some examples of nutritional disorders? What are some of the ways that diet can affect human health, including cardiovascular health & the likelihood of cancer?
Obesity, too much food. Malnutrition, not enough food or not the right kinds
Protein deficiency - vitamin B can be an issue because w/o it the body cannot create protein from amino acids.

Saturated fats play a role in heart disease too much LDL, alcohol intake related to cancer as well as fat intake - reservatol in wine may help with fats

What is ingestion?
Ingestion is the consumption of a substance by an organism.

What are omnivores, herbivores and carnivores?
Omnivores eat everything, herbivores eat only plant life, carnivores eat other living organisms other than plant life. (meat eaters)

What would be an example of a fluid feeder?
Fluid feeders are organisms that feed on the fluids of other animals or even plants. Examples of fluid feeders include:
Aphids
Ticks
Mosquitoes
Leeches
Hummingbirds

What are bulk feeders?
organisms that obtain food by eating pieces of other organisms or swallowing them whole

What, technically, does the word digestion mean?
Digestion is the process of metabolism whereby a biological entity processes a substance in order to chemically and mechanically convert the substance for the body to use.

What are two reasons why digestion is necessary?
To break down food into a form that the body can use it
To eliminate waste from the body

Do different organisms, in general, use the same monomers, or do different kinds of organisms (plants vs. animals, for example) use different kinds of monomers?
(Make sure you review and know what monomers are! And which polymers are made from which monomers!)
Animals do - plants do not

Where does digestion begin?
Digestion begins in the mouth - food starts to be broken down by our saliva

How is saliva useful in food processing and digestion?
To facilitate movement of the food through the mouth and along the tongue, it is necessary for saliva to be present. Usually, the sensations of sight, taste, and smell associated with food set in motion a series of neural responses that induce the formation of saliva by the salivary glands in the mouth.

What kinds of molecules are digested by saliva, and by what enzyme?
Amylase, an enzyme in the saliva, begins the process of breaking complex carbohydrates into simple sugars.

What monomer(s) would these molecules be broken down into?
Glucose

What other kinds of digestion occur in the mouth?
The physical breaking down of food by the teeth

What is the role of the tongue?
To manipulate the food in the mouth so that it is coated with saliva, can be chewed, and passed along to the pharynx

How does our body deal with the potentially dangerous situation that the food and breathing passages both open into the pharynx?
The trachea and the esophagus are in parallel alignment in the throat. The epiglottis works as a barrier which closes off the trachea when swallowing so that food is not allowed into the airway.

What happens when our bodies don’t deal with this situation properly?
We aspirate food - suck food particles into our airway and choke.

What is the role of the esophagus? Would the esophagus perform its role properly even if you were upside down?
The esophagus moves the bolus (masticated food) into the stomach by peristalsis. Yes, you can swallow if you are upside down because of peristalsis.

How does the esophagus function change during vomiting compare to esophagus function during ordinary food processing?
Reverse peristalsis. 2 sets of muscles one lenghtwise one crosswise move food to the stomach. In reverse peristalsis, these muscles can also force food back up through the esophagus.

When might vomiting be a useful response?
When one has consumed a poisonous substance

What is the primary role of the stomach?
To store and digest food

What property of the stomach allows us to eat and eat and eat at Thanksgiving?
The stomach is expandable and can hold up to two liters of food.

Is the pH of the stomach high or low?
The pH level of the stomach is high due to the presence of hydrochloric acid.

Why does this matter in digestion?
Because acids are necessary for breaking down food.

What ordinarily keeps the stomach contents from returning back into the esophagus?
The esophageal sphincter - sometimes is faulty or leaky and can result in acid reflux or heartburn

How long does the stomach ordinarily take to empty after a meal?
2 to 6 hours to empty

What substances are absorbed in the stomach?
Alcohol, aspirin, some drugs, caffeine

How do you think the effects (both good and bad) of these substances might differ depending on whether or not you’d eaten before ingesting them?
The rate of absorption would be slowed if you were to consume food before consuming drugs or alcohol.

What are the primary roles of the small intestine?
Chemical digestion and absorption.

What kinds of macromolecules are digested in the small intestine?
Carbohydrates, proteins, nucleic acids, fats

Why does the surface area of the small intestinal wall matter?
Because a large surface area is needed so that the maximum amount of nutrients can be absorbed into the bloodstream.

Does the small intestine have lots of surface area or minimal surface area?
The small intestine has a large surface area due to many folds, projections and microvilli.

Where do the various nutrients/molecules/monomers go after being absorbed by cells of the wall of the small intestine?
To capillaries that lie beneath the walls of the small intestine

And then where do they go after that?
Into the bloodstream and onward to cells for nourishment or fat for storage.

What is the function of the large intestine?
To reclaim water that would otherwise be lost, an to eliminate waste matter from the body.

What are the waste products of digestion called and what are they made of?
Feces. This waste is made up primarily of indigestible materials as well as water, salts, mucus, cellular debris from the intestines, bacteria, and cellulose and other types of fiber. Like the human body itself, these waste products are mostly water: about 75%, compared with 25% solid matter. Much of what goes into producing excrement has nothing to do with what enters the digestive system, so even if a person were starving he or she would continue to excrete feces.

If the large intestine cannot efficiently function, what is the result – and why?
We would not be able to eliminate waste material from our body.

Would this result ever be a good thing? Why or why not?
No, it would not be a good thing. The back up of bacteria would be detrimental to overall health and the mass of the feces would be extremely uncomfortable and could cause rupture. - perotonitis

In what way does the large intestine function similarly to the esophagus?
Peristalsis

Is elimination of waste products controlled by voluntary or involuntary muscles?
Both

Where are these control muscles found?
In the sphincter of the anus

Lecture 13: Animal Organization (Structure and Function) (Chapter 33)

2007-10-23T10:46:00.000-07:00

Lecture 13: Animal Organization (Structure and Function) (Chapter 33)

What does “structure fits function” mean? Give an example. What mechanism or process is responsible for the relationship between structures and their function?
That an organism's anatomy is adapted to meet its functional needs.

What is anatomy?
Anatomy is the study of the body's structure.

What is physiology?
Physiology is the study of how the body functions.

What are the levels in the hierarchy of animal structure?
Cell, Tissue, Organs, Organ Systems, Oganism

Which of these levels are present in a unicellular organism?
Cell

Which of these levels are present in a mouse or in a human being?
All

What is a tissue?
A group of cells with similar structure and function.

What are the four major types of tissues, and what would be examples of each type?
Epithelial Tissue - Skin
Connective Tissue - Tendons, ligaments, adipose tissue, blood, cartilage, bone
Muscle Tissue - Skeletal Muscle, Smooth Muscle (organ muscle), Cardiac Muscle
Nervous Tissue - Nerve cells, Neurons

What are some of the materials that animals exchange with their environment?
Oxygen and carbon dioxide
Water, Food - Excrement, Decomposed Tissue - puts nutirents back into the soil

How does the rate of diffusion of molecules across small distances compare to the rate of diffusion across large distances?
Diffusion is effective for short distances only.

What would happen to the inner cells of multicellular organisms if they had to rely on diffusion to get oxygen to those inner cells?
They would suffer from tissue death.

How do multicellular organisms solve this problem?

They have a circulatory system that carries oxygen to the cells.

What is homeostasis?

A biological state of balance.

Challenge Question: Why (specifically) do “warm-blooded” animals need more oxygen (for their size) than “cold-blooded” organisms do?

"Warm-blooded" animals stay warm by not sweating; by keeping the blood to the centre of their bodies; by covering their bodies in a thick layer of insulation; by shivering; by making heat energy in their vital organs. For a "warm-blooded" animal to stay warm in a cold environment requires energy. Therefore, these animals must eat more food and breathe more oxygen when the weather is cold.

Lecture 12: Cellular respiration

2007-10-23T10:44:00.000-07:00

Lecture 12: Cellular respiration (Chapter 8)

Cellular Respiration Overview Review Questions

What kinds of organisms have mitochondria?
Animals

Do plants have mitochondria?
Nope, they have chloroplasts.

What gas is produced by cellular respiration?
Carbon Dioxide

What gas is used/consumed during the process of cellular respiration?
Oxygen

How is fermentation different from cellular respiration?
Fermentation is done in an anaerobic environment and produces significantly less ATP.

How would you summarize the overall process of cellular respiration (what is the starting molecule? What is the goal?)?
Glucose - ATP

Why does this process have so many small steps?
To minimize the loss of energy.

From a cellular perspective, why is oxygen required for organisms like us?
So that we can synthesize the maximum amount of ATP

What do the terms aerobic and anaerobic mean?
Aerobic - in the presence of oxygen
Anaerobic - in the absence of oxygen

What is the first step that leads to the process of cellular respiration?
Glycolysis (includes the Preparatory Cycle that breaks down pyruvate to a 3 carbon molecule that is attached to an acetyl group.

What does this term mean?
It's Greek for Sweet Rupture. It refers to a breaking down of sugar/glucose molecules.

Where in the cell does this process occur?
In the cell cytoplasm

How much ATP does it produce? (A lot? A little?)
A little

What is the second step in the overall process of cellular respiration?
The Citric Acid Cycle

Where does it occur?
In the mitochondria

What are some of the important kinds of molecules produced during this step?
NADH, FADH, ATP,

What is the third step in the process of cellular respiration?
The Electron Transport Chain

What are high energy electrons used for during this process?
To move glucose electrons and pass them along where they meet up with O2, which then combines with hydrogen atoms and becomes water. As electrons move down their concentration gradient, energy is released and stored as ATP and later used for synthesis by chemiosmosis.

Why is energy needed to move H ions across the membrane in the first part of this process?
Because H+ movement into the mitochondria requires a form of active transport.

What kind of molecule do the H ions flow through in the final part of this process?
Oxygen

What molecule is produced as a result of energy released by the H ion movement? H2O

Why, specifically, is O2 required for this process?
Because they are electron carriers in this process.

Why is carbon monoxide (CO) such an effective poison?
What does an uncoupler do?
Because it stops hemoglobin from accepting oxygen molecules.

The mechanisms by which carbon monoxide produces toxic effects are not yet fully understood, but hemoglobin, myoglobin, and mitochondrial cytochrome oxidase are thought to be compromised.

In the absence of oxygen, what alternative processes do some cells run to get ATP?
Fermentation

How much ATP are these cells able to get?
2

What other molecules are produced as a result of these alternative processes?
Lactate, CO2. (alcohol in plants)

What would be produced if, while trying to use yeast to make wine, you pumped oxygen into the tank containing the mixture of grape juice and yeast? Why?
Grape juice.
Because you would stop the fermentation process by adding oxygen.

Lecture 11: Photosynthesis

2007-10-23T10:42:00.000-07:00

Lecture 11: Photosynthesis Photosynthesis & Cellular Respiration Overview Questions
In what parts of the cell do the processes of photosynthesis & cellular respiration occur?
Chloroplasts and mitochondria, respectively.

How does the role of chloroplasts in making energy available compare to the role of mitochondria in making energy available? (Review Q: How do chloroplasts & mitochondria compare in size to the cells of bacteria?)
They have opposite inputs and outputs with the exception that they both create ATP.
They both have aerobic and anaerobic methods for this process.

Smaller surface area to volume ratio makes the components for synthesizing ATP more quickly passable through cells.

Energy harvesting/ electron transport chains Review Q: what is chemical energy? What is potential energy?
Energy associated with the interaction of atoms in a molecule.
Stored energy in the form of starch, glycogen or adipose tissue.

Why is it important that electron transfers / electron transfer reactions occur in small steps?
To minimize the energy loss between transfers.

What is a concentration gradient?
Gradual change in chemical concentration from one point to another.

Electrons are passed from one electron carrier to another in a transport chain.
What specific work is the energy released by those electron transfers used to accomplish?
The creation of NADPH and ATP
In photosystem I - At the end of the electron transport chain lies the molecule nicotine adenine dinucleotide (NADP+). Using the energy released by the flow of electrons, two electrons from the electron transport chain combine with a hydrogen ion and NADP+ to form NADPH.

In Photosystem II, the electrons are passed through a different electron transport chain. As they pass along the cascade of electron carrier molecules, the electrons give up some of their energy to fuel the production of ATP, formed by the addition of one phosphorus atom to adenosine diphosphate (ADP).

What kind of macromolecule do the H+ ions move through to cross back through the membrane? (What is the name of this macromolecule? What does the name mean?)
Porin - a protein that makes up the outer wall of the mitochondria. It acts like a sieve and filters out larger molecules. The name means PORE.

Are the H+ ions moving up or down their concentration gradient as they move through this macromolecular passage? What is the energy released by their movement used for?
The H+ ions are moving down their concentration gradient.
The phosphorylization of ADP - making ATP

Photosynthesis specifically
What are the overall inputs and outputs of the two stages of photosynthesis?
Input - water, CO2
Output - Oxygen and Glucose

What kinds of organisms does photosynthesis take place in?
Plants and Algae

What organelle does photosynthesis take place in?
Chloroplast

What is the initial energy source for photosynthesis?
Solar energy

What kind of molecule is broken down to release the oxygen produced by photosynthesis?
Water

Why is this oxygen production important in the biosphere?
Because it supports the existence of organisms.

What kind of pigment molecule is most important in photosynthesis?
Chlorophyll

What wavelengths of light do plants mostly absorb?
Violet blue and orange

What wavelengths of light don’t plants absorb?
Green (yellow)

What is the 1st stage of photosynthesis?
The Light Reaction Cycle or The Light Dependent Cycle

PS I and PS II take place in this first phase.

What happens during this stage? (See the questions above about electron transfer chains to answer this question.)
The light dependent reaction produces oxygen gas and converts ADP and NADP+ into the energy carriers ATP and NADPH.

What are some of the ways that herbicides could disrupt this process?
Herbicides can block energy transfer by inhibiting the enzymes ability to catalyze a chemical reaction. Some herbicides punch a hole in the plant membrane, ruining the gradient.

What are the products (outputs) of this first stage?
The energy carriers ATP and NADPH.

Where do these products go next, and why? The energy carriers ATP and NADPH. They move on to the Stroma for the Calvin Cycle where they use ATP/NADPH and carbon dioxide to produce sugar.

What gas is released when water is split to provide a new electron for chlorophyll?
Oxygen

Why do shade plants need more antenna chlorophyll than sun plants? How can you tell that a shade plant has more antenna chlorophyll (and reaction center chlorophyll) than a sun plant?
Because the antenna are light harvesting tools for the plant and they need to make the most of any light available to them. Their leaves are thinner and usually darker.

What other kinds of pigments are important in photosynthesis? What is their function? How, specifically, do they dissipate (=get rid of) the excess energy? When and where would you see evidence of the existence of these pigments? Carotenoids - oranges, red, golds
They disperse excess energy as heat
In the fall when chlorophyll starts to break down

What is the 2nd stage of photosynthesis?
The Calvin Cycle or The Light Independent Cycle

What products of the light reactions are used in this second stage?
ATP and NADPH

What atmospheric molecule is taken up during this stage?
CO2

What is the most common protein on earth and what is its function?
With regard to plants and algae - it is Rubisco

RuBisCO, is an enzyme that is used in the Calvin cycle to catalyze the first major step of carbon fixation, a process by which the atoms of atmospheric carbon dioxide are made available to organisms in the form of energy-rich molecules such as sucrose.

RuBisCO is apparently the most abundant protein in leaves, and it may be the most abundant protein on Earth.

What is the product of this stage of photosynthesis?
Glucose

How does carbon dioxide get into leaves?
through the stomata - small openings on the underside of a plant's leaves.

What is the disadvantage of this process?
Water loss

What are some of the ways that plants have evolved to get around the disadvantages of stomatal opening?
C4 Photosynthesis : C4 plants.
Stomata are open during the day.
Photosynthesis takes place in inner cells (requires special anatomy called Kranz Anatomy)
Adaptive Value:
Photosynthesizes faster than C3 plants under high light intensity and high temperatures because the CO2 is delivered directly to RUBISCO, not allowing it to grab oxygen and undergo photorespiration.
Has better Water Use Efficiency because PEP Carboxylase brings in CO2 faster and so does not need to keep stomata open as much (less water lost by transpiration) for the same amount of CO2 gain for photosynthesis.

CAM Photosynthesis : CAM plants. CAM stands for Crassulacean Acid Metabolism
Called CAM after the plant family in which it was first found (Crassulaceae) and because the CO2 is stored in the form of an acid before use in photosynthesis.
Stomata open at night (when evaporation rates are usually lower) and are usually closed during the day. The CO2 is converted to an acid and stored during the night. During the day, the acid is broken down and the CO2 is released to RUBISCO for photosynthesis
Adaptive Value:
Better Water Use Efficiency than C3 plants under arid conditions due to opening stomata at night when transpiration rates are lower (no sunlight, lower temperatures, lower wind speeds, etc.).
May CAM-idle. When conditions are extremely arid, CAM plants can just leave their stomata closed night and day.

What are the disadvantages of these solutions?
Limited photosynthesis

What kinds of plants use these different solutions?
C4 - Many Summer Annuals and Corn
CAM - Cactus, Bromeliads, some Orchids...

Lecture 10: Biodiversity

2007-10-23T09:24:00.000-07:00

Lecture 10: Biodiversity (the short version)

How long ago did life apparently appear on earth?
Approximately 3.5 billion years ago

What are the two domains of prokaryotes?
What are some of the especially extreme forms of Archaea?
Bacteria and Archaea
Archaeans may be the only organisms that can live in extreme habitats such as thermal vents or hypersaline water. They may be extremely abundant in environments that are hostile to all other life forms. However, archaeans are not restricted to extreme environments; new research is showing that archaeans are also quite abundant in the plankton of the open sea. Much is still to be learned about these microbes, but it is clear that the Archaea is a remarkably diverse and successful clade of organisms.
Examples: Halobacteria survive in extreme salinity, Methanobacteria-high temps, Thermoproteus - live in sulfur

What are eukaryotes? What kingdoms of organisms are eukaryotes?
Eukaryotes most likely evolved from prokaryotes. They are the organisms of the 5 kingdom domain Eukarya - Plants, Animals, Algae, Fungi and Protista. They share similar microstructures such as DNA, nucleus, ATP

What are some of the characteristics of members of the plant kingdom?
Photosynthesis, cellulose, sexual reproduction, multi celled

What are some of the characteristics that plants evolved as they adapted to land? Non-flowering plants, more effective seed dispersal, seed coatings for protection from enironmental changes, evolution of leaf characteristics to slow water loss, absorb more sun...

What are some of the characteristics of members of the fungal kingdom?
Thin and threadlike (hyphae), can mass together, can thread into the body of another organism, reproduce by spores, they can be harmful or useful.

What are some of the characteristics of members of the animal kingdom? Where do they digest their food?
Multicellular, heterotrophs, internal digestion, embryological development pattern lots of diversity.

What are some examples of some of the simplest kinds of animals
Sponges, Cnidarians, Hydras, Jellies, Sea Anemones, Coral,

Where do they mostly live?
Aquatic environments - salt water

What does this suggest about where the ancestors of animals probably lived?
That they lived in an aquatic environment as well.

What characteristic (hint: it is related to how their embryos develop) is shared by mollusks, annelids, and arthropods?
In embryological development, these organisms make their mouths first.

Can you give at least one example of each of these phyla (= plural of phylum, btw)?
Mollusk: snail, slug, clam, octopus, squid
Annelids: earthworms, leeches, marine worms
Arthropods: Spiders, lobsters, barnacles, ticks, millipedes
Insects

Which of these phyla is the most diverse/ has the most species?
Insects

Which of these three phyla includes the most intelligent animal species found in any of these three groups?
Insects

What characteristic is shared by all arthropods?
An exoskeleton

What characteristic is shared by echinoderms and chordates? (Hint: it is also related to how their embryos develop.)
They make their anuses first.

Which of these phyla do we belong to?
Chordates

Can you give one example of an echinoderm?
Sea urchin, sea star, sea cucumber

What sub-phylum do we belong to within the Phylum Chordata? What characteristic gives our sub-phylum its name?
We belong to the sub-phylum vertebrates. Vertebrates share the formation of skulls and backbones, endoskeletons, hinged jaws,

What are the six major groups within our sub-phylum?
Mammals, Bony Fish, Cartilaginous Fish, Amphibians, Reptiles, Birds

What are some of the characteristics that adapted reptiles for life on land?
Scaly waterproof skin, amniotic egg(can lay on land), behavior to regulate body temperature.

What are some of the characteristics that reptiles share with birds?
Eggs, scales, anatomy

What are the characteristics of mammals?
Fur, mammary glands, self-regulating body temperature, internal embryonic development.

What are some of the characteristics that mammals share with reptiles?

What is a monotreme and how is both like reptile and like a mammal?
Animals that lay eggs instead of give live birth. Reptile: they lay eggs. Mammal: they are warm blooded, they have mammary glands, they have fur.

Lecture 9 (Chapter 6): Energy and Enzymes

2007-10-23T08:40:00.000-07:00

Lecture 9 (Chapter 6): Energy and Enzymes

How is matter different than energy?
Energy does not have mass or take up space.

What is energy?
Energy is the capacity to do work and bring about change; occurs in a variety of forms.

What is potential/stored energy?
It is stored energy, often in the form or glycogen which is broken down by glycolysis and then the citric acid cycle or fermentation or it can be stored in the form of fat/adipose tissue which is broken down by hydrolysis, glycolysis and the citric acid cycle. (I think, anyway...researching)

Where is energy stored in molecules?
Energy is stored in the covalent bonds of molecules.

How does the energy get out?
Energy is released when the covalent bonds it is stored in are broken.

What happens (in terms of energy usage, storage or release) when chemical reactions rearrange matter?

What is cellular respiration & how does it relate to energy storage & release?
It is the cell's way of releasing a stored form of energy and synthesizing it to a much more easily used form of E.

How does photosynthesis relate to energy storage & release?
It converts energy from sunlight into a form of chemical energy and stores it as starch.

What is ATP used for?
ATP is a usable form of chemical energy in a cell, created from glucose.

What is the ATP cycle?

What bond is broken (or created) during the ATP cycle?

The tri-phosphorous bone. ATP is broken down to ADP and P.

What happens when that bond is broken? (What would you expect to happen to the ATP cycle if the available supply of phosphorus/phosphate in the cell was very very low?)
Energy is released.
I would expect to see lower amounts of energy in the organism.

What is an enzyme?
Enzymes are a special kind of protein.

What do enzymes do?
Enzymes speed up or catalyze chemical reactions.

What features of an enzyme determine the specific function it can perform? (What would happen to enzyme function if you changed the amino acid sequence of the protein? Why?)
The shape/structure of an enzyme determines the specific feature it can perform. If the arrangement of the groups on the active site was even slightly different, a substrate wouldn't fit the active site on the enzyme.

What is the active site?
Active sites are cracks or hollows on the surface of the enzyme caused by the way the protein folds itself up into its tertiary structure. Molecules of just the right shape, and with just the right arrangement of attractive groups (see later) can fit into these active sites. Other molecules won't fit or won't have the right groups to bind to the surface of the active site.

What happens at the active site?
It is where the substrate binds and where the reaction occurs. In biology and biochemistry, the reactant in an enzyme reaction is known as the substrate. (consider competitive and non-competitive inhibition)

What kinds of cellular/environmental factors can affect enzyme function? Incompatible pH levels or temperatures will affect enzyme function by affecting their ability to maintain their structures (see denaturing).

What are co-factors & co-enzymes? Give an example.
Coenzyme - FAD, NAD+, NADP
Nonprotein organic molecule that aids the action of the enzyme to which it is loosely bound.
Cofactor
Nonprotein adjunct required by an enzyme in order to function; many cofactors are metal ions, others are coenzymes.

What do enzyme inhibitors do?
They stop enzymes from binding with their substrates.

Give an example. Major example below...but also weed killers, poisons, etc.
Feedback Inhibition
The first step in the citric acid (TCA) cycle involves combining acetyl CoA with a molecule of oxaloacetate or oxaloacetic acid to form a molecule of citric acid or citrate.
The enzyme which catalyzes this step, citrate synthase, is inhibited by ATP. When the cell has a low concentration of ATP, in other words, is low in energy, the citric acid (TCA) cycle operates, feeds the electron transport chain, and ATP is produced. As the energy store of the cell builds up and the concentration of ATP increases, the TCA cycle or citric acid cycle shuts down because the ATP inhibits the citrate synthase and stops the formation of citrate (or citric acid) which is needed for the cycle to operate.

How are competitive inhibitors different than non-competitive inhibitors?
There are some important differences between competitive inhibition and feedback inhibition.

In competitive inhibition the inhibitor is similar in structure to the substrate and binds to the enzyme at the active site, preventing the substrate from binding.

In feedback inhibition, the inhibitor binds to the enzyme at a site away from the active site and acts by altering the shape of the enzyme in such a way that it is incapable of catalyzing the reaction.

Feedback inhibition is a natural part of the process by which an organism regulates the chemical reactions that take place in its cells. In that sense it is done on purpose. Competitive inhibition usually involves inhibitors, commonly called poisons, that do not belong in the cell.

Lecture 8 (Chapter 5) Membrane Structure and Function

2007-10-23T07:40:00.000-07:00

Lecture 8 (Chapter 5) Membrane structure and function

Which two kinds of biological macromolecules make up the structure of biological membranes?
Lipids and proteins

How does the structure of the membrane make it difficult for some kinds of molecules to pass through the membrane?
The cell membrane is selectively permeable.

Can water pass directly through the lipids of the membrane? Why should you expect that it would not be able to do so?
Water, while polar, is small enough to freely move across the plasma membrane. One would think that the hydrophobic tails of the inner layer of membrane would either impede or inhibit water's movement into the cell and that active transport would be required, rather than the passive transport method of osmosis.

(Review: What are polar and non-polar molecules? What does it mean to say that a molecule is hydrophobic?)
Electrons are not always shared equally between two bonding atoms: one atom might exert more of a force on the electron cloud than the other. This "pull" is termed electronegativity and measures the attraction for electrons a particular atom has. The unequal sharing of electrons within a bond leads to the formation of an electric dipole: a separation of positive and negative electric charge.
Atoms with high electronegativities - such as fluorine, oxygen, and nitrogen - exert a greater pull on electrons than atoms with lower electronegativities. In a bonding situation this can lead to unequal sharing of electrons between atoms as electrons will spend more time closer to the atom with the higher electronegativity.
Bonds can fall between one of two extremes - being completely non-polar or completely polar. A completely non-polar bond occurs when the electronegativities are identical and therefore possess a difference of zero. A completely polar bond is more correctly termed ionic bonding and occurs when the difference between electronegativities is large enough that one atom takes an electron from the other. The terms "polar" and "non-polar" bonds usually refer to covalent bonds. To determine the polarity of a covalent bond using numerical means, the difference between the electronegativity of the atoms is taken. If the result is between 0.5 and 2 then, generally, the bond is polar.

A molecule is hydrophobic if it is not soluble in water. Hydrophobic molecules are non-polar meaning

What might we expect to happen to membranes at very high temperatures? Why? (Think about what happens to margarine or butter at high temperatures.)
Membranes consist of mainly lipids and proteins. In high temperatures we could expect that they would not be able to maintain their structure. (proteins are denatured and lipids melt as bonds are dissolved)

What are some of the functions of membrane proteins?
On the outside of the membrane: glycoprotein transport, cellular id, receptors that can grab certain molecules.
On the inside of a membrane: Enzymes catalyze the chemical reactions in response to outside signals.

What is diffusion? Does it require energy or not?
When molecules spread randomly from areas where they are highly concentrated to areas where they have a lower concentration (passive transport). No energy is needed for this reaction.

What is a concentration gradient?
The graduated difference in concentration of a solute
A concentration gradient—a smooth decrease in concentration from high to low

Which two types of molecules mostly move in and out of cells by diffusion?
Water and oxygen

What is osmosis?
Osmosis is a special type of diffusion where water molecules cross the plasma membrane.

What kind of molecule undergoes osmosis?
Water

Compared to proteins, are these molecules large or small?
Smaller?

What are the requirements for osmosis?
A hypotonic or hypertonic environment for the cell.

Does osmosis require energy input?
Nope

What does it mean that water “follows the solutes”? Review: What are solutions, solutes, and solvents?
Water goes where the concentration of a solute is high so that it can disperse it.
Solute
Substance that is dissolved in a solvent, making a solution.
Solution
Fluid (the solvent) that contains a dissolved substance (the solute)
Solvent
Liquid portion of a solution that serves to dissolve the solute.

What is facilitated diffusion?
When molecules are too large or polar, a carrier protein will provide large pores so that the molecule can pass through the membrane.

What kinds of molecules or macromolecules facilitate this kind of diffusion?
Protein

(What does facilitate mean?) Does this process require energy or not?
Facilitate means to make possible and although the name suggests otherwise, it does not require energy.

What is the driving force for facilitated diffusion? This means: what makes facilitated diffusion work? What is a concentration gradient? (Gee, I wonder if that is a clue.)
The driving force of facilitated diffusion is the concentration gradient of the cell environment.

What is active transport? Does this process require energy or not?
It is the transport(pumping) of molecules against a concentration gradient (from regions of low concentration to regions of high concentration) with the aid of proteins in the cell membrane and energy from ATP.

How does active transport work?
Proteins involved in active transport are called pumps because just as a water pump uses energy to move water against the force of gravity, proteins use energy to move a substances against its concentration gradient. One type of pump that is active in all animal cells and is especially associated with nerve and muscle cells, moves sodium ions (Na+) to the outside of a cell and potassium ions K+ to the inside of a cell. These events are linked and the carrier protein is called a sodium-potassium pump.

What kinds of molecules (macromolecules) are involved in helping active transport happen?
Proteins/carrier proteins

What are exocytosis and endocytosis?
Exocytosis is a process in which an intracellular vesicle fuses with the plasma membrane so that the vesicle's contents are are released outside the cell.

Endocytosis is a process by which substances are moved into the cell from the environment by phagocytosis (cellular eating) or pinocytosis (cellular drinking).

How are they the same and how are the different from each other?
(Why are these two processes important in the transport of really big molecules or structures?)
They are both accomplished by the formation of vesicles at the plasma membrane. It is the way that large molecules are able to enter or exit a cell.

Do exocytosis and endocytosis require energy or not?
Yes

2007-10-23T06:20:00.000-07:00

Lecture 7 (Chapter 4): Cells! Cell structure and function

How big are the biggest cells?
A frog’s egg is the biggest cell at 1mm - I have no idea if this is the right answer.

How does the size of mitochondria compare to the size of the average bacterial cell?
It is comparable in size because mitochondria is believed to have evolved from bacteria.

Why does the surface area to volume ratio matter?
Because the larger the cell, the longer it takes for molecules to get to the center of it. Smaller cells have less distance to be traveled.

(Is diffusion to the center of a cell faster in small cells or in large cells?
Faster in smaller cells

In terms of size and structure, how do prokaryotic cells compare to eukaryotic cells?
Prokaryotic cells are smaller and simpler. They do not have a membrane bonded nucleus, they have no organelles. They do have a nucleoid region, and DNA.

What structures do eukaryotic cells have that prokaryotic cells do not?
They do not have a membrane bonded nucleus, they have no organelles. They do have a nuclear circle/region, and DNA.

What is an organelle?
Normal structures responsible for energy production in cells. In animals, mitochondria. In plants, chloroplasts. Mitochondria are located in the cytoplasm outside the nucleus of the cell. They consist of two sets of membranes, a smooth continuous outer coat and an inner membrane arranged in tubules or in folds that form plate-like double membranes (cristae).
The mitochondria are the principal energy source of the cell (thanks to the cytochrome enzymes of terminal electron transport and the enzymes of the citric acid cycle, fatty acid oxidation, and oxidative phosphorylation). The mitochondria convert nutrients into energy as well as doing many other specialized tasks.
Each mitochondrion has a chromosome composed of DNA that is otherwise quite different from the better known chromosomes in the nucleus. The mitochondrial chromosome is much smaller. It is round (whereas the chromosomes in the nucleus are shaped like rods). And there are many copies of the mitochondrial chromosome in every cell (whereas there is normally only one set of chromosomes in the nucleus).
No matter whether we are male or female, we inherit our mitochondrial chromosome from our mother. In other words, the mitochondrial chromosome is transmitted in a matrilinear manner. We have Eve to thank for our mitochondrial chromosome.

What is cellular metabolism?
The chemical activity of cells

What are 3 differences between plant cells and animal cells?
Differences between plant and animal cells reflect ancestry and function.
Plants have cellulose
Chloroplasts
Flagellum and centrioles

What is the role of the nucleus?
The nucleus is the cells genetic control center

What important kind of macromolecule is found there?
Nucleic Acids – particularly DNA - RNA goes back and forth

Does this macromolecule contain nitrogen or not?
Yes

What is the nuclear envelope? What is a nuclear pore & what is its purpose?
A double membrane that surrounds the nucleus in eukaryotic and is connected to the endoplasmic reticulum, has pores that allow substances to pass between the nucleus and the cytoplasm.

A nuclear pore is an opening in the nuclear envelope that permits the passage of proteins into the nucleus and ribosomal subunits out of the nucleus.

What is the role of the rough ER (endoplasmic reticulum)?
The endoplasmic reticulum manufactures, processes, and transports a wide variety of biochemical compounds for use inside and outside of the cell. Consequently, many of the proteins found in the cisternal space of the endoplasmic reticulum lumen are there only transiently as they pass on their way to other locations. Other proteins, however, are targeted to constantly remain in the lumen and are known as endoplasmic reticulum resident proteins. These special proteins, which are necessary for the endoplasmic reticulum to carry out its normal functions, contain a specialized retention signal consisting of a specific sequence of amino acids that enables them to be retained by the organelle. An example of an important endoplasmic reticulum resident protein is the chaperone protein known as BiP (formally: the chaperone immunoglobulin-binding protein), which identifies other proteins that have been improperly built or processed and keeps them from being sent to their final destinations.

There are two basic kinds of endoplasmic reticulum morphologies: rough and smooth. The rough endoplasmic reticulum is involved mainly with the production and processing of proteins that will be exported, or secreted, from the cell. The ribosomes assemble amino acids into protein units, which are transported into the rough endoplasmic reticulum for further processing. These proteins may be either transmembrane proteins, which become embedded in the membrane of the endoplasmic reticulum, or water-soluble proteins, which are able to pass completely through the membrane into the lumen. Those that reach the inside of the endoplasmic reticulum are folded into the correct three-dimensional conformation, as a flattened cardboard box might be opened up and folded into its proper shape in order to become a useful container. Chemicals, such as carbohydrates or sugars, are added, then the endoplasmic reticulum either transports the completed proteins to areas of the cell where they are needed, or they are sent to the Golgi apparatus for further processing and modification.

It is the rough endoplasmic reticulum that is directly continuous with the nuclear envelope (as illustrated in Figure 1), which is also studded with ribosomes, and the two organelles are thought to have evolved simultaneously in ancient cells.

What do the roots endo, plasm, and reticulum mean?
Endo: within (gk-endon)
Plasm: formative or formed material (as of a cell or tissue) (German -plasma)
Reticulum: A netlike formation or structure; a network (Lat diminutive of rete, meaning "net")

What makes the rough ER look rough?
The surface of rough endoplasmic reticulum is covered with ribosomes, giving it a bumpy appearance when viewed through the microscope.

What are the roles of the smooth ER?
Most proteins exported from the endoplasmic reticulum exit the organelle in vesicles budded from the smooth portion, which has a more even appearance than rough endoplasmic reticulum when viewed through the electron microscope because of the lack of ribosomes. The smooth endoplasmic reticulum in most cells is much less extensive than the rough endoplasmic reticulum and is sometimes alternatively termed transitional. Smooth endoplasmic reticulum is chiefly involved, however, with the production of lipids (fats), building blocks for carbohydrate metabolism, and the detoxification of drugs and poisons. Therefore, in some specialized cells, such as those that are occupied chiefly in lipid and carbohydrate metabolism (brain and muscle) or detoxification (liver), the smooth endoplasmic reticulum is much more extensive and is crucial to cellular function. Smooth endoplasmic reticulum also plays a role in various cellular activities through its storage of calcium and involvement in calcium metabolism. In muscle cells, smooth endoplasmic reticulum releases calcium to trigger muscle contractions. Presented in Figure 2 is a fluorescence digital image taken through the microscope of the endoplasmic reticulum network in a bovine (cow) pulmonary artery endothelial cell grown in culture.

What is the Golgi apparatus mostly made of?
The Golgi is composed of membrane-bound sacs known as cisternae. Between five and eight are usually present; however, as many as sixty have been observed.
The primary function of the Golgi apparatus is to process and package the macromolecules such as proteins and lipids that are synthesized by the cell. It is particularly important in the processing of proteins for secretion. The Golgi apparatus forms a part of the endomembrane system of eukaryotic cells.

What do lysosomes do?
Lysosomes are organelles that contain digestive enzymes (acid hydrolases). They digest excess or worn out organelles, food particles, and engulfed viruses or bacteria. The membrane surrounding a lysosome prevents the digestive enzymes inside from destroying the cell. Lysosomes fuse with vacuoles and dispense their enzymes into the vacuoles, digesting their contents. They are built in the Golgi apparatus. They are frequently nicknamed "suicide-bags" or "suicide-sacs" by cell biologists due to their role in autolysis.

What does the word/root lyse mean?
The name lysosome derives from the Greek words lysis, which means dissolution or destruction, and soma, which means body.

What would happen if lysosomes within a cell burst?
Never in normal conditions are the lysosomes allowed to rupture. But in uncontrolled cell death called necrosis, where trauma may rupture the cell and its organelles, the lysosome can rupture digesting the surrounding proteins and killing the cell.

What is and what causes a lysosomal storage disease?
Lysosomal storage diseases are caused by a lack of enzymes that normally eliminate unwanted substances in the cells of the body. The enzymes are found in sac-like structures in cells called lysosomes. Lysosomes act as the "recycling center" of each cell, breaking down unwanted material into simple products for the cell to use to build new material. The lack of certain enzymes causes a buildup of the substances that the enzyme would normally eliminate, and deposits accumulate in many cells of the body. Abnormal storage causes inefficient functioning and damage of the body's cells, which can lead to serious health problems.
There are more than 40 known lysosomal storage diseases, including

Fabry disease - causes kidney and heart problems, pain and a skin rash
Gaucher disease - causes the spleen to enlarge, anemia and bone lesions if untreated
Hurler syndrome - causes deformities of the skeleton and facial features, enlargement of the spleen and liver, joint stiffness, clouding of the cornea, mental retardation and deafness
Niemann-Pick B disease - leads to enlargement of the spleen and liver, as well as lung disease
Pompe disease - an often fatal storage disease in which glycogen builds up in the liver, heart and muscle, especially during infancy (also known as acid maltase deficiency)
Tay-Sachs disease - a lysosomal storage disease that occurs more commonly in people of Eastern European Ashkenazi descent and causes degeneration of the brain in infants Many of these disorders are rare, but some occur more often in certain ethnic groups. Because these diseases follow several patterns of inheritance, a person's risk of passing this condition on to his or her children depends on the disease and the individual's family background.

What is the role of chloroplasts? What kind of organisms are they found in?
Choloroplasts convert solar energy to chemical energy. They are found in plants.

Where is it hypothesized that the first chloroplasts came from?
Chloroplasts are derived from cyanobacteria that were engulfed by primitive cells many hundreds of millions of years ago. Instead of being digested and used as food, the cyanobacteria were kept alive to produce food for their host cells by photosynthesis. The bacteria in effect became solar-powered food factories for their host cells. Over time the bacteria became so highly specialised for photosynthesis and integrated into their host cells, that they could no longer survive on their own - they had become chloroplasts.

What is the evidence for this relationship?
Similarities noted between the structure of chloroplasts/mitochondria and the structure of ancient bacteria shows that evolution from those older bacteria is likely.

What is the role of mitochondria?
Mitochondria breaks down chemical bonds to harvest energy.

What kind of organisms are they found in?
Animal organisms.

Are they found in plant cells?
Nope

What are some of the functions of the cytoskeleton?
They help create structure and organize acitivities within the cells.

What is a microtubule?
A small cylindrical organelle composed of tubulin protein around an empty central core; present in the cytoplasm, centrioles, cilia, and flagella.

What is a flagellum & where might you find one?
A long slender extension used for locomotion by some bacteria, protozoans and sperm. With regard to cytology - you would find them in the phospholipid membrane of a cell.

What are the fundamental, cellular features shared by all life forms on this planet?
Cells enclosed by membranes made of lipids and proteins.
DNA as genetic material.
Similar metabolic processes: synthesis, breakdown, energy processing - all done by enzymes.

Lecture 6: Basic Chemistry & Chem of Biological Molecules (Chapters 2 & 3)

2007-10-22T14:51:00.000-07:00

Lecture 6: Basic Chemistry & Chem of Biological Molecules (Chapters 2 & 3)

What is the reductionist approach to science?
With regard to science, reductionism is the theory that complex organisms can be reduced and defined by simpler more fundamental organisms. “To understand the whole, look at the parts.”

What are the levels of life’s organization?
LEVEL 1 – Atoms
Smallest unit of an element, composed of protons (+), neutrons (=) and electrons (-)

LEVEL 2 – Molecules
Union of two or more atoms of the same or different elements

LEVEL 3 - Cells
Are the basic unit of structure and function in living things.
May serve a specific function within the organism
Examples- blood cells, nerve cells, bone cells, etc.

LEVEL 2 - Tissues
Made up of cells that are similar in structure and function and which work together to perform a specific activity
Examples - blood, nervous, bone, etc. Humans have 4 basic tissues: connective, epithelial, muscle, and nerve.

LEVEL 3 - Organs
Made up of tissues that work together to perform a specific activity
Examples - heart, brain, skin, etc.

LEVEL4 - Organ Systems
Groups of two or more tissues that work together to perform a specific function for the organism.
Examples - circulatory system, nervous system, skeletal system, etc.
The Human body has 11 organ systems - circulatory, digestive, endocrine, excretory (urinary), immune(lymphatic), integumentary(skin), muscular, nervous, reproductive, respiratory, and skeletal.

LEVEL 5 - Organisms
Entire living things that can carry out all basic life processes. Meaning they can take in materials, release energy from food, release wastes, grow, respond to the environment, and reproduce.
Usually made up of organ systems, but an organism may be made up of only one cell such as bacteria or protist.
Examples - bacteria, amoeba, mushroom, sunflower, human

Be able to give an example of how biological function at the organism level is affected by the chemical level.
Dehydration, DNA, Cellular Respiration...

What is matter?
Matter is anything that takes up space and has mass. It only exists in 3 states: solid, liquid or gas.

What are chemical elements?
Chemical elements are substances that cannot be broken down into simpler substances with different properties.
A chemical element, or element, is a type of atom that is defined by its atomic number; that is, by the number of protons in its nucleus.

What is the smallest possible piece of an element called?
An atom is the smallest piece of an element, which still displays properties of the element.

Which four elements make up most of your body (what are their names) & what are the chemical symbols for those elements?
Oxygen: #8 on the periodic table. Its symbol is O
Carbon: # 6 on the periodic table. Its symbol is C
Nitrogen: # 7 on the periodic table. Its symbol is N
Hydrogen: #1 on the periodic table. Its symbol is H

What is a molecule?
A molecule is the smallest part of a compound that still has the properties of the compound.

What is a compound?
A compound is a molecule that contains at least two different elements.
All compounds are molecules but not all molecules are compounds.

How is a compound the same as the molecule?
Two or more atoms joined together.
Molecular hydrogen (H2), molecular oxygen (O2) and molecular nitrogen (N2) are not compounds because each is composed of a single element.

How is it different?
In a molecule, the two or more atoms of the same element have joined. In a compound, the atoms that have joined are from different elements.

Water (H2O), carbon dioxide (CO2) and methane (CH4) are compounds because each is made from more than one element. The smallest bit of each of these substances would be referred to as a molecule. For example, a single molecule of molecular hydrogen is made from two atoms of hydrogen while a single molecule of water is made from two atoms of hydrogen and one atom of oxygen.

(We may be given a formula for a common material (such as O2 or CO2), we need to be able to tell if it is a compound or a molecule, neither or both. (Assume that if the atoms of a material are joined by an ionic bond, she will write the formula in a form such as Na+Cl-.))

What is an atom?
An atom is the smallest piece of an element which still contains properties of the element.

What are the three kinds of subatomic particles found in atoms?
Protons, Neutrons and Electrons

What are their charges?
Proton +
Neutron =
Electron -

Where in the atom are each of the particles found?
Protons and neutrons are found in the nucleus of the atom.

Which two particles are big and which one is smallest?
Protons and neutrons are the larger particles and electrons are the smallest.

Which particle is most critical in determining what kind of element an atom is?
The number of protons determines the type of element an atom is. The number of protons found in the nucleus of an atom is referred to as the atom's atomic number.

What is an ion?
A positive ion is formed when some electrons "leave" their atom, so the protons(+) in the core are more and "win", so the atom becomes an + ion.
A negative ion is formed when an atom "steals" electrons from another atom, so its electrons(-) are more than the protons(+) and so it becomes negatively charged.

What is an isotope?
Isotopes are two forms of the same element that have different numbers of neutrons in the nucleus (two isotopes have the same number of protons, but a different number of neutrons).

Which particle is different in number from one isotope of an element to another isotope of the same element?
Each element has a number of different isotopes and this is determined by the number of neutrons in the nucleus. For example, the isotope oxygen-15 has 8 protons and 7 neutrons, oxygen-16 (the most common isotope of oxygen) has 8 protons and 8 neutrons and oxygen-17 has 8 protons and 9 neutrons. Different isotopes of the one element are almost physically and chemically identical.

How (without counting particles) could a scientist distinguish one isotope of an element from another isotope?
A neutral atom has the same number of electrons as protons. Thus, different isotopes of a given element all have the same number of protons and electrons and the same electronic structure;

Because protons are positively charged, they repel each other. Neutrons, which are electrically neutral, allow some separation between the positively charged protons, reducing the electrostatic repulsion. Neutrons also stabilize the nucleus because at short ranges they attract each other and protons equally by the strong nuclear force, and this also offsets the electrical repulsion between protons. For this reason, one or more neutrons are necessary for two or more protons to be bound into a nucleus. As the number of protons increases, additional neutrons are needed to form a stable nucleus; for example, although the neutron to proton ratio of 3He is 1:2, the neutron/proton ratio of 238U is greater than 3:2. If too many or too few neutrons are present, the nucleus is unstable and subject to nuclear decay.

How does the arrangement of electrons determine the chemical properties of each kind of atom?
Electrons are arranged in electron shells. The inner shells are filled first. The outermost shell may not be filled all the way. The further away from the nucleus that the shell is, the more energy the electrons there have. Electron arrangement in shells determines how an atom behaves because the number of electrons in the outer shell determines how interactive that atom is can be with other atoms. If the shell is nearly full or almost empty it is very reactive.

What is (or what makes up) a chemical bond?
A chemical bond is the physical process responsible for the attractive interactions between atoms and molecules, and that which confers stability to diatomic and polyatomic chemical compounds.
Bonds vary widely in their strength. Generally covalent and ionic bonds are often described as "strong", whereas hydrogen bonds and van der Waals' bonds are generally considered to be "weak". Care should be taken because the strongest of the "weak" bonds can be stronger than the weakest of the "strong" bonds.

If an atom loses an electron, what will the overall charge on the atom be? What will be the charge on the atom if the atom gains an electron?
If an atom loses an electron, the protons will outnumber the electrons and it will change from its neutral state to a positive ionic state.
If an atom gains an electron, the electrons will outnumber the protons and it will change from its neutral state to a negative ionic state.

What is an ionic bond? Give an example of a compound held together by an ionic bond.
In an ionic bond, the atoms are bound by attraction of opposite ions, whereas, in ionic materials, the geometry follows maximum packing rules.
An ionic bond (or electrovalent bond) is a type of chemical bond based on electrostatic forces between two oppositely-charged ions.

What is a covalent bond?
In a covalent bond, atoms are bound by sharing at least one pair of electrons. It is a strong bond. Can be single(one pair), double, or triple.

Are covalent bonds found in molecules? (Quick review: Are all molecules also compounds? Why or why not?)
Yes, covalent bonds form molecules. Chemical reactions occur as bonds are broken and made. Energy may be released or used by chemical reactions. Our bodies store energy by forming covalent bonds in chemical reactions.

What is a nonpolar covalent bond?
Nonpolar covalent bonds have equal electron sharing.

What is a polar covalent bond?
In polar covalent bonds, one atom pulls harder on the electrons/gets more of the negative charge and creates slightly positive and negative parts in a polar molecule
If the electronegativities of the two atoms in the bond are exactly equal or very close to equal, then the bond is non-polar covalent. This is always the case if the two atoms bonded are identical to each other, but sometimes two atoms have very similar electronegativities to each other, resulting in a non-polar bond.
If the electronegativities are similar, but not equal, then the bond is polar covalent (if the difference is greater than 0.5 but less than 1.7)
If the electronegativities are very different, then the bond is ionic (if the difference is greater than 1.7).
NOTE #1: The difference between a non-polar covalent, polar covalent bond and an ionic bond is just one of degree -- it is not black and white, but rather a gradual increase. As the difference in electronegativity increases the bond gets more and more polar until it is considered ionic. NOTE #2: Only bonds are called "covalent," but "ionic" can refer to both bonds and compounds. A compound that has covalent bonds in it is called "molecular," and a compound that has ionic bonds in it is called "ionic."

Which atom(s) in a (polar) water molecule pull more strongly on the shared electron pair? Which atoms pull more weakly? Which atoms in water have a slight negative charge and which ones have a slight positive charge?

What is a hydrogen bond? What kinds of molecules (polar or nonpolar) form hydrogen bonds? Compared to covalent bonds, are hydrogen bonds strong or weak?
A hydrogen bond is a special type of bond that exists between an electronegative atom and a hydrogen atom bonded to another electronegative atom. This type of bond always involves a hydrogen atom, thus the name. Hydrogen bonds occur between two polar molecules.
The typical hydrogen bond is stronger than van der Waals forces, but weaker than covalent, ionic and metallic bonds.

What is a solution?
A solution is a liquid with a complete mixture of 2 or more substances.
Saline – Table salt and water NaCI/H2O

What is a solvent?
A solvent is dissolving agent
Water

What is a solute?
A solute is a dissolvable substance (hydrogen bonds form between
Salt, sugar

What solvent is most important for life on earth?
Water

Why is this substance such a versatile solvent (what are some of the characteristics that is has that make it a good solvent)?
A water molecule is formed when two atoms of hydrogen bond covalently with an atom of oxygen. In a covalent bond electrons are shared between atoms. In water the sharing is not equal. The oxygen atom attracts the electrons more strongly than the hydrogen. This gives water an asymmetrical distribution of charge. Molecules that have ends with partial negative and positive charges are known as polar molecules. It is this polar property that allows water to separate polar solute molecules and explains why water can dissolve so many substances.
Water is a good solvent due to its polarity. The solvent properties of water are vital in biology, because many biochemical reactions take place only within aqueous solutions
When an ionic or polar compound enters water, it is surrounded by water molecules. The relatively small size of water molecules typically allows many water molecules to surround one molecule of solute. The partially negative dipoles of the water are attracted to positively charged components of the solute, and vice versa for the positive dipoles.

What are acids?
An acid is any compound or ion which yields hydrogen ions in water solution

What is an example of an acid found in the human body?
Hydrochloric Acid
Lactic Acid
Pyruvic Acid

What are bases?
A base is any compound or ion which yields hydroxyl ions in water solution.

What is the pH scale used for?
The pH scale is used to measure the acidity or alkalinity of a solution.

What is the pH of pure water?
Pure water is a 7 on the pH scale

What is the pH of lemon juice? (Is the pH of acids a big number or a smaller number?)
Lemon juice is 2 on the pH scale – acids have lower numbers on the pH scale. 7 is neutral, anything lower is considered acidic, anything higher is considered alkaline or base.

What is the pH of bleach?
12

What do chemical reactions do? Give an example of a simple chemical reaction.
A chemical reaction changes a substance into a new one that has a new chemical identity.
When wood burns in the presence of oxygen: once wood is turned to ash, it has become an entirely different mixture than it was before.

What is synthesis?
The combining of separate elements or substances to form a coherent whole.

What is lysis?
The dissolution or breaking apart of cells or bonds

What are organic compounds?
An organic compound is any member of a large class of chemical compounds whose molecules contain carbon;

What is a hydrocarbon made of?
A hydrocarbon is a compound of carbon and hydrogen

What is a carbon skeleton?
A carbon skeleton is a chain of Carbon molecules. They vary in length, can be branched or not, can have single or double bonds, they are usually arranged in rings. Their shape is important for recognition by other molecules.

What are functional groups used for?
Functional groups are specific groups of atoms within molecules that determine the characteristic chemical reactions of those molecules.

What kind of atom (of which element) are functional groups usually attached to?
They usually attach to carbon atoms/carbon skeletons

What are the two kinds of functional groups I want you to know about & what are some of their characteristics?
COOH and NH2
COOH is called the carboxyl group and thus the organic acids are also called as carboxylic acids.
NH2 – Amines (amino acids)

What is a macromolecule?
From the strict perspective of chemistry, a "molecule" consists of a number of atoms linked by covalent bonds.
The term macromolecule is used to describe different forms of compounds of molecules. Living things are composed of macromolecule like proteins, carbohydrates, lipids and nucleic acids..
Carbohydrate is a macromolecule which is made up of monosaccharide monomers
Protein is a macromolecule that is made up of amino acid monomers
Lipids are macromolecules that are made up of fatty acid and glycerol monomers
Nucleic Acids are macromolecules made up of nucleotide monomers.

How is a macromolecule different than or similar to a polymer?
The term macromolecule as used in polymer science refers only to a single molecule. For example, a single polymeric molecule is appropriately described as a "macromolecule" or "polymer molecule" rather than a "polymer", which suggests a substance composed of macromolecules. [2].

What is a polymer?
A polymer is a substance composed of molecules with large molecular mass composed of repeating structural units, or monomers, connected by covalent chemical bonds. The word is derived from the Greek, πολυ, polu, "many"; and μέρος, meros, "part"). Well known examples of polymers include plastics, DNA and proteins.
What are monomers? A monomer (from Greek mono "one" and meros "part") is a small molecule that may become chemically bonded to other monomers to form a polymer.

Amino acids are natural monomers, and polymerize to form proteins. Glucose monomers can also polymerize to form starches, and glycogen polymers. In this case the polymerization reaction is known as a dehydration or condensation reaction (due to the formation of water (H2O) as one of the products) where a hydrogen atom and a hydroxyl (-OH) group are lost to form H2O and an oxygen molecule bonds between each monomer unit.

What is a carbohydrate?
A macromolecule formed of monosaccharide bonds, along with carbon, hydrogen and oxygen.

Are simple sugar molecules (such as glucose) small or large compared to most macromolecules?
They are larger and need the help of insulin to enter cells. Glucose's size and structure make it hard for the molecule to pass through the outer membranes of many of the body's cells. Insulin helps to fix this problem. Specifically, insulin bonds with the outer membrane of cells to increase permeability. This enables glucose to pass through the cell membrane more easily and gives the cell access to more energy. Without insulin, it is extremely difficult for glucose in the blood to be used by the body's cells as energy. Conversely, an abundance of insulin increases the rate at which glucose is used by the cells and therefore lowers the amount of glucose left in the bloodstream

What are monosaccharides? Give two examples.
Monosaccharides are single molecules of sugars. Examples would be fructose and glucose.

What are the two forms that sugar molecules can be in?
Hexose – 6 carbon atoms
Pentose – 5 carbon atoms

Since two monosaccharides can have exactly the same chemical formula (for example, C6H12O6), what does make them different from one another?
The arrangement of their bonds

What are monosaccharides used for in cells?
A major source of cellular fuel – used in cellular respiration to form ATP

What is a disaccharide? What is the three examples from lecture?
A carbohydrate formed from the bond of two simple sugars
Sucrose = glucose and fructose
Maltose = glucose and galactose
Lactose = Glucose and Galactose

What are polysaccharides?
Long chains of sugars (polymers of monosaccharides)

What kind of monomer units are they made of?
Glucose

What common polysaccharide is found in plants as an energy storage molecule?
Starch

What kinds of human foods are rich in this polysaccharide?
Corn, potatoes, grains

What kind of polysaccharide is made in animals?
Glycogen

What is its function?
Glycogen is a simple sugar in “storage”. When energy is needed, glycogen will be broken down to release sugar molecules. This is called hydrolysis.

What polysaccharide is a major component of wood?
Cellulose

What is fiber?
The bond between glucose monomers in plants (cellulose)

Can humans digest this polysaccharide?
No

Can any organisms digest this polysaccharide?
Microorganisms can digest (decomposition). Cows can also break it down.

What are lipids? Can you give an example?
Lipids are organic compounds that are insoluble in water.

Are lipids made of monomer units?
Yes, they are made of glycerol and fatty acids

What does hydrophobic mean? (Why don’t oil and vinegar mix?)
In chemistry, it means that a compound is not soluble in water.

How do saturated fatty acids differ from unsaturated fatty acids?
Saturated fatty acids have no double bonds between carbons – they are saturated with

Why does this matter to humans?
Because the consumption of saturated fats has been linked to cardiovascular disease.

What are phospholipids & where would you find them?
The molecules that form the bulk of the plasma membrane that surrounds cells in a bi-layer. They have hydrophilic heads and hydrophobic tails.

What are waxes? What are they used for by biological organisms?
Long chain fatty acids that bond with long chain alcohols.
They are used to form a protective barrier, to slow water loss, repel insects, trap dust. Maintenance of fur and skin, car wax ear wax, candles, honeycomb

What kind of macromolecule are steroids? What are some of the types of steroids in organisms?
Steroids are a lipid which has a different structure than fats. They have skeletons of 4 fused carbon rings – each steroid differs primarily by the type of functional group attached to the carbon skeleton. Examples are: cholesterol, testosterone and estrogen.

What are proteins?
Biological polymers of amino acid monomers
Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.

What kinds of monomer units are they made of?
Amino Acids

What kind of atom (or element) is found in proteins but is not found in carbohydrates or in lipids?
Nitrogen

What is an enzyme?
Enzymes are a type of protein that bring reactants together speeding chemical reactions in cells. They are specific to one type of reaction and function at body temperature.

Why does the three-dimensional shape of proteins matter?
It determines its function in the cells and body of the organism.

What creates/determines the three dimensional shape of proteins?
The amino acid sequence determines the shape of protein molecules.

What happens if the three dimensional shape of a protein is changed?
A cell’s proteins may not be functional because they have mis-folded. Cystic fibrosis and Alzheimer’s are associated with misshapen proteins.
Chaperone proteins appear to be present to ensure that protein cells fold correctly. Prions are being researched for the relation to causing cells to fold incorrectly.

Why do high temperature & acidic environments affect protein function?
High temperatures and acids will denature a protein. In other words it makes the molecule incapable of holding its structure.

What are nucleic acids? Are they polymers?
Nucleic acids are polymers of nucleotides w/ specific functions in cells. DNA is the genetic material/coding that stores information regarding its own replication and the order in which Amino Acids are joined to make a protein. RNA communicates this information outside of the cells.

What are the monomer units of nucleic acids?
Nucleotides

What three parts is a nucleotide made of?
Phosphate, a pentose sugar and a nitrogen base.
Deoxyribose is the pentose sugar found in DNA
Ribose is the pentose sugar found in RNA

Do nucleotides contain nitrogen?
Yes

What are the two kinds of nucleic acids?
DNA and RNA

Where are they found in the cell?
The cell’s nucleus

Why are these polymers called nucleic acids?
Because they are found at the cell’s nucleus

Which kind of nucleic acid carries the master copy of an individual’s genetic material?
DNA