Bio Final

Question 1

Give a biological example for each property/processes associated with life that we covered in class. Give examples that are different from those in the book and used in class

Answer 1

1. energy: they acquire and use energy ie. photosynthesis, respiration, fermentation, digestion
2. cells: made up of membrane-bound units that regulate the passage of materials between exterior and interior spaces
3. information: process hereditary / genetic information encoded in genes. ie. DNA, RNA
4. replication: every organism replicates itself; reproduction
5. evolution: organisms are the product of evolution, and populations continue to evolve; ie. giraffe with tongue that can eat thorny plants

Question 2

In science, what is a hypothesis, and what is a theory? (see pages 7-8). How are they different?

Answer 2

hypothesis: testable statement to explain phenomena or observations – must be testable and falsifiable
theory: an explanation for a very general class of phenomena or observations that are supported by a wide body of evidence. Proposed explanations for broad patterns in nature

Question 3

What is a “control” in an experiment? Why is it important?

Answer 3

checks for factors, other than the one being tested, that might influence the experiment’s outcome. (also controlling for the possibility that the manipulation itself affected the behavior)

Question 4

What are the two components of cell theory?

Answer 4

1. all living organisms are made of one or more cells ( You must have a cell in order to make another cell.)
2. all cells come from preexisting cells (If you must have a cell to make another, then all cells must be related)

Question 5

Approximately 96% of the human body is comprised of what four elements?

Answer 5

hydrogen, carbon, nitrogen, oxygen

Question 6

What is the difference between a nonpolar and polar covalent bond?

Answer 6

1. nonpolar covalent (ie. hydrogen molecule): electrons halfway b/t 2 atoms, shared equally;
2. polar covalent (h2o); electrons shared unequally and one side is more electronegative and there’s partial charges on atoms; asymmetric sharing of electrons; Water is an example of a polar molecule. equal electronegativity between atom’s electrons that are shared equally or symmetrically -Oil is an example of an nonpolar molecule(this is why water and oil do not mix).

Question 7

What is an isotope? Give two examples of how are isotopes are useful in the biological sciences.

Answer 7

isotopes (varying neutrons for the same element): most are stable. Isotopes are used in biology for carbon dating and radioactive tracers in things such as CAT scans.

Question 8

specific heat capacity

Answer 8

he amount of energy required to raise the temperature of 1 gram of a substance by 1 degree Celsius; water has a high specific heat because hydrogen bonds must be broken before heat can be transferred and the water molecules begin to move faster. As molecules increase in overall polarity (and their ability to form hydrogen bonds), it takes an extraordinarily large amount of energy to change their temperature

Question 9

surface tension

Answer 9

water organizes to maximize H bonds, breaking bonds requires energy ; enhanced attraction between the surface of water meniscus results in tension that minimizes the total surface area; when water molecules are at the surface, there are no water molecules above them for hydrogen bonding, they exhibit stronger attractive forces between their nearest molecules.

Question 10

adhesion

Answer 10

attraction between unlike molecules, usually analyzed in regard to interactions between a liquid and a solid surface (water molecules adhere to glass and pull upward at perimeter) chalk on a chalkboard

Question 11

cohesion

Answer 11

attraction between like molecules (water is cohesive because it stays toughener because of the hydrogen bonds that form between individual molecules); water molecules at surface form H bonds with water molecules and resist the upward pull of adhesion; allows capillary action – water attracted to objects with electric charge

Question 12

why water is such an effective solvent:

Answer 12

both of the O-H bonds are polar, so the oxygen atom has a partial negative charge and hydrogen has a partial positive
molecule is bent —

the partial negative charge sticks out from the partial positive charges, giving it overall polarity

Question 13

Using scientific terminology involving bonds and molecules, explain how salt dissolves in water.

Answer 13

hydration shells: negatively charged O side of water attracted to positively charged Na+ ion; and the positively charged side of water is attracted to the negatively charged Cl- ion.
Covalent bonds are stronger than ionic, so they’re more willing to form easily. They break ionic bonds and form covalent bonds.

Question 14

e able to recognize the following functional groups (hydroxyl, carboxyl, carbonyl, sulfhydryl, methyl, phosphate, amino) listed in the table of your textbook and in your lecture notes. Look up the structure of estradiol, cysteine, and glucose and identify the functional groups in each.

Answer 14

OH Hydroxyl CH Methyl NH Amino SH Sulfhydryl
COO or CHOO Carboxyl CO or CHO Carbonyl
Phosphate PO (POOOO)

Question 15

What is a polymer?

Answer 15

polymer: “many-parts” large number of monomers together
polymerization: linking monomers together = to form proteins

Question 16

What type of chemical reactions add monomers together to form polymers? Are these reactions spontaneous or do they require energy?

Answer 16

monomers polymerize through condensation reactions (aka. dehydration reactions); requires energy – endergonic

Question 17

What type of chemical reactions break polymers down into their monomer building blocks? Are these reactions spontaneous or do they require energy?

Answer 17

hydrolysis: breaks polymers apart by adding a water molecule, separating one monomer from the polymer chain (opposite of condensation reactions); dominates because it increases entropy and is favorable energetically; they do not require much energy = exergonic!

Question 18

How are proteins denatured? What happens to the biological activity of a denatured protein and why?

Answer 18

denatured proteins: unfolded by treating with compounds that break hydrogen bonds and S-S bonds; it makes ribonuclease unable to function normally (ie. no longer break apart nucleic acids)

physical and chemical changes deactivate protein by denaturation (temp. pH, salt). ie. cook an egg, high fevers.

Question 19

What are the four levels of protein structure (describe the different levels of structure)? What type of chemical bonds are responsible for each level?

Answer 19

rimary: sequence of amino acids
secondary: polypeptides form A-helix or B-sheets - H bonds in core structure
tertiary: interactions between amino acid side chains (curly) - unique folds b/c of covalent bonds, ionic bonds, H bonds, hydrophobicity, and van der Waals, R-groups
quaternary: complex, multiple subunits form function of protein b/c of covalent bonds, ionic bonds, H bonds, hydrophobicity, and van der Waals

Question 20

What is the basic structure of an amino acid?

Answer 20

amino acid: building blocks of proteins / polypeptides, 20 types differ in side groups; All amino acids contain a Hydrogen. The examples are: H, NH2, COOH, and distinct side chains.

structure: include 1 amino group + carboxyl group, plus central carbon with hydrogen

Charged side chains (acidic or basic?): acidic = positive, basic = negative

R-group: polar or electronegatively charged side groups will react

amino acid = peptide
50 or less: oligopeptide
50+: polypeptide
when 50+ and functional = protein

Question 21

What is a peptide bond?

Answer 21

peptide bond: bond responsible for linking monomers; bond forming between carboxyl group of one amino acid and the amino group of another; the C-N covalent bond resulting from a condensation reaction; very stable (compared to links in other types of macromolecules) because valence electrons on nitrogen is partially shared in the C-N bond — sharing is enough that bonds have characteristics of a double bond

carboxyl + amino group = peptide bond

aminos: act as base
carboxyl: acts as acid

Question 22

Name 2 diseases associated with protein misfolding. For each of these diseases, explain the following:
What are the symptoms of this disease/disorder?
what protein is misfolded? How does misfolding affect the function of the protein in the cell?
how does misfolding contribute to the symptoms of this disease/disorder?

Answer 22

mad cow disease in cattle: PrP is a normal component of mammalian cells, but improperly folded version of the protein represents the infectious form of the prion
sponge-brain illnesses: sheep, cows, goats, and humans afflicted with these undergo massive degeneration of the brain; spongiform encephalopathy can be inherited and the disease is transmitted when individuals eat tissues containing the infectious form of PrP; all prion illnesses are fatal.
Alzheimers Disease: Symptom: confusion, memory loss. Misfolding proteins creates plaques that stick together. These plaques interfere with neurons in the brain, which eventually kills the neurons, resulting in memory loss. B-amyloid precursor protein APP: transmembrane protein in brain 40aa highly processed, B-deposits cause plaque to form in brain; neurofibrillary tangles – microtubule stability – progressive loss of synaptic connections

Question 23

What are chaperone proteins? Why are they important in the cell

Answer 23

chaperonins: aid in protein folding:
unfolded protein enters cylinder
cap attaches, cylinder changes shape (hydrophobic inside now!)
cap comes off, protein released

Question 24

What is an enzyme? How do they work

Answer 24

enzyme: a protein that functions as a catalyst; enzymes also: lock and key — enzymes are lock and keys are substrates that fit into the lock and react

Question 25

substrates:

Answer 25

reactant molecules enzymes bring them together in a precise orientation so atoms involved in reaction can interact. 54 Many reactions can be activated by changes in temperature or acidity (low pH) — which are deadly to cells; cells use special proteins (enzymes) to perform complex synthesis and decomposition reactions in our body. (anat)

Question 26

What is meant by the activation energy (EA)? What do enzymes do to the EA of a reaction

Answer 26

activation energy: the amount of energy required to start a reaction; required to break bonds in reactants so new bonds can form in products E^A
Enzymes promote chemical reactions by lowering the activation energy required to make it possible for chemical reactions (ie. breakdown of sugars) to proceed under conditions compatible with life; they speed up reactions without themselves being changed or consumed — they proceed until equilibrium is reached. (anat)

Question 27

exergonic reaction

Answer 27

spontaneous: downhill, degradative, catabolic, releases energy, moves from lower free energy to greater stability. spontaneous: happen on its own (break bonds) – but can be slow. Heat works!
1. products are less ordered than reactants
2. products have lower potential energy than reactants

Question 28

endergonic

Answer 28

non-spontaneous
products are more ordered than reactants
reactants have lower potential energy than products
require input of energy – uphill!

Question 29

1st law of thermodynamics

Answer 29

energy is conserved (can’t be created / destroyed)

Question 30

2nd law of thermodynamics

Answer 30

entropy increases in isolated systems

Question 31

What is the monomer called that makes up a carbohydrate molecule

Answer 31

monosaccharide: “one sugar” — C3H603 1-2-1 C-H-O

Question 32

What is the general molecular formula for a carbohydrate

Answer 32

(CH20)n ie. C1H2O1, C6H12O

Question 33

What is a carbohydrate made up of two monosaccharides called? Three monosaccharides? What is a large polymer of carbohydrate made up of many monomers of sugar called?

Answer 33

two monosaccharides: disaccharide
monomers called monosaccharide “one sugar”
small polymers: oligosaccharides “few sugars”
large polymers: polysaccharides “many sugars”

Question 34

hen sugars consisting of 5 or more carbons cannot exist in the form of linear chains — the bond responsible for ring formation occurs only between the carbon containing the carbonyl group and one of the carbons with a hydroxyl group and one of the carbons with a hydroxyl group;

Answer 34

glucose is an example — cyclic structure forms a bond with oxygen atom and transfers its hydrogen to the carbonyl, turning it into a hydroxyl group; the newly formed Cq hydroxyl group can be oriented to produce alpha or beta glucose configurations:

Question 35

What mechanisms could have led to the accumulation of carbohydrates in early oceans?
chemical evolution:

Answer 35

sugars are synthesized on dust particles and other debris in interstellar space and could have rained down onto earth as the planet was forming as well as being synthesized in the hot water near ancient undersea volcanoes;
synthesis of sugars could have been catalyzed by minerals found in walls of deep-sea hydrothermal vents

Question 36

Why don’t scientists believe that carbohydrates played little to no role in the origin of life? (What evidence supports this idea

Answer 36

Most saccharides are readily synthesized under conditions that mimic conditions of early earth. ie. when formaldehyde molecules CH2O are heated in solution, they react with one another to form almost all the pentoses and hexoses.

Question 37

How do monosaccharides join to form polysaccharides?

Answer 37

They form when enzymes catalyze the formation of glycosidic linkages between monosaccharides that are in the alpha or beta form; they are long chains of monosaccharides, but some branch extensively; among linear forms, it is common for adjacent strands to be connected by hydrogen bonding or other types of linkages.

Question 38

What is the special covalent bond formed between two monosaccharides in a disaccharide (or polysaccharide for that matter)?

Answer 38

glycosidic linkage: monosaccharides polymerize when a condensation reaction occurs between 2 hydroxyl groups, resulting in a covalent interaction (analogous to peptide bonds in proteins, but peptide bonds form between same locations in their monomers, giving proteins a backbone structure, but this isn’t true with polysaccharides); glycosidic linkages form between hydroxyl groups and every monosaccharide contains at least 2 hydroxyls, the location and geometry of glycosidic linkages can vary widely!

Question 39

Describe four functions of carbohydrates in organisms

Answer 39

1. serve as a substrate for synthesizing more complex molecules; ie. RNA contains 5-carbon sugar ribose and dnA contains modified sugar, nucleotides consist of ribose or deoxyribose, a phosphate group, a nitrogenous base Sugar acts as a subunit of each of these monomers. serve as precursor to larger molecules
2. provide fibrous structural materials: cellulose in cell walls of plants and algae; chitin: structural support in cell walls of fungi and external skeletons of insects & crustaceans; peptidoglycan: structural support in bacterial cell walls
3. indicate cell identity: immune system – chains outside the cell membrane
4. store chemical energy: starch – energy storage in root veggies and glycogen – energy storage in animal cells

Question 40

Cellulose is a polymer, specifically a carbohydrate polymer (polysaccharide). Cellulose is composed primarily of what types of monomers?

Answer 40

a polymer of B-glucose monomers joined by

B-1, 4-glycosidic linkages. each glucose monomer in the chain is flipped in relation to the adjacent monomer.

Question 41

If you want to break down starch into monomers of glucose, would this involve dehydration reaction/condensation or hydrolysis?

Answer 41

hydrolysis!

Question 42

Explain which carbohydrates are used in cell-to-cell recognition. Where are these carbohydrates located in the cell?

Answer 42

structural polymers tend to be repetitive, with 1 or 2 types of monosaccharides, but complex carbs are different. Some have enormous structural diversity — the linkages between them vary a lot. they are capable of displaying information to other cells through their structure. polysaccharides act as an identification badge on outer surface of plasma membrane that surrounds the cell. glycoproteins project outward from cell surface into environment glycoprotein: has 1 or more carb covalently bonded to it: cell recognition and cell-cell signaling; each cell has these on its surface that identify it as part of our body and not foreign — recognition and communication — ie. sperm only bind to eggs of their own species 79

Question 43

Name a structural carbohydrate found in animals.

Answer 43

polysaccharides like chitin (insects exoskeleton), and peptidoglycan form cell walls (bacteria), giving it structural strength,

Question 44

What is an enzyme?

Answer 44

catalysts: bring substrates together in a precise orientation that makes reactions more likely
enzymes: speed up reactions like a lock and key — substrates fit into enzymes and react; very large compared to substrates and roughly globular. Enzymes are not rigid and static, but flexible and dynamic; many of them change shape and conformation when reactant molecules bind to the active site. 2. What is the activation energy (EA)? (Explain in terms of what this term means during the progress of a chemical reaction) What effects do enzymes have on the activation energy?

Question 45

Name two functions enzymes that explain how they can speed up chemical reactions.

Answer 45

1. bring substrates together: when 1 or more substrates enter active site, they are held in place through H bonding or weak interactions with amino acids; once substrate is bound, 1 or more R groups come into play. the degree of interaction between substrate and enzyme increases and reaching maximum when temp unable condition (transition state) is formed — when the key is in the lock.
2. lower activation energy: activation energy: a certain amount of kinetic energy is required to strain the chemical bonds in substrates so they can achieve a transition state.

Question 46

enzyme catalysis is a 3-step process:

Answer 46

nitiation: enzymes orient reactions as they bind at spots within the active site
transition: (facilitation) lower activation energy (moving) stabilized by a change in enzyme’s shape; interactions b/t substrate and R groups lower activation energy required for reaction
termination: kick out products; reaction products have less affinity for active site, binding ends, enzyme returns to its original conformation and products are released. 147

Question 47

Describe factors that can alter enzyme activit

Answer 47

1. temperature: affects folding and movement of enzyme and kinetic energy of its substrates
2. ph: concentration of protons in a solution affects structure and function — affects the charge on carboxyl and amino groups in residue side chains and the active site’s ability to participate in reactions that involve the transfer of protons or electrons
3. interactions with other molecules: other molecules (other enzymes) regulate most of the cell’s enzymatic activity — often changing the structure and their activity either activates or inactivates enzymes
4. modifications of its primary structure:

Question 48

NON-COVALENT MODS

Answer 48

a) competitive inhibition: regulatory molecule is similar in size and shape to enzyme’s natural substrate and inhibits catalysis by binding to the enzyme’s active site — it competes with the substrate for access to the active site
b) allosteric regulation: the regulatory molecule binds at a location other than the active site and changes the shape of the enzyme — binding event changes the shape of the enzyme that makes the active site available or unavailable.

Question 49

COVALENT MODS

Answer 49

chemical change in primary structure — reversible or not The changes often result from cleavage of peptide bonds that make up primary structure of enzymes. ie. Trypsin. Most comment: addition of one or more phosphate group — enzyme is phosphorylated instead of the substrate, and the transfer of a phosphate from ATP to the enzyme may be catalyzed by the enzyme itself or by a different enzyme. It adds a negative charge to one or more amino acid residues in a protein, electrons in that part of protein change configuration. enzyme’s conformation changes.

Question 50

3 enzyme helpers:

Answer 50

1. cofactors: inorganic ions (metal) which reversibly interact with enzymes
2. coenzymes: organic molecules that reversibly interact with enzymes (electron carries NADH FADH2)
3. prosthetic group: non-amino acid atoms or molecules that are attached permanently to proteins (ie. retinal, which converts light energy into chemical energy)

Question 51

free energy change in a reaction

Answer 51

the change in enthalpy minus change in entropy multiplied by temperature in Kelvin.

Question 52

What were the 4 steps of the Oparin-Haldane theory of chemical evolution

Answer 52

1.H2, N2, HCN, NH3, CO2 present in atmosphere combine to form simple organic compounds
2. compounds react and form building blocks (aminos, sugars, nucleotides)
3. building blocks link to form larger polymers
the first polymer replicated itself

Question 53

What are the building blocks of nucleic acids called?

Answer 53

nucleotides: nucleic acids are made up of monomers called nucleotides; have three components:
Phosphate group, 5 carbon sugar (deoxyribose ribose), N-base

Question 54

What is the structure of a nucleotide? Can you name and recognize the three components of the nucleotide?

Answer 54

nucleotides: nucleic acids are made up of monomers called nucleotides; have three components:
1. phosphate group (bonded to sugar molecule) attached to 5’ carbon
2. a five-carbon sugar (bonded to the nitrogenous base); organic compound bearing reactive hydroxyl (-OH) functional groups
3. Nitrogenous base ATGC (U)

Question 55

What are the 4 nitrogen containing bases that make up nucleotides in a DNA molecule? What about an RNA molecule?

Answer 55

2 structural group the nitrogenous bases belong to:

1. purine: adenine and guanine (AG): two rings are linked together by 9 atoms (*think 9 and “nine” at the end of A and G)
2. pyrimidine: cytosine, thymine, (CT) and in RNA instead uracil (U): linked together by 6 atoms that make a single ring in each pyrimidine

Question 56

How does the structure of purines differ from that of pyrimidines?

Answer 56

Purines are large, made up of 9 atoms

Pyrimidines are smaller, have a single molecule structure made up of 6 atoms, also include an RNA substituted U instead of T in DNA

Question 57

Name 3 ways that DNA differs from RNA in terms of structure

Answer 57

1. drops an oxygen on 2’ carbon
2. has U instead of T
3. single strand instead of double

Question 58

Name 3 types of RNA that exist in cells. What are the functions of each of these different types of RNA?

Answer 58

tRNA: translation
mRNA: transcription
rRNA: translation 
snRNA: transcript processing eukaryotes
miRNA: micro-RNA -- piRNA + siRNA

Question 59

What is meant when geneticists say that DNA is directional? What do they mean when they say that DNA has an anti-parallel arrangement?

Answer 59

directional: the sugar-phosphate backbone is directional— one end has an unlinked 5’ phosphate while the other has an unlinked 3’ phosphate — the groups aren’t linked to another nucleotide. DNA is always written from 5’-3’ direction which is the same way DNA and RNA are synthesized — bases are added only at the 3’ end of the growing molecule
complementary trands are antiparallel: one strand is 5’->3’ and some are 3’->5’

Question 60

What are the two main functions of DNA in the cell?

Answer 60

carries information required for organisms growth and reproduction
serves as a mold or template for synthesis of a complementary strand and contains information required for a copy of itself to be made.

Question 61

Which of the bases pair together in a DNA double helix (through hydrogen bonding)? How many hydrogen bonds do each pair form with one another?

Answer 61

AT GC bases are complementary:
A-T pair has 2 hydrogen bonds
G-C has 3 hydrogen bonds (making it stronger than AT)

Question 62

Describe the different levels of structure of a DNA molecule? What bonds or forces support these levels?

Answer 62

1. primary: the order (sequence) of the different nitrogenous bases in a nucleic acid forms the primary structure of the molecule; hydrogen bond
2. secondary: 2 DNA molecules (strands) that run in opposite directions (orientations) of each other — twisted into a double helix, held together by hydrogen bonds by AT GC pairs and hydrophobic interactions that drive bases into the interior of the helix: hydrogen bonding, hydrophobicity, and van der waals interactions, phosphodiester linkages
3. tertiary: NONE

Question 63

Describe the different levels of structure of an RNA molecule? What bonds or forces support these levels?

Answer 63

1. primary structure: consists of sugar-phosphate backbone formed by phosphodiester linkages and a sequence of 4 types of N bases extending from backbone.
2. secondary structure: This forms a hairpin structure — stem and loop configuration folds with unpaired bases on one side; complementary base pairing between purine and pyrimidine bases; A forms hydrogen bonds with uracil — 3 hydrogen bonds form between G and C and 2 hydrogen bonds form between A and U. They form hydrogen bonds on the same strand (rather than DNA second strand) — when bases on one part of RNA fold over and align with ribonucleotides on another part of the same strand, 2 sugar-P strands are antiparallel; hydrogen bonding b/t complementary bases results in stable double helix.
3. tertiary: folds that form distinctive three-dimensional shapes like tRNA; molecules are much more diverse in size, shape, reactivity than DNA

Question 64

Give an example of an activated nucleotide? What is meant by “activated” in such a molecule? How can activated nucleotides be used in the cell?

Answer 64

the potential energy of the nucleotide monomers is first raised by reactions that add two phosphate groups to the ribonucleotides or deoxyribonucleotides, creating nucleoside triphosphate: ATP = activated nucleotides; can be used to store and provide energy through high potential energy

Question 65

What is the name of the type of covalent bond that exists between neighboring nucleotides

Answer 65

The phosphodiester bond

Question 66

Who first put together the detailed model of the structure of DNA? What work by other scientists contributed to identification of the correct structure of DNA?

Answer 66

Watson & Crick; X-ray crystallography Rosalind Franklin using DNA with X-rays and analyzing scattered radiation; Maurice Wilkins calculated distances b/t groups and molecules (Franklin-Wilkins), Erwin Chargaff — 2 empirical rules analyzing N bases in DNA samples from organisms

Question 67

What are Chargaffs rules? In other words, what did Chargaff discover while analyzing the nucleotide contents of DNA found in different organisms?

Answer 67

1. # of purines matches the # of pyrimidines

2. # of Ts and As in DNA are equal and Cs and Gs in DNA are equal

Question 68

Hershey and Chase:

Answer 68

VIRUS: To find out what the genes are made of that virus’s inject into cells to make them a host. Most people believed that it had to be proteins or DNA. By raising virus’s in a radioactive isotope of both phosphorus and nitrogen. The experimenter then had the virus attach to a host cell to starts replication. They then put the cells and virus capsids into a blender to separate them. They then centrifuged them which separated the solvents and a pellet. Between two samples of radioactive isotopes, they found that DNA was radioactive in the pellet of the test tube from the specific isotope it was raised in. Versus a different radioactive isotope that was found in the solution. This showed that DNA was being passed on from the virus, into the host cell.

Question 69

Meselson & Stahl:

Answer 69

coli: Predicted that DNA was synthesized in three possible ways:
1. conservative (old strands rejoin while new strands join)
2. semiconservative (old strand joins with a new strand),
3. dispersive: segments old and new; dispersive (segments of the old helix is removed and copied). By introducing an isotope of nitrogen during synthesia they were able to predict the traits of each generational offspring that each method would produce. The isotope of nitrogen is slightly heavier than neutral nitrogen so the density gradient of each generation will show a specific pattern for each method. The resulting density gradient conflicts with the conservative and dispersive method, but is consistent with the traits the semiconservative replication would produce.

Question 70

Describe 2 properties (limitations) of DNA polymerase III and explain how each affect how DNA synthesis is performed on the leading and lagging strands.

Answer 70

1 .it builds off of RNA primer

2. builds in 3’ direction
3. it stops at edge of RNA primer

Question 71

In eukaryotes, why do chromosomes shorten after repeated cell divisions

Answer 71

the last 50-100 nucleotides break off with each cell division
telomeres: non-coding placeholders

Question 72

Why can’t DNA polymerase function at the very end of a chromosome?

Answer 72

DNA polymerase is unable to add DNA near tip, no synthesizing DNA without a primer — so single strand DNA stays single – it has no template

Question 73

Can you list 3 mutagens in the environment?

Answer 73

Physical - UV radiation particles
Chemical: carcinogens
Biological: Virus

Question 74

Describe a repair system, discussed in class, that cells use to repair thymine dimers

Answer 74

Nucleotide excision repair will detect the damaged nucleotide and use enzymes to remove and replace the nucleotide.

Question 75

Describe a human hereditary disease related to a defect in DNA repair

Answer 75

Xeroderma Pigmentosum is a hereditary disease that causes defects in the nucleotide excision repair mechanism which causes an accumulation of damaged DNA which will inevitably causes diseases such as cancer.

Question 76

1. What do all lipids have in common?

Answer 76

Hydrophobic (insoluble in water)
Hydrocarbons: molecules containing only carbon + hydrogen (Many are carbon containing compounds found in living organisms and are nonpolar.)

Question 77

What are hydrocarbons? Are hydrocarbons polar or nonpolar? Why?

Answer 77

Molecule that contains only Hydrogen + Carbon.

They are nonpolar: because the difference in electronegativity between hydrogen and carbon is less than 1

Question 78

Describe 3 different functions for lipids in your body and give an example of each.

Answer 78

1. Energy storage: fats, fuelled
2. Cell membranes: Phospholipids
3. Cell Communication: Hormones (testosterone / estradiol)

Question 79

What structural characteristics of fats determine their fluidity?
fluidity:

Answer 79

the viscosity (the state of being thick, sticky, and semifluid in consistency) of the lipid bilayer of a cell membrane;

1. saturation: Having any double bonds as opposed to having all single bonds;
2. length of hydrocarbon chain

Question 80

Describe the structure of a triglyceride type of fat.

Answer 80

3 hydrocarbon chains joined to a glycerol head by ester linkages

Question 81

Name the 3 types or categories of fats in the cell.

Answer 81

fats
phospholipids
steroids

Question 82

What is the difference between a saturated and unsaturated fatty acid? Which is more fluid at room temperature? Why?

Answer 82

Saturated fats: (saturated with H) only single bonded carbons and hydrogens; single covalent bonds
Unsaturated fats: 1 or more doubled bonded carbons, more fluid at room temperature because they create a kink in the chain which forces more space in between the lipid molecules;

Question 83

What are phospholipids used for in cells? How does their structure suit their function?

Answer 83

1. energy storage
2. acts as pigment that capture or respond to sunlight
3. serve as signals between cells
4. form water proof coating on leaves and skin
5. act as vitamins used in many cellular processes

Question 84

How are phospholipids similar and different from triglycerides

Answer 84

same: made up of hydrocarbon chains attached to a head.
different: the head that hydrocarbon chains binds to:
Phospholipids attached to a phosphate group
Triglycerides attached to a glyceride head

Question 85

What is meant by an amphipathic molecule

Answer 85

contain both hydrophilic + hydrophobic elements.
Hydrophilic heads interacts with water
Hydrophobic tails interact with one another

Question 86

What evidence is there that supports a “fluid mosaic” model of membrane structure?

Answer 86

I. Membrane is fluid and contains many proteins and lipids (things that move around).
Enzymes move to where they need to (pathways)
Receptors involved in cell communication can align with internal signaling molecules.

II. Membrane is selectively permeable (things coming into and out of the cell are tightly regulated)
Maintain proper pH and ionic concentrations for cellular reactions to occur
Maintain electrochemical gradients necessary for cell signalling
Helps control reaction timing and sequences

Question 87

What molecules are able to diffuse across the phospholipid bilayer of the plasma membrane? What properties of these molecules enable them to diffuse across the membrane? What molecules are not able to diffuse across the membrane and what characteristics do these molecules have that prevent them from crossing the membrane?

Answer 87

Selectively permeability :
EASY: O2, CO2, N2 - They are small and nonpolar molecules are able to diffuse directly across the phospholipid bilayer.
MEDIUM: H20 (small, uncharged polar molecules)
HARDER: Glucose, sucrose
HARD: Cl-, K+, and Na+ - Molecules that are large or polar will not diffuse across a phospholipid bilayer.

Biologically important ions to know: Na+, K-, Cl-, Ca2+,

Question 88

In what ways is the cell membrane a dynamic “fluid” structure? Why is this important in the cell? In what way is it a “mosaic” structure?

Answer 88

The cell membrane is “fluid” because: phospholipids move easily within the membrane, but they stay connected to each other because common hydrophobic tail and hydrophilic heads will try to stay connected as much as possible. Even if a phosphate bond is broken with another phosphate group they will quickly reform with other phosphate groups.

It is important because: it allows the cell to be able to move and expand based on it’s needs and not break when it is bumped into or forced into a different area. If it did not bend and move base on outside input then it would be much more prone tearing and dying.

The cell membrane is a mosaic because: proteins embedded in the phospholipid bilayer allow and control the rate of molecular exchange inside and outside the cell. Proteins can be amphipathic with nonpolar side chains in the middle of the protein and polar side changes on the exposed ends on either side of the cell wall.

Question 89

Explain how cholesterol act as a “temperature buffer” in the cell membrane? Why is this important?

Answer 89

Cholesterol maintains optimum membrane fluidity. This keeps the membrane functional in warm and cool conditions; reduces permeability at high temps, more dense, hydrophobic protects, insulates (permeability to glycerol is higher)

Question 90

hat are the relative concentrations of sodium, chloride, potassium, and calcium inside and outside of the plasma membrane of the cell? You should be able to predict the chemical and electrical gradients of these ions.

Answer 90

Intracellular: lots of PO4, Proteins, more K+, fewer Cl-
Extracellular: More Cl-, More Na+, Less K+, Ca2+

Question 91

How can you predict electrical gradient?

Answer 91

Ion channels: move through channels down their concentration gradient and down their electrical gradient toward unlike charges

Question 92

Can you name a steroid hormone? What molecule are steroids derived from?

Answer 92

Estradiol and testosterone

Steroids are derived from cholesterol

Question 93

What are aquaporins

Answer 93

Aquaporins (AQP): integral membrane proteins that serve as channels in the transfer of water, and in some cases, small solutes across the membrane.
They are conserved in bacteria, plants, and animals.

Question 94

What are the main differences between passive and active transport? Give examples of each type of transport and be able to describe why it is passive or why it is active. Also explain which type of transport is spontaneous and which is not a spontaneous process.

Answer 94

passive transport / facilitated diffusion: down a concentration gradient; requires no energy – small molecules, nonpolar (diffusion)

active transport: up a concentration gradient, polar; requires energy / uphill

Question 95

*17. A brain cell (neuron) and a liver cell (hepatocyte) have very different functions. It should not be surprising that the protein composition of their cell membranes is different. Describe how might the protein membrane composition of a neuron differ from a liver cell?

Answer 95

neuron: voltage gated channels, membrane potentials (charge difference across membrane)
liver: ligand-gated channels – lock and key

Question 96

18. What is a meant by a gated channel? Give an example of a gated channel.

Answer 96

Ion gated channel: They respond to chemical and electrical signals in the cell. They tightly control the flow of ions through Voltage and Ligand gated channels. Structure of ion channels determine which ions travel through based on:
size
charge

Ion channels: move through channels down their concentration gradient and down their electrical gradient toward unlike charges

Examples:
Voltage-gated channel
sodium and potassium channels
calcium channels

Ligand-gated channel
Nictotinic acetylcholine receptor (a special sodium channel)

Question 97

What is osmosis? Can you predict the direction of the flow of water across a semipermeable membrane (permeable to water but not solute)?

Answer 97

“Diffusion of Water” from an area of high concentration to a low concentration.

Question 98

Can you predict what will happen to cells placed into a hypotonic solution? Cells placed into hypertonic solution? Cells placed into isotonic solution?

Answer 98

Hypotonic: They will grow in size as they try to equalize with the outside solution.
Hypertonic: They shrink in size in order to try and equalize with the outside solution.
Isotonic: Nothing.

Question 99

What happens when you add detergent to cells? Explain the mechanism behind the ability of detergent to disrupt cell membranes and how they can be used to separate proteins from cell membranes.

Answer 99

The cell membrane breaks down. Detergent breaks down the phospholipid bilayer of the cell. They separate proteins by breaking the phospholipids away.

Question 100

Can ions diffuse across the cell membrane? Why or Why not?

Answer 100

Yes, but only through Active Transport

Question 101

Passive Transport= Facilitated Diffusion

Answer 101

Downhill or spontaneous process, requires no input of energy

Question 102

Active Transport=

Answer 102

Uphill or nonspontaneous process, requires energy to occur.
Ions move down concentration gradients. They also move down their electrical gradients(towards unlike charge)
Ions respond to “Electrochemical Gradients”

Question 103

What is an electrochemical gradient?

Answer 103

-Is a gradient of electrochemical potential, usually for an ion that can move across a membrane. The gradient consists of two parts, the electrical potential and a difference in the chemical concentration across a membrane.

Question 104

What are the symptoms of cystic fibrosis? What parts of the body are affected by cystic fibrosis? What molecule in the cell is responsible for the symptoms of cystic fibrosis? What is the cystic fibrosis transmembrane conductance regulator (CFTR)? What is transported by the CFTR and in what direction is it transported? Is the CFTR an example of passive transport or active transport? How does the mutation in the molecule affect its function and how does it affect osmosis in the body? Describe how a dysfunctional CFTR channel leads to the symptoms of cystic fibrosis?

Answer 104

Cystic Fibrosis is a mutation in the chloride channel CFTR (cystic fibrosis transmembrane conductance regulator); In 70-85% of CF cases, mutation is 3-bp deletion = loss of phenylalanine # 508; Mutations in gene encoding CFTR protein, eliminates its function

Part of body affected: Build up in lungs, digestive tract, reproductive tract, tears

How molecule affects function: Prevents transport of chloride (and indirectly sodium); Salts get retained intracellularly and the chlorine channel is non-existent or dysfunction, so chlorine is trapped inside and the sodium channels become overactive, pulling sodium in and stealing water from extracellular fluid (where the mucus is) which become hypertonic to extracellular fluid (in lungs, intestines, sweat glands, reproductive tract); Water is pulled from mucus lining in lungs.Mucus dries out and gets thick and cannot move properly.

Question 105

Consider the sodium potassium pump (Na+/K+ ATPase). Can you explain how the sodium potassium pump works? Why is it considered to be an active transporter protein (explain what is transported, in what directions the items are transported and what gradients exist and whether the protein transports the items down or against these gradients)? What provides the energy to run this pump?

Answer 105

sodium more on outside of cell, usually.

When sodiums comes out of cell, they fit into shape, ATP comes and attaches and break sup phosphate groups and attaching to the protein changes shape and opens and allows K+ to fit if not same the shape of receptor and phosphate group is kicked off, therefore, the channel opens and K+ goes inside cell.

Question 106

Why is the function of Na+/K+ ATPase important to a cell?

Answer 106

Maintains gradient and transport of K+ and Na+ ; it changes the shape so they can move in and out of the cell; It’s important because it pumps sodium out so the cell doesn’t lyse / explode. Potassium needs to be more inside the cell. Cell wants 140 concentration inside of K+.

Outside: 
Na+
Cl- (Chlorine)
Inside more:
K+
Ca+

Question 107

What are the three domains of life? Give a specific (specific organism, specific species) example of each.

Answer 107

bacteria: organism - species - MRSA, staphylococcus
archaea: organism - species - Thermophilia
eukarya: organism - species - yeast, tetrahymena

Question 108

Why do they say that the bacteria and Archaea are ubiquitous (omnipresent)? Back up your statement using examples.

Answer 108

Bacteria + archaea:
ancient: oldest fossils are 3.5 billion years old
abundant: most dominant forms of life by volume, we have more bacteria on our body than cells in our body; # of bacteria and archaea alive today 5X10^30
ubiquitous: in soils, oceans, organisms, form biofilms on surfaces
diverse
1. abundance: diverse in the number of species and abundant – 1 trillion cells in our body are outnumbered 10-1 by bacterial and archaeal cells living on and in you; a teaspoon of good quality soil contains billions of microbial cells; marine archaea = 10,000 individuals per milliliter in world’s oceans; bacteria and archaea living under the ocean makes up 10% of the world’s mass; number of bacteria and archaea alive today = 5X10^30; bacteria and archaea are the dominant life forms in terms of volume of living material
2. habitat diversity: they’re found almost everywhere; they live in environments where others can’t live (oxygen free mud, hot springs, salt flats), they are found as deep as 10,000 meters of seawater and at temps over 120 degrees; there are more prokaryotes than eukaryotes

Question 109

What is an extremophile? Can you provide a specific example of one extremophile that is important for research in biotechnology? Where is this extremophile found? Explain what enzyme in this organism is used in biotechnology. What is the technology that uses this enzyme? What property of this enzyme allows it to be used for this application?

Answer 109

: archaea - extreme environment lovers; they live in high-salt, high-temp, low-temp, or high pressure habitats

enzymes isolated from some of these are used in research, forensics, sequencing tech, conservation genetics, food sciences, molecules research, evolution research

example: an archaean grows close to hydrothermal vents that its surroundings are at 121C, a record high for life; it helps us understand the tree of life, develop industrial applications, and explore the structure and function of enzymes; the genomes of extremophiles have been sequenced and expeditions to seek new species because the first forms of life lived at high temperature and pressure environments and lacked oxygen – this may explain how life on earth began and also give us evidence of extraterrestrial life. Also, enzymes that function at high temps and pressures may be useful in industrial processes
enzyme: DNA polymerase Taq polymerase; Thermus aquaticus – bacterium that lives in hot water springs in Yellowstone

technology: PCR - Taq polymerase chain reaction in research and commercial settings - isolated from Thermus aquaticus, thermostable, tolerates rapid changes in temp, used to copy DNA in PCR, can make millions of copies before it loses activity
properties: it’s stable up to 95C

Types: OneTaq, Deep Vent, Top Taq, VeriQuest Taq, Terra PCR direct

Question 110

Why are we humans so interested in studying the bacteria and Archaea? In other words, of what importance are these organisms to our lives?

Answer 110

1. origin of life
2. extraterrestrial life
3. commercial applications (taq poly)
4. medical importance: thousands of bacteria species live in and on our body, only a tiny fraction of those can disrupt normal body function “pathogenic”; pathogenic forms come from several different lineages, and tend to affect tissues at entry points of body (wounds, pores) in the respiratory and gastrointestinal tract and the urogenital canal.
5. bioremediation: using bacteria and archaea to clean up pollution to something less toxic and more processable .

Question 111

Can you name at least one type of pathogenic bacteria? What disease/illness is caused by this bacteria?

Answer 111

Anthrax: autoimmune
Firmicutes: staphlococcus/Streptococcus: affect nervous system, respiratory tract, skin, wounds, etc. disease: tetanus, acnes, shock, boils, pneumonia, strep throat, scarlet fever

Question 112

Who was Robert Koch?

Answer 112

Koch’s postulates: they define what is pathogenic (causes disease)
microbe must be present in individuals suffering from disease and absent in healthy individuals
organism must be isolated and grown in pure culture away from host organism
if organism from pure culture are injected into a healthy experimental animal, disease symptoms should appear
the organism should be isolated from the diseased experimental animal, again, grown in pure culture and demonstrated by size, shape, color to be the same as original organism.

Question 113

Germ theory of disease:

Answer 113

laid the foundation for modern medicine, initially its greatest impact was sanitation – efforts to prevent pathogen transmission

Question 114

What is meant by virulence? Why do we say that virulence is a heritable trait?

Answer 114

virulence: ability to cause disease is a heritable trait that varies among individuals in a population; natural selection operates on this trait. Some e.coli strains are harmless and some produce toxins that can kill cells in digestive tract

Question 115

Why do scientists believe that we may see more antibiotic-resistant strains of pathogenic bacteria? Some even believe that we are about to enter a “post-antibiotic era”.

Answer 115

Extensive use of antibiotics in late 20th century in clinics and animal feed led to the evolution of drug resistant strains of pathogenic bacteria – one study found that there are soil-dwelling bacteria in natural environments that actually use them as food. We may be entering the post-antibiotic era in medicine. Bacteria usually grow in biofilms (dense colonies enmeshed in polysaccharide-rich matrix helping shield them from antibiotics. Yikes: these are growing on catheters in hospitals!

Ribosomal additions to protect themselves from anti-bacteria?/?/?/

Question 116

What is metagenomics? What is the goal of metagenomics? How do we study metagenomes?

Answer 116

metagenomics: way to study communities of microbes by sequencing their genomes.

goal: The goal is to identify and characterize communities of organisms that are not able to be cultured in the lab (greater than 99%) environmental sequencing which allows biologists to rapidly identify and characterize organisms that have never been seen.;
to document the presence of bacteria and archaea in the environmental sample that cannot be grown in culture

determine profile of microbes that live in our bodies
healthy people have different bacteria than sick ones
key to using microbes to boost health

Question 117

What is bioremediation? How are bacteria and Archaea used for bioremediation?

Answer 117

bioremediation: bacteria are placed in contaminated sites to assist in cleanup; bacteria consume/breakdown hazardous contaminants forming less toxic byproducts, also add nitrogen
organic solvents
wastewater
oil spills
chlorines / dioxins

Question 118

Describe 3 examples illustrating how the Bacteria are diverse in structure. Describe 3 examples in which bacteria are diverse in function. Describe 3 examples in which bacteria are diverse in metabolism.

Answer 118

Bacteria are diverse in structure

size: range in size from smallest of free-living cells (“mycoplasmas” which are .015um^3) to the largest known (“thiomargarita namibiensis, 200X10^6 um^3); ie. one billion mycoplasma cells could fit into a namibiensis
shape: filaments, spheres, rods, chains, spirals
motility: many are motile, swimming movements using rotating flagella; they swim ahead or tumble, which allows them to change directions; gliding movement (creep along surface)

Bacteria are diverse in metabolism – they produce ATP in 3 ways: page 538
phototrophs: “light feeders” use light energy to excite electrons. ATP is produced by photophosphorylation:
Chemoorganotrophs: oxidize organic molecules with high potential energies (ie. sugars)
Chemolithotrophs:oxidize inorganic molecules using ammonia and methane

Question 119

What two types of bacteria are distinguished with the gram stain? What parts (structures) of the bacteria are stained by the Gram Stain method? What is different about the compositions of these structures in the two groups of bacteria that are detected by the stain?

Answer 119

Gram positive

gram negative

Question 120

What is an Autotroph? What is a heterotroph?

Answer 120

Autotroph: self-feeders synthesize building blocks from simple molecules( cO2 / CH4) organisms that manufacture their own building block compounds
Heterotroph: other-feeders absorb organics from environment (and other orgs) organisms that acquire building block compounds from other organisms

Question 121

What are Protists? Are protists single-celled organisms or multi-celled organisms. Give examples.

Answer 121

all eukaryotes that aren’t plants, animals, and fungi. They are multicellular and most are unicellular; they don’t make up a monolithic group; represent some of single common ancestor;

Question 122

What type of environment are protists usually found? Why are they studied by scientists (What makes them important)?

Answer 122

Found: environments surrounded by water: ie. wet soils, aquatic habitats, inside bodies of other organisms
Why studied:
medically: cause disease like malaria, food crops, parasites in humans, algal blooms, drug resistance
ecologically: aquatic food chains, climate change
evolution: understand evolution of life on earth

Question 123

Name a specific type of protist that causes disease (See table 30.1 in your text). Name the disease that is caused by the Protist.

Answer 123

Leishmania: causes skin sores / affect internal organs - spleen and liver
Malaria: most infection disease in world; enters through blood - infects liver cells and in your brain.
Phytophthora infestans: responsible for irish potato famine
giardia: diarrhea can last several weeks

Question 124

What are algal blooms? What are red tides? What type of protist are often reproducing to cause the algal blooms? Why are we concerned with algal blooms such as red tides?

Answer 124

algal blooms: unicellular species have rapid population growth due to photosynthetic protists (dinoflagellates) – some synthesize toxins to protect themselves from predation by copepods. Have high concentrations of pigments (xanthophylls) which discolor water.
toxins released by dinos build up in shellfish (paralytic shellfish poisoning where saxitoxin blocks ion channels – weakness + paralysis)

Red Tides: caused by algal bloom: Shell fish poisoning – feeding on protist-fed shellfish; saxotoxins block ion channels and it affect nerve cells (block signal from travelling); muscle weakness, paralysis, prickling sensation ni mouth

Why concerned: harmful to people because clams and shellfish filter protists out of the water as food, which causes high levels of toxins to build up. Saxitoxins – cause prickling in mouth, muscle weakness, and paralysis.

Question 125

Compare and contrast the structure (including composition) and function of flagella found in Bacteria/Archaea with those found in the Eukaryotes?

Answer 125

Prokaryotes: (Bacteria/Archaea) – small, nucleoid (DNA location), few permanent internal membranes, no nuclear membrane (nor mitochondria), DNA circular, binary fission/budding reproduce, rotating flagella, cytoskeleton proteins help cell division, cytoplasm contains all contents of cell different than outside, cell wall counteracts forces of osmosis (gives shape + rigidity) – may be polysaccharide on outside)
Eukaryotes: large, DNA in nucleus, membrane-bound parts, DNA linear, mitosis/meiosis reproduce, tubulin cilia flap

Question 126

What is the endosymbiont theory? Who proposed the endosymbiont theory? Describe the evidence for this theory (Hint: we talked about 5 lines of evidence to back up this theory).

Answer 126

endosymbiont theory: symbiotic relationship allowed host to occupy new environments with oxygen. mitochondria originated when a bacterial cell took up residence in another cell 2 billion years ago
Proposed by: Lynn Marguilus: proposed that modern mitochondria are remnants of ancestral aerobic bacterium that took up residence in archaeal host.
Evidence: mutual advantage:
host supplied bacteria with protection and carbon compounds from prey
bacterium produced much more ATP than the host cell could synthesize on its own

evidence slides:
mitochondria are same size as bacteria
have their own circular DNA molecules (like bacteria)
have their own ribosomes which are poisoned by same antibiotics that inhibit bacterial ribosomes
have double membranes consistent with engulfing mechanism
divide by binary fission as bacteria do

Question 127

How do scientists hypothesize that the nuclear envelope and endomembrane system evolved? What is the evidence for this hypothesis?

Answer 127

1. membrane infoldings surround chromosomes
2. eukaryotic cells arises with enfoldings forming nuclear envelope and ER; enfolding became detached from plasma membrane, giving rise to ER and nuclear envelope

infoldings of plasma membrane led to development of the membrane bound organelles – nuclear envelope, ER, golgi, mitochondria, chloroplasts

Question 128

What is secondary endosymbiosis? What is the evidence for secondary endosymbiosis?

Answer 128

photosynthetic eukaryotic cells: The photosynthetic protist was engulfed by predatory protist, nucleus formed from photosynthetic protist (which was lost in process), organelle has four membranes.

Evidence: chloroplasts have bacteria-like characteristics (same as mitochondria list)
modern examples of cyanobacteria living inside protists and animals

Question 129

What is the cytosol? How is the aqueous environment on the inside of the cell different from the outside of the cell?

Answer 129

cytosol: fluid between plasma membrane and organelles – small volume.
small volume of cytosol reduces the effect of total surface area to volume ratio (exchange of nutrients and waste products)

Question 130

What parts of the cell are included in the endomembrane system?

Answer 130

golgi apparatus
endoplasmic reticulum
lysosomes

Question 131

What is a lysosome? Describe its structure and function.

Answer 131

ontain hydrolytic enzymes break down macromolecules into building blocks to be reused by cell;
hydrolases function at pH5;
used in phagocytosis + recycling cellular organelles; found only in animal cells

Question 132

What inherited disease is caused by a lysosome dysfunction? Explain the symptoms of this disease

Answer 132

Build up of a lipid that is normally broken down in the lysosome of cells in CNS
Tay-sachs: lipis build up around nerve cells because they are not broken down in the normal way. Infants losing sight, hearing, and movement, death usually within 3 years.

Question 133

Where is the RER found in the cell? Name 3 functions of the RER. Describe why the RER is called the “Rough” endoplasmic reticulum.

Answer 133

protein synthesis, proteins produced here end up in the plasma membrane, secreted from cell

Question 134

Name 3 functions of the smooth endoplasmic reticulum (SER)

Answer 134

lipid synthesis
detox
stores CA2+ for cell signalling

Question 135

What is a peroxisome? What is the function of a peroxisome? Why is compartmentalization with membranes particularly important for this organelle?

Answer 135

globular organelles that are centers for reduction oxidation; single membrane + originate as buds in ER.
byproducts include H202
enzymes that oxidize h202 into water and oxygen
If it didn’t have a membrane, it would just eat up all the cell’s parts.

Question 136

Mitochondria

Answer 136

Mitochondria is where ATP is made during cellular respiration; How structure allows it to perform its function:
double membrane
inner membrane folded into cristae – contains proteins in electron transport chain + ATP synthase
innermost region is matrix

Question 137

chloroplast

Answer 137

Organelles in plants and most algae where sunlight converted into energy
double membrane
membrane-bound stacks of thylakoids
structural proteins, pigments, and enzymes responsible for photosynthesis are embedded in thylakoid membranes

Question 138

Name 3 types of protein filaments that make up the cytoskeleton. Describe a function of each type of filament and give an example of the filament.

Answer 138

actin filaments: strands with double helix (microfilaments) / acting
intermediate filaments: fibers wound into thicker cables // keratin, lamin, others
microtubules: alpha and beta tubulin

Question 139

Name 3 types of motor proteins in our cells. Give an example illustrating the function of each of these two types of motor proteins. p 133

Answer 139

actin
myosin
dynein

Question 140

What is the point of cellular respiration (what is the purpose of cellular respiration)?

Answer 140

To make energy quickly – oxidizing glucose to make ATP (energy released is used to make ATP)

Question 141

When individuals hear the word “respiration” they often are thinking of ventilation. How would you explain the difference between ventilation and cellular respiration?

Answer 141

Cellular respiration has nothing to do breathing. Ventilation does. Cellular respiration is the process of making energy from glucose.

Question 142

Steps of cellular respiration

Answer 142

1. glycolysis: occurs in cytoplasm of eukaryotes and prokaryotes; one 6-carbon molecule of glucose is broken into pyruvate (two molecules of 3-carbon compound), ATP is produced from ADP and NAD is reduced to make NADH.
2. pyruvate processing: occurs in matrix of mitochondria or cytoplasm of prokaryotes; pyruvate is processed (oxidized) to release one CO2 molecule and remaining two carbons are used to form acetyl CoA – results in more NAD+ being reduced to NADH
3. citric acid cycle (KREBS): to two molecules of CO2, more ATP and NADH are produced and FAD is reduced to form FADH2
4. electron transport and oxidative phosphorylation: occurs in inner membrane of mitochondria or plasma membrane of prokaryotes; electrons from NADH and FADH2 move through proteins (ETC - electron transport chain) – energy released in chain of redox reactions is used to create a proton gradient across the membrane; protons flow back across the membrane to make ATP (this mode links the phosphorylation of ADP with oxidation of NADH and FADH2)

Question 143

How many high energy molecules are produced (nucleotides, electron carriers)? What substances feed in and what comes out?

Answer 143

1. glycolysis: 10 reactions, happens in cytoplasm // glucose goes in, 2 pyruvate comes out
   1st 4 reactions: energy investment! (using ATP to start reaction), 1st + 3rd requires input of energy (2 ATP molecules), starts with 6-carbon molecules that gets split into two 3-carbon molecules;
   2nd 5 reactions: energy payoff! 2 NAD+ molecules get reduced into 2 NADH molecules, also 2 ATP (net) molecules getting made; 2 NADH + 2 ATP (net) energy produced) ; 6th NAD+ —> NADH // 7th + 10th generate 4 ATP (2 each), 2 actually gained along with 2 pyruvate = enzyme catalyzes transfer of ADP to ATP
   where: cytoplasm
   input: glucose
   output: pyruvate
   energy: 2 ATP

substrate level phosphorylation: enzyme reactions resulting in ATP production

2. pyruvate processing: take 2 pyruvates to make 2 CoA out and 2 NADH out(no ATP)
   where: matrix of mitochondria
   input: pyruvate
   output: 2 Acetyl CoA
   energy: 2 NADH
3. Krebs/Citric Acid: redox reaction; to two molecules of CO2, more ATP and NADH are produced and FAD is reduced to form FADH2
   where: matrix of mitochondria
   input: 2 Acetyl CoA
   output: 2 (4????) CO2
   energy: 6 NADH, 2 FADH 2, and 2 GTP (later gets turned into ATP)
4. oxidative phosphorylation / electron transport: final electron acceptor is O2
   where: inner membrane of mitochondria
   input: NADH (complex 1) + FADH 2 (complex 2) —> (complex 3) —> (electron donated to make 02)
   output: 25 H+s + 0 + electron makes H20
   energy: makes 25 ATP.

Question 144

ATP Synthase:

Answer 144

in intermembrane space – Higher H+ concentration outside than inside, the H+ from the outside go in through ATP synthase and move rotor and connects phosphate group to ADP to make ATP. Makes 25 ATP.
ATP Synthase: chemiosmosis: process of cranking out ATP into the matrix

Question 145

What are redox chemical reactions? Give 2 examples of redox reactions from your text or lecture. In these examples state what is being oxidized and what is being reduced.

Answer 145

redox: reactions are assisted by enzymes
reduction :molecule is “reduced” by gaining electrons. They often are accompanied by protons, so look for molecules that gain hydrogen ions.
oxidation: molecule is “oxidized” when it loses electrons (and maybe lose hydrogens too)
Oxidation: energy rich molecule to product
enzymes that use NAD++ as cofactor for oxidation reactinos bind NAD+ and the substrate
2 electrons and proton are transfered to NAD+, forming NADH; second proton is donated to the solution
NADH diffuses away and donates electrons to other molecules
reduction: product to energy rich molecule; opposite of above?

Question 146

How do enzymes contribute to the redox reactions?

Answer 146

substrate level phosphorylation: when an enzyme catalyses a reaction that results in the production of ATP; reactions 7+10 – transfer of phosphate group from substrate to ADP to form ATP

in cells, enzymes routinely break down fats to release the glycerol and convert the fatty acids into acetyl CoA molecules; glycerol can be processed and enter glycolysis; acetyl CoA enters the citric acid cycle

Question 147

How does the production of ATP by substrate level phosphorylation differ from the production of ATP through chemiosmosis? In your answer define each of the two types of ATP production and describe where specifically each process takes place in the cell.

Answer 147

Phosphorylation uses the electron transport chain during this process–you get 2 ATP out of it (4?) – bulk of ATP comes through chemiosmosis (like 34 ATP!) … movement of electrons generate this

Question 148

What is the point of fermentation? Why are some organisms unable to carry out aerobic respiration?

Answer 148

To make energy without oxygen.

Question 149

Name two high-energy electron carriers

Answer 149

NADH

FADH2

Question 150

Name two high-energy nucleotides

Answer 150

ATP and GTP

Question 151

How many and what type of high energy nucleotides are produced in glycolysis from 1 molecule of glucose?

Answer 151

2 ATP, 2 NADH (is NADH a nucleotide?)

Question 152

Where is pyruvate converted to Acetyl-CoA? If you assume that all the products of glycolysis are converted to Acetyl-CoA, how many Acetyl-CoA will be produced from 1 molecule of glucose?

Answer 152

The matrix of the Mitochondria. 2 Acetyl-CoA.

Question 153

in addition to Acetyl-CoA and NADH, what else is generated in the oxidation of pyruvate into Acetyl-CoA?

Answer 153

CO2

Question 154

How many NADH are generated when 2 molecules of pyruvate are converted to 2 molecules of Acetyl-CoA?

Answer 154

6 NADH

2 FADH 2

Question 155

What molecules feed into the citric acid cycle? How many will be coming from 1 molecule of glucose?

Answer 155

2-Pyruvate feed in. 2 Acetyl and 2-CO2 CoA come out.

Question 156

What high-energy electron carriers are generated by the citric acid cycle?

Answer 156

6-NADH and 2 FADH2

Question 157

How many of each type of electron carrier will be produced in the citric acid cycle if two Acetyl-CoA molecules go into the cycle? How many and what type of high energy nucleotides are directly generated in this cycle?

Answer 157

2-GtP (later converted into ATP),

Question 158

Which protein complex in the electron transport chain accepts electrons from NADH molecules? What molecule accepts electrons from FADH2?

Answer 158

NADH gives up electrons to Complex I. FADH2 gives up electrons to Complex 2.

Question 159

Describe the direction in which protons are pumped by complexes 1, 3, and 4 in the electron transport chain? Note: mitochondria is not a sufficient answer. Describe the specific parts of the mitochondria from which protons are pumped and what part where they are pumped too by these complexes.

Answer 159

Complexes 1,3,4 pump H+ against their gradient into the intermembrane space. They are being pumped into the intermembrane space.

Question 160

About how many total ATP are generated by the complete oxidation of one molecule of glucose into CO2? How many of these ATP are generated by chemiosmosis? Where do the remaining ATP come from?

Answer 160

The total number of ATP=29. 2 From Glycolosis, 2 from Citric Acid Cycle, and 25 from Chemiosmosis.

Question 161

How many ATP are generated from 1 glucose molecule in the process of yeast fermentation? Are yeast prokaryotes or eukaryotes?

Answer 161

2 ATP through alcohol fermentation. Yeast are Eukaryotes.

Question 162

Can you give 3 examples of how ATP is used in a cell to do work? (Hint, think of 3 things that require energy for the cell to do, we have talked about many types of work done in the cell). NEED SPECIFICS

Answer 162

1. DNA synthesis
2. To separate chromosomes during Anaphase
3. to pump elements across the cell membrane that are too large to diffuse, polar, or against their gradient.

Question 163

2. What is the endosymbiont theory? Can you describe all of the evidence supporting the endosymbiont theory?

Answer 163

evidence slides:
mitochondria are same size as bacteria
have their own circular DNA molecules (like bacteria)
have their own ribosomes which are poisoned by same antibiotics that inhibit bacterial ribosomes
have double membranes consistent with engulfing mechanism
divide by binary fission as bacteria do

Question 164

zygote

Answer 164

the cell that results from fertilization; when two haploid gametes fuse during fertilization, a full complement of chromosomes is restored

Question 165

Haploid

Answer 165

having one set of chromosomes; a cell or individual with one set of chromosomes

Question 166

Diploid:

Answer 166

having two sets of chromosomes; a cell or individual organism with two sets — one from mother and one from father

Question 167

aneuploid

Answer 167

the state of having an abnormal number of copies of a certain chromosome

Question 168

G1 (gap 1) phase

Answer 168

gap between end of M and start of S phase

Question 169

motor proteins:

Answer 169

class of proteins whose major function is to convert the chemical energy of ATP into motion – dynein, kinesin, myosin

Question 170

Tumor suppressor gene

Answer 170

a protein that prevents cell division, such as when cell has DNA damage – mutant genes that code for tumor supp. are associated with cancer

Question 171

Proto-oncogene

Answer 171

(slide) proteins required for normal cell growth – if mutated they become active when they shouldn’t be – uncontrolled cell growth = cancer

Question 172

Oncogene:

Answer 172

any gene whose protein product stimulates cell division at all times and thus promotes cancer development; often mutated form of a gene involved in regulating cell cycle

Question 173

Cyclin-dependent protein kinase (Cdk)

Answer 173

any several related protein kinases that are functional only when bound to a cyclin and are activated by other modifications; involved in control of cell cycle; cannot’ be switched off! They can be phosphorylated and inactivated; as cyclin concentrations decrease, CDKs become inactive

Question 174

M-phase promoting factor (MPF):

Answer 174

a complex of cyclin and dependent kinase that, when activated, phosphorylates a number of specific proteins needed to initiate mitosis in eukaryotic cells

Question 175

gametogenesis

Answer 175

process where haploid daughter cells, each containing one of each homologous chromosomes eventually go on to form egg cells or sperm cells

Question 176

tetrad

Answer 176

the structure formed by synapses homologous chromosomes during prophase of meiosis I

Question 177

nondisjunction

Answer 177

if both homologs in meiosos I or both sister chromatids in meiosis II move to same pole of parent cell, the products will be abnormal

Question 178

aneuploidy

Answer 178

cells have too many or too few chromosomes of particular type

Question 179

monosomy

Answer 179

the state of having only one copy of particular type of chromosome in an otherwise diploid cell

Question 180

What are three purposes of eukaryotic cell replication by mitosis?

Answer 180

1. growth
2. wound repair
3. reproduction

Question 181

Compare and Contrast prokaryotic cell division with eukaryotic cell division. What is prokaryotic cell division called?

Answer 181

prokaryotic: divide by binary fission whenever nutrients available and cells are large enough
eukaryotic: nuclear division cell cycles – somatic cells divide to produce 2 genetically identical daughter cells / and division for germ line cells to produce genetically different haploid gametes

Question 182

What is the role of the cytoskeleton such as actin filaments and microtubules during mitosis?

Answer 182

spindle apparatus forms: composed of microtubules originating from microtubule organizing centers (centrosome w/centrioles in animal cells); they move chromosomse

vesicles from golgi apparatus carry components to build a new cell wall using these polar microtubules via motor proteins; the furrow appears because a ring of actin filaments forms just inside membrane – myosin motor proteins bind to these actin filaments and use ATP to contract in a way that cause actin filaments to slide; myosin moves the ring of actin on the inside of membrane, the ring shrinks in size and tightens. Actin and myosin filaments slide past each other, tightening the ring further, until original membrane pinches in two and cell division is complete.

Question 183

DNA is organized around proteins. Why is it necessary to condense DNA into compact structures before cell division can occur?

Answer 183

DNA wrapped around globular histone proteins– chromatin; during interphase, the chromatin is relaxed / uncondensed, forming long, thin strands.

Question 184

How might the cell cycle of a developing embryonic cell differ from a neuron? How about from a skin cell?

Answer 184

intestine: 2 times a day
neuron + muscle: many do not divide
liver cells: replicate once per year. If liver is damaged, remaining cells divide every 1-2 days.

Question 185

In broad terms, what conditions must be met before a cell can divide? Specifically, what is “checked” at the G1 checkpoint? The G2 checkpoint? The M-phase Checkpoint?

Answer 185

Synthesis phase: DNA replication before a cell can divide (meiosis / mitosis) the DNA must be replicated so there will be enough for daughter cells.

G1 + G2: growth, replicating organelles and increase in size
G1: determines if cell will go through cycle and divide or exit;
size: daughter cells large enough to function
nutrients available
social signals: signalling molecules from other cells (social signals)
damage to DNA: physical damage – repairable or not / apoptosis
G2: After S phase: DNA damaged or chromosomes not replicated correctly – removable of inactivating phosphate blocked; when MPF is not turned on, cells remain in G2; related to size, too
M-Phase: (2)
kinetochores attached properly to spindle apparatus;
chromosomes might not separate correctly

Question 186

What is a protein kinase? How are these enzymes involved in cell cycle regulation?

Answer 186

kinase: polypeptide subunit catalyzes transfer of phosphate group from ATP to target proteni (regulatory protein)

Question 187

Describe how MPF regulates cell division at the M-checkpoint.

Answer 187

appears to signal “start M phase”
maek of distinct polypeptide subunits – concentration of kinase is more or less constant throughout cycle; cyclins: their concentrations fluctuate throughout cell cycles; concentration of cyclin associated with MPF during interphase and peaks in M phase; timing is key, MPF is only functional when bound to cyclin (which regulates MPF dimer)
kinase: catalyzes transfer to a target protein
cyclin: regulates MPF dimer

MFP is a CDK: activates proteins necessary to start M-phase by phosphorylating them
molecule that initiates mitosis was M-phase promoting factor
is a type of cyclin-dependent protein kinase (CDK)
kinases put a phosphate group on target proteins

CDKs phosphorylate proteins that are necessary for the next stage: types
PF activates proteins necessary to start mitosis
another maintains cells in G0 phase
activates proteins necessary to push cell from G1 into S

Important to regulate: because of cancer
Pronto-oncogenes: two types of defects cause cancer
Ex: defective Ras protein triggers uncontrolled cell growth

Question 188

Cell cycle:

Answer 188

Mitosis: two sister chromatids separate into separate genetically identical daughter cells; 5 phase:

prophase: chromosomes condense – DNA wraps tightly around histones and scaffolding proteins (tightly packed);
prometaphase: nuclear envelope breaks down, microtubules contact kinetochores
metaphase: chromosomes all line up independently at the metaphase plate (middle”), spindle apparatus complete (centrioles at opposite poles of cell)
anaphase: sister chromatids separate into daughter chromosomes and are pulled apart
telophase: nuclear envelope reforms, chromosomes de-condense
cytokinesis: in plant cells, cell plate forms in location of metaphase plate // in animal cells, furrow forms (actin and myosin contractile ring constricts cytoplasm)

Question 189

Know the differences between mitosis and meiosis including: how the phases differ and what types of cells undergo each process).

Answer 189

Mitosis:

1. cell divisions: 1
2. # of chromosomes in daughter cell compared to parent: same
3. synapsis of homologs: no
4. # of crossing over: none
5. makeup of chromosomes in daughter cells: identical
6. role: asexual reproduction in some eukaryotes, cell division for growth
7. homologous chromosomes pairing timing: don’t pair at all
8. align @ plate: individual chromosomes line up single file
9. result: identical daughters

Meiosis:

1. cell divisions: 2
2. # of chromosomes in daughter cells compared to parent: half
3. synapsis of homologs: 1 + per pair of homologous chromosomes
4. # of crossing over: different - various combos of maternal/paternal chromosomes, both are mixed within chromosomes
5. role: 1/2’ing chromosomes in cells that produce gametes
6. homologous chromosomes pairing timing: early
7. align @ plate: homologous paired up
   result: non-identical daughters (unique)

Question 190

What are two processes in meiosis that generate genetic diversity in the gametes? In what phases of meiosis do these processes occur? Could you draw diagrams of each of these phases, and label: homologous chromosomes, centromere, sister chromatids.

Answer 190

independent assortment
crossing over
random fertilization
random mating

Question 191

How many chromosomes are in a human somatic cell? Human gamete?

Answer 191

somatic cell: 23

human gamete: 46

Question 192

What is the term that refers to failure of chromosomes to separate correctly during Meiosis I or meiosis II? What is the result of this in terms of the effects on the resulting daughter cells?

Answer 192

nondisjunction: when sister chromatids in meiosis II move to same pole – homologs / sister chromatids fail to separate (disjoin)
aneuploidy: too many or too few chromosomes

Question 193

Name 3 genetic disorders than are caused by the inability of chromosomes to separate correctly during meiosis. In each of these diseases, state which chromosomes are affected, and the symptoms of the genetic disorder. Name two factors that increases the likelihood of these disorders occurring.

Answer 193

Patau Syndrome:
Kinefelter Syndrome:
Turner Syndrome:
Down Syndrome: 23

Question 194

Be able to identify the pedigrees showing X-linked dominant, X-linked recessive, autosomal dominant and autosomal recessive patterns of inheritance.

Answer 194

Autosomal vs. Sex-linked:

If a trait appears about equally often in males and females, then it’s likely to be autosomal; but if males express trait more often, then alleles responsible is likely to be recessive and found on X chromosome.
X linked recessive traits: males express trait more often than females; appearance of X-linked recessive usually skips a generation in pedigree. Most X-linked traits are recessive. 278
X-linked dominant: an affected male will pass the trait to all his daughters and none to his sons; because daughters have their father’s only X chromosome; heterozygous female will pass the trait to 1/2 daughters and 1/2 sons
Y-linked traits: very few genes occurs on Y. They are involved with male specific sexual development; there are no known human Y-linked traits.

Question 195

Recombinant

Answer 195

the combination of alleles on X chromosome is different from combinations of alleles present in the mother

Question 196

Which would lead to a higher frequency of recombination, genes that are very far apart, or genes that are very close together? Why?

Answer 196

Genes that are very close together are less likely to separate during crossing over

Question 197

Discuss all the factors that you now know about that affects a person’s phenotype.

Answer 197

Environment: an individual’s phenotype is often as much a product of environment as it is a product of genotype:
temp
sunlight
nutrients available
competition
mother’s hormone levels during development of embryo

   2.  Interactions between genes: genes work together to control a single trait when gene-by-gene interactions occur, one trait is influenced by alleles of two or more genes  one gene influences many traits: pleiotrophic

Question 198

What are quantitative traits. Name 3 examples of quantitative traits.

Answer 198

quantitative traits: continuously varying traits that don’t like to fall into one category; are produced by the independent actions of many genes (some have greater effects than others); are greatly influenced by environment; when the frequency of different trait values observed are plotted on histogram (freq. distribution), they often form a bell shaped curve (normal distribution) p 275

Question 199

What is polygenic inheritance?

Answer 199

polygenic inheritance: each gene adds a small amount to the value of the phenotype; this is why offspring resemble their parents; ie. blood pressure

Question 200

polygenic inheritance: each gene adds a small amount to the value of the phenotype; this is why offspring resemble their parents; ie. blood pressure

Answer 200

pleitrophic: gene that influences many traits — more genes influence more than 1 trait;
ie. mutations in one gene cause Marfan syndrome; FBN1 alleles is dominant to wild-type alleles; people with FBN1 are tall, have long limbs, fingers, abnormally shaped chest, heart problems, etc.

Question 201

monohybrid cross

Answer 201

they evenly get split apart and all the options are the same…ie Bb x 4

Question 202

dihybrid cross:

Answer 202

they can swap – there are multiple options - 3 different options

Question 203

A hypothetical polypeptide is made from an extremely short gene which has the following structure:
5‘ GCATGCATACGACTTAATG 3‘
3’ CGTACGTATGCTGAATTAC 5’

Answer 203

3’ CGUACGUAUGCUGAAUUAC 5’

5’ GCAUGCAUACGACUUAAUG 3’

Question 204

Exceptions to central dogma:

Answer 204

many genes code for RNA molecules that do not function as mRNAs, they are not translated into proteins
info sometimes even flows from RNA back to DNA. ie. reverse transcriptase: when RNA viruses infect a cell, this polymerase synthesizes a DNA version of RNA genes; ex: AIDS / HIV – uses reverse transcriptase

Question 205

It is common to use phrases such as “genes code for proteins”. This is largely correct, in that genes provide the information to build proteins. However the statement “genes code for proteins” is imprecise. Give an example where a gene DOES NOT code for a complete protein.

Answer 205

Stop codons / start codons specify methionine

introns

Question 206

Transcription and translation are terms borrowed from linguistics that are used to describe the conversion of genetic information in the form of DNA into RNA and protein. Explain why each of these terms is appropriate for its respective step in the flow of genetic information. p 308

Answer 206

transcription: making a copy of information; conveys the idea that DNA acts as a permanent record – an information archive or blueprint, which is copied, during transcription, to produce short-lived form (mRNA)
translation: converting info from one language to another; the transfer of info from one type of molecule to another – from language of nucleic acids to language of proteins – also referred to simply as protein synthesis;

Roles of transcription & translation:
DNA is transcribed to RNA by RNA polymerase; Transcription: is the process of copying hereditary info in DNA to RNA
Messenger RNA is translated to proteins in ribosomes; translation: is the process of using the information in nucleic acids to synthesize proteins

Question 207

) Describe the structure of prokaryotic RNA polymerase. What part of the enzyme is responsible for binding the specific region of the promoter to initiate transcription?

Answer 207

large subunit: forms E, P, A binding sites for tRNA, channel for growing polypeptide, area to catalyze formation of peptide bonds
small subunit: binds to mRNA + provide site for complementary binding b/t anticodon on tRNA + codon on mRNA

Question 208

responsible for binding promoter region to initiate transcription:

Answer 208

small subunit

Question 209

How is DNA polymerase similar to RNA polymerase? How are they different?

Answer 209

RNA polymerase: enzyme / protein that catalyzes the synthesis of RNA; it synthesizes RNA molecules according to the information provided by base sequences in particular stretch of DNA’
5’-3’ direction, do not require a primer

The sequence of bases in DNA specifies the sequences of bases in an RNA molecules, which specifies the sequence of amino acids in a protein; genes ultimately code for proteins

DNA polymerase:
5’-3’ direction, require a primer to begin transcription

Question 210

Describe the roles of the promoter and transcription factors in the initiation of eukaryotic transcription

Answer 210

promoters: sections of DNA that promote the start of transcription

promoters vary more than bacterial promoters; most include a sequence (TATA box) centered 30 base pairs upstream of transcription start site
transcription begins when basal transcription protein factors (like a sigma) bind to a promoter — in response, RNA polymerase binds to site; They assemble at the promoter, and RNA polymerase follows 320
initiating transcription: initiation: where and in which direction transcription takes place on DNA template; promoters: sections of DNA that promote the start of transcription; transcription begins when basal transcription protein factors bind to a promoter — in response, RNA polymerase binds to site; They assemble at the promoter, and RNA polymerase follows

also:
elongating polypeptide: RNA polymerase begins moving along the DNA template synthesizing RNA
terminating translation: transcription terminates after RNA is cleaved downstream of poly(A) sequence; eventually, RNA polymerase falls off; termination: transcription stops when RNA polymerase transcribes a DNA sequence that functions as a termination signal — as soon as its synthesized, this portion of RNA folds back on itself and forms a short double helix held together by complementary base pairing (hairpin structure)

Question 211

How does transcription of a gene eventually end in prokaryotes? How does transcription end in eukaryotes?

Answer 211

Prokaryotes: sigma: detachable protein subunit binds to polymerase before transcription begins; makes the initial contact with the DNA of the promoter;
Prokaryotes: termination: transcription stops when RNA polymerase transcribes a DNA sequence that functions as a termination signal — as soon as its synthesized, this portion of RNA folds back on itself and forms a short double helix held together by complementary base pairing (hairpin structure)

Eurk transcription terminates after RNA is cleaved downstream of poly(A) sequence; eventually, RNA polymerase falls off; hairpin forms and changes interactions with polymerase

Question 212

Describe how an mRNA strand gets processed (in eukaryotic organisms) before it is translated. Why is processing necessary?

Answer 212

RNA processing: occurs in nucleus; any modification (such as splicing or polyA tail addition) needed to convert a primary transcript into mature RNA;

primary transcript: the initial product when genes of any type are transcribed — pre-mRNA.
must be processed to produce a mature RNA 321

in these transcripts, stretches of RNA (introns) are spliced out and exons are joined together

ALSO:
Splicing: introns are removed from growing RNA strand; pieces of primary transcript are removed and remaining segments are joined; occurs in nucleus while transcription is underway and results in RNA that contains uninterrupted genetic message. Four steps:
snRNPs bind to 5’ exon-intron boundary (marked by GU) to key A near end of intron
other snRNPs arrive to form multipart spliceosome, which contains 145 proteins and RNAs
intron forms loop plus single-stranded stem (lariat) with A at its connecting point
lariat is cut out, a phosphodiester linkage links eons on either side, producing continuous coding sequence (the mRNA)333

cap & tail: serve as recognition signals for translation and protect the message from degradation y ribonuclease (makes mature mRNA) 323
function: protect mRNAs from degradation by ribonucleases (enzymes that degrade RNA) and enhance the efficiency of translation 324

Question 213

What is a codon? Describe an experiment that interpreted the genetic code for the first time. p 3

Answer 213

codon: group of 3 bases that specifies a particular amino acid — many of the 64 codons that are possible might specify the same amino acid

Question 214

Describe the process of initiating translation, elongating a polypeptide, and terminating translation.

Answer 214

translation:
protein synthesis initiation: // ribosome binding site / Shine-Dalgarno Sequence: 3 steps: a. mRNA binds to small subunit (ribosome binding site sequence binds to complementary sequence in an RNA molecule in small subunit helped by initiation factors - promoter / basal transcription factro; b. initiator aminoacyl tRNA binds to start codon c. large subunit of ribosome binds, completing ribosome assembly, translation can now begin 329
elongation: extending when both the P site and the A site are occupied by tRNAS and the amino acids on the tRNAs are in the ribosomes active site; this is where peptide bond formation occurs; 3 steps: a. arrival of aminoacyl tRNA b. peptide bond formation c. translocation (repeat down the length of mRNA). RNA polymerase adds nucleotides. Splitting phosphate groups from NTPs provides energy for transcription
termination: Termination signal in DNA is transcribed into mRNA & causes all to disassociate; release factor: polyA – cap and tail, migrates to ribosom ; recognizing the stop codon and files the A site when translocating ribosome reaches one of the stop codons — UAA, UAG, UGA 331

Question 215

What is a reading frame? Describe how a point mutation can change the reading frame

Answer 215

point mutation: a single-base change — if a mistake is made during DNA synthesis or DNA repair, a change in sequence of bases results 313
reading frame: single addition or deletion mutation throws the sequence of codons out of register;
Crick + Brenner: confirmed that codons are 3 bases long; also were able to produce DNA sequences that had deletions or additions of 2 base pairs or 3 base pairs

Question 216

What is a point mutation? \

Answer 216

mutation: any permanent change in organisms DNA — modification in a cell’s information archive — a change in genotype, mutations create new alleles
point mutation: a single-base change — if a mistake is made during DNA synthesis or DNA repair, a change in sequence of bases results

Question 217

missense mutations:

Answer 217

point mutations that case changes in amino sequence of proteins (ie, like forest mice colonized beach habitats, altered melacortin receptor gene resulting in whiter rat coats, camouflaging them in beaches, and the alleles created by point mutation increased frequency in beach-dwelling populations) 313

Question 218

silent mutation

Answer 218

a point mutation that doesn’t change the amino acid sequence of the gene product

Question 219

frameshift mutation

Answer 219

major disruptions of proteins — single addition or deleting throw off sequence of codons out of register and alters meaning of all subsequent codons

Question 220

nonsense mutation

Answer 220

large effecting — occur when codon that specifies amino acid is changed by mutation to one that specifies a stop codon — causes early termination of polypeptide chain and results in non-functional protein.

Question 221

3 categories of mutations:

Answer 221

beneficial: increase fitness of the organism — its ability to survive and reproduce — in certain environments; the G-to-A mutation is beneficial in beach habitats because it camouflages mice
neutral: no effect on fitness — silent mutations are usually neutral
deleterious: because organisms tend to be well-adapted to environment, and mutations are random changes in genotype, many lower fitness; they are harmful or deleterious. G-to-A mutation would be deleterious in forest habitat 313

Question 222

What is meant by the term “charged tRNA”? Describe the enzyme responsible for charging the tRNA molecule

Answer 222

Allows right amino acid to be attached:
input of energy - ATP to attach amino acid to tRNA
enzymes: aminoacyl tRNA synthetase catalyzed addition of amino to tRNAs “charging” a tRNA – the combo of tRNA molecule covalently linked to an amino acid; this synthetase bound to a tRNA has just been charged with an amino acid, so the two structures fit together tightly, making it possible for enzyme and it’s tRNA and amino acid substrates to interact in a precise way. 327
for each 20 aminos, there is a different synthetase and one or more tRNAs
Subtle shaped and base sequenced allow enzymes to recognize correct tRNA for correct amino acid.

Question 223

What amino acid begins almost every eukaryotic polypeptide?

Answer 223

Met / AUG

Question 224

How does a charged tRNA deliver an amino acid to a growing polypeptide chain in the correct order?

Answer 224

anticodon and codon (mRNA/tRNA) are complementary; Each aminoacyl-tRNA synthetase has a binding site for a particular amino acid and a particular tRNA; subtle differences in shape and base sequence allow enzymes to recognize the correct tRNA for the correct amin

Question 225

During elongation of the polypeptide in translation, the ribosome must move along the mRNA to “read” new codons. This movement is called translocation and requires energy. What form of energy is used by the cell for this translocation process?

Answer 225

translocation: occurs when proteins (elongation factors) help move the ribosome relative to the mRNA so that translation occurs in the 5’—>3’ direction, requires GTP! 331

Question 226

What is a large scale mutation? Give 3 examples of large scale genetic mutations and use diagrams to illustrate each.

Answer 226

chromosome mutations:
inversion
translocation
deletion
duplication

Question 227

Name three different types of mutagens and give a specific example of one type.

Answer 227

beneficial: beach mouse G-to-A mutation
neutral: silent
deleterious: G-to-A would be bad in forest

Question 228

Are all mutations deleterious?

Answer 228

No, some are neutral (no negative effect, a change that gives the species a similar adapatability to its environment) and others are beneficial (beach mouse)

Question 229

How are the major discoveries of Gregor Mendel and the work of Thomas Hunt Morgan related?

Answer 229

Mendel: established basic patterns of inheritance, independent assortment, recessive/dominant 266 (discovered chromosomes contain genes that can be inherited)
Morgan discovered: X-linked inheritance — chromosomes contain genes and can be inherited! 269

Question 230

What was the major contribution of Morgan’s work to our understanding of genetic inheritance?

Answer 230

X-linked traits (and as a result sex-linked and Y linked traits, too)

Question 231

How could Morgan tell that the trait for white eyes was on the X, rather than the Y chromosome?

Answer 231

All the F1 had red eyes; in continued crosses, he obtained white-eyed female flies; when
reciprocal cross: b/t white-eyed female and red-eyed male, all F1 females had red eyes, but all F1 males had white eyes. 268

Question 232

What is the difference between Mendel’s law of segregation and Mendel’s law of independent assortment? Why does a monohybrid cross illustrate Mendel’s law of segregation while a dihybrid cross is necessary to illustrate Mendel’s law of independent assortment?

Answer 232

principle of segregation: reappearance of recessive phenotype and 3:1 ratio in F2 individuals — 2 members of each gene pair must segregate into different gamete cells during formation of eggs and sperm; each gamete contains one allele of each gene 262
independent assortment: alleles of different genes are transmitted independently of one another 265

Question 233

Explain the Beadle and Tatum experiment. What did this show?

Answer 233

Beadle & Tatum: thought that we should be able to discover what genes do by making them defective; knock out a gene by damaging it and then infer what gene does by observing the phenotype of the mutant individual 305

found N.crassa mutants that could not make certain compounds
one mutant could not make pyridoxine (B6) even tho normal ones can.
Inability to synthesize pyridoxine was due to a defect in a single gene – the inability to synthesize other molecules was due to defects in other genes
results inspired one-gene, one-enzyme hypothesis – the N.crassa lacked the enzyme due to a genetic defect and was unable to synthesize the compound
implication: knock-out mutant studies showed that each gene contains info needed to make an enzyme