BR Bio Set 2

Question 1

antibody mechs

Answer 1

1. opsonization: coating leads to phagocytosis
2. neutralization by coating
3. complement activation by creating an antibody-antigen complex that is recognized by a complement protein, thus triggering an immune response (eg. membrane attack complex lyses the cell)

Question 2

types of antibodies

Answer 2

IgA: found in milk; protects the nursing infant

IgD: unknown

IgE: binds to mast cells and is involved w allergic reactions

IgG: able to cross the placenta; most abundant and is produced within days after IgM antibody is secreted

IgM: produced a few days after detection of an antigen, making it the first antibody produced in response to an antigen

Question 3

antibody structure

Answer 3

Composed of four subunits arranged in a Y configuration
= 2 lights chains + 2 heavy chains, Joined together by disulfide bonds

within each subunit is a variable and constant domain

• Variable regions are located at the terminal ends of the chains, differing in the amino acid sequence; Also the location of the antigen binding site
• Constant regions are found in the lower portion of the Ig

Question 4

D vs L configuration

Answer 4

in sugars; look at their fisher projection

dependent on the chiral carbon that is most distant from the carbonyl carbon, referred to as a reference carbon

D if hydroxyl group on reference carbon is to the right
L …. to the left

Question 5

Cholesterol

be able to draw structure

Answer 5

synthesized in the cytosol and generally exists as the cholesterol ester; major constituent of eukaryotic animal plasma membrane and is an intermediate in the biosynthesis of all human steroid hormones

Has a fairly rigid set of four fused non polar rings + polar hydroxyl group, thus granting it a slightly amphiphilic attribute

Question 6

smooth ER

Answer 6

lacks ribosomes; appears more tubular in shape; involved in the synthesis of a majority of the cell’s membrane lipids; also involved in hydroxylation reactions that aid in the detoxification of drugs (basically makes a substance more water soluble, thus making it easier to eliminate in the body)

In hepatocytes, important for catabolism of liver glycogen
In other cells, can help regulate Ca2+ levels

Question 7

rough ER

Answer 7

studded w ribosomes; generally flat and sheet like

Embedded ribosomes synthesize membrane and secretory proteins that are then passed through the RER and into the lumen, where post-translational modification begins via hydroxylation and glycosidation events

Proteins after this modification are then shuttled to the Golgi apparatus, where modification continues even more

After golgi, the proteins are sent to their final destinations

Question 8

golgi apparatus

• regions
• pathway

Answer 8

complex of cisternae (flattened membranes)

• • Cis cisterna region: face the nucleus and ER
• • Trans: face plasma membrane
• • Medial: located btwn the cis and trans cisternae

As a protein is passed from the cis to trans cisterna, diff chemical modifications occur, involved glycosylation (addition of carbohydrates), sulfation (addition of inorganic sulfate), proteolysis (reducing the size of the protein)

Once the proteins reach the trans face, they are sorted and concentrated into vesicles that are destined for different regions of the cell

Question 9

Peroxisomes

Answer 9

single membrane-bounded organelles found within the cellular cytoplasm, contains lots of enzymes (like lysosome) but notably contains catalase, which degrade hydrogen peroxide

Peroxisome can generate hydrogen peroxide, which is a potentially damaging oxidant
– Used in the dissipation of heat

Question 10

viral interactions w host cells

• adsorption
• host range

Answer 10

Adsorption: interaction of that virus w the host cell’s surface to facilitate binding prior to entry

Host range: restriction on the specific organisms or cell types that a virus can infect
– Dependent on interaction of that virus w the host cell’s surface proteins, glycoproteins, and glycolipids

Question 11

metabolism v catabolism v anabolism

Answer 11

Metabolism: refer to all processes that occur within living organisms

Catabolism: breakdown of complex molecules into smaller and simpler products, usually accompanied by the release of energy

Anabolism: building up or becoming more complex development of a molecule; biosynthesis of small precursor molecules into larger and more complex

Question 12

how do we regenerate NAD+ in order to continue glycolyssi

Answer 12

Pyruvate acted on by lactate dehydrogenase to yield lactate and NAD+

Occurs when oxygen becomes a limiting factor, thus becoming an anaerobic reaction → ie in muscles during exercise

Lactate will be transported by blood to liver, where it is converted back into pyruvate

Pyruvate can be converted back into glucose via gluconeogenesis since two lactates (C3H6O3) can make one glucose (C6H12O6)

ALTERNATIVELY,
Pyruvate can be acted on by pyruvate decarboxylase to yield acetaldehyde and CO2 via alcoholic fermentation → acetaldehyde can be acted on by alcohol dehydrogenase to yield ethanol and NAD+

Question 13

regulation of glycolysis

Answer 13

Irreversible at hexokinase, phosphofructokinase, and pyruvate kinase → act as control points

High levels of ATP allosterically inhibit phosphofructokinase

[H+] from conversion of pyruvate into lactate also allosterically inhibits phosphofructokinase → surplus of hydrogen ions causes drop in pH, leading to acidosis

Citrate from the Krebs cycle also inhibit phosphofructokinase

High levels of AMP promote / stimulate phosphofructokinase

Question 14

Complexes of ETC, pathway

Answer 14

Complex 1 (NADH-Q reductase): reduced NADH + H+ passes two electrons and two hydrogens to the oxidized flavin mononucleotide (FMN) prosthetic group assoc w this complex → results in production of reduced FMNH2 and regeneration of oxidized NAD+
-- Electrons from FMNH2 are passed to a series of iron-sulfur clusters (Fe-S) where iron atoms cycle btwn the reduced ferrous (Fe2+) and the oxidized ferric (Fe3+) states, allowing electrons to eventually be passed from a reduced Fe-S moiety to the oxidized CoenzymeQ (CoQ; aka quinone)

Complex 2 (Succinate-Q reductase): recall that when succinate is oxidized to fumarate in the Krebs cycle by the enzyme succinate dehydrogenase, FADH2 is generated → this FADH2 needs to be reoxidized by immediately passing its electrons to an Fe-S protein which funnels them into the oxidized form of CoQ (very similar to what happens in Complex 1), allowing the regeneration of FAD

At the end of the Fe-S complex (found in both Complex 1 and 2), there is a quinone / CoQ (coenzyme Q) that collects all of the electrons from the various substrates into one pocket, becoming CoQH (ubiquinol) → we need to reoxidize CoQ now
– Nomenclature: reduced quinone is dihydroquinone, oxidized quinone is just quinone → BUT reduced CoQ is ubiquinone and oxidized CoQ is ubiquinol

Complex 3 (Cytochrome Reductase): contain cytochrome (b and c) and an Fe-S protein

• • As CoQH2 transfers one electron at a time to an Fe-S protein in the complex, it is converted to CoQH· (semiquinone) and will react w the reduced cytochrome b (Cyt b2+) to give CoQH2 and the oxidized form of cytochrome b (Cyt b3+)
• • Cyt b3+ can then oxidize another molecule of CoQH· to CoQ
• • The electrons are eventually passed to the reduced form of cytochrome c

Complex 4 (Cytochrome Oxidase, an enzyme): consists of two heme groups (heme a and heme a3) which each have a copper atom associated w it

• • Copper atoms can alternate btwn +1 and +2 oxidation states
• • Electrons are passed from cyt c to heme a to heme a3 then to oxygen, where the transfer of four electrons to molecular reduction leads to its reduction into two molecules of water
• ** this is the only step that actually requires oxygen

Question 15

cytochromes

Answer 15

aka electron carriers; electron transporting proteins that contain a heme prosthetic group w an iron atom (alternating btwn Fe2+ and Fe3+)

• —- Cyt b acts as the go-btwn that allows interactions btwn CoQH and Fe-S to occur
• —- Cyt c has an iron atom of the heme group bonded to a sulfur atom of a Met residue on one side and nitrogen atom on the other side

Question 16

how is ATP production related to ETC

Answer 16

Note: ATPase is NOT a part of the respiratory pathway (aka the ETC)
– Oxidation takes place in the ETC / respiratory unit
– Phosphorylation takes place at the ATPase
THUS, the process of OXIDATIVE PHOSPHORYLATION is this bridge btwn the effects of the ETC and the production of ATP.

Rearrangement of enzymes passing back and forth thru oxidized vs reduced states removed hydrogen ions from the matrix of the mitochondria, pumping them across the membrane to the intermembrane space → thought to be translocated across the first four complexes

Movement of hydrogen ions down their gradient and through the ATPase allow for phosphorylation of ADP into ATP.

Question 17

two shuttles

Answer 17

Recall that glycolysis occurs in the cytosol but still generates 1 NADH for each G3P that it processes → thus 2 NADHs are extramitochondrial but can be transported into the mitochondrial matrix by one of two shuttle systems

Glycerol phosphate shuttle: 2 NADH yields 2 ATP → cost of 1 ATP; found in the majority of body cells

Malate-aspartate shuttle: 2 NADH yields 3 ATP → no ATP cost; found only in heart, brain, and kidney

Question 18

Pentose Phosphate Pathway

Answer 18

generate reducing power in the form of NADPH and five carbon sugars (eg ribose-5-phosphate)

Glucose-6-phosphate has many fates → glycolysis or PPP
– Glycolysis: enzyme phosphofructokinase will yield fructose-6-phosphate

vs. PPP: enzyme glucose-6-phosphate dehydrogenase used at the C-1 carbon will yield 6-phosphoglucono-d-lactone
» Then, if acted on by enzyme lactonase, will yield 6-phosphogluconate
» Then, if acted on by 6-phosphogluconate dehydrogenase with addition of NADP, will yield NADPH and beta-keto-intermediate
» Then, with removal of CO2, will yield ribulose-5-phosphate
» Then, if acted on by phosphopentose isomerase, will yield enediol intermediate
» Then, can be interconverted to yield ribose-5-phosphate
» This end product of PPP can be incorporated into biomolecules such as RNA, DNA, ATP, and NAD.

Question 19

hydrogen peroxide conversion

• reduction of oxygen yields what
• tocopherols
• superoxide dismutase
• glutathione peroxidase
• deficiency in glycose 6 dehydrogenase?

Answer 19

As oxygen becomes reduced, it goes thru a number of intermediates before it is converted into water; these intermediates are “toxic” and can cause cellular damage → incl the superoxide radical hydrogen peroxide and hydroxyl free radical

Tocopherols (Vitamin C / E) and ergothioneine can act as free radical scavengers (aka antioxidants) and convert them into less toxic substances

Superoxide dismutase (SOD) can catalyze the conversion of superoxide radical into hydrogen peroxide (another toxic component) and oxygen → the enzyme catalase can then react w hydrogen peroxide, converting it into water and oxygen

Glutathione peroxidase can react w hydrogen peroxide and reduce it into water

• • Reduced glutathione (GSH) reacts w peroxide to form water and the oxidized form of glutathione (GSSG)
• • GSSG can be reduced back to the sulfhydryl form by NADPH, with the help of the enzyme glutathione reductase

Individuals deficient in Glucose-6-Phosphate dehydrogenase are unable to form NADPH, thus are unable to form GSH, thus peroxides are free to continue causing damage

Question 20

how to deal w unsaturated FAs during beta oxidation

Answer 20

FAs w double bonds in them → two scenarios

Encounter a double bond in the beta, gamma-position AFTER beta-oxidation

• • Need to convert it to double bond at the alpha, beta position via isomerase
• • Basically changing it from cis to trans

Encounter a double bond at the alpha, beta-position AFTER beta-oxidation
Ur chilling

Question 21

Mendel’s Laws of Heredity

Answer 21

Law of Segregation: alternative alleles segregate from each other in heterozygous individuals and retain their identity

Law of Independent Assortment: segregation of one gene pair is independent of other gene pair during the formation of gametes

• • Independent assortment of genes will occur if they are located on different chromosomes or are far apart on the same chromosome
• • Genes that are farther apart will recombine more frequently than those that are closer together

Question 22

auxotroph vs prototroph

eg. tryptophan auxotroph

Answer 22

Auxotroph: mutant that will grow only when its medium is supplemented with a particular compound which is not required by the normal wild type organism → will not grow on minimal medium

Prototroph: wild type organism → will grow on minimal medium

eg. Eg. Tryptophan auxotroph will grow on a complete medium but will not grow on a minimal medium unless it has been supplemented w tryptophan.

Question 23

How to Read a Pedigree

Answer 23

Square (male) vs Circle (female)

If the shape is filled in, then the individual is affected with a given defect

If the shape is slashed through, that individual is heterozygous for a given defect

Reproduction denoted by a horizontal line and offspring denoted by vertical

Offspring read from left to right, oldest to youngest

Different generations reside on separate horizontal lines

Question 24

types of DNA

Answer 24

B DNA is the most commonly found form of DNA. It is a right handed helix, has about 10.5 bp per turn, has bases that are oriented essentially 90 degrees to the helical axis, and each turn is about 3.4 Angstroms. It also has distinguishable major and minor grooves.

In A-DNA, the minor groove is very indistinguishable and the bases are hence shifted about 20 degrees from the helical axis. There are about 12 bp per turn. This form is most commonly encountered in anhydrous environments and is also right handed.

Z DNA is extremely different in that it is a left handed helix, with about 12 bp per turn. The bases are alternating purines and pyrimidines, in which the purines are in the syn conformation about the N-glycosidic bond and the pyrimidines are in the anti conformation (only one they can be in) about the N-glycosidic bond.

Question 25

supercoiling

Answer 25

greatly changes the overall form of DNA not only by making it more compact but also by altering accessibility to the major and minor grooves → introduction requires input of energy Positive supercoiling: twisting of DNA around its own axis in the right-handed direction Negative supercoiling: above but in left-handed direction

Question 26

Linking number (L) Topoisomers Topoisomerases

Answer 26

The number of times that one DNA strand can be wound around another DNA strand is referred to as its linking number (L) Topoisomers: DNA molecules that differ only in their linking number Topoisomerases: enzymes that can alter the degree of the linking number in DNA - - Type 1: reversibly cleave one strand of DNA and relaxes negatively supercoiled DNA - - Type 2: reversible cleave both strands of DNA and adds supercoils

Question 27

Polymerase Chain Reaction:

Answer 27

process by which we amplify DNA; requires use of Taq DNA polymerase from a thermophilic bacteria, thus allowing the polymerase to be stable at temperatures up to 90 degrees Celsius (meaning it doesn’t denature) Process: 1. Heat so that ends will begin to separate 2. Addition of excess primers 3. Cooling so that primers will hydrogen bond to their complement areas 4. Addition of dNTPs and Taq DNA polymerase 5. Now have twice as much DNA as before ** Can repeat this without adding extra Taq DNA polymerase = MAX AMPLIFICATION !!

Question 28

Comparison of DNA to RNA polymerases

Answer 28

Both proceed in the 5’ to 3’ direction DNA polymerase uses dNTP’s (releasing PPi) vs RNA polymerasebuses NTP’s (also releasing PPi) Both polymerases require a DNA bubble for operation DNA replication is semiconservative thru DNA polymerase vs RNA polymerase conserves the DNA strands bc the strands eventually rewind DNA polymerase requires a primer with a free 3’-OH group to initiate chain elongation vs RNA polymerase does not require a primer DNA directed DNA polymerase is almost always involved in synthesizing DNA bidirectionally, thus both DNA strands are being copied vs DNA directed RNA polymerase only allows one strand of DNA to be copied at a given time

Question 29

Wobble Rules in Base Pairing

Answer 29

Wobble refers to the steric freedom in the pairing of the third base of the codon 1. U can pair for A (Standard) or G (non-standard) 2. G can pair with C (standard) or U (non-standard) 3. Inosine can pair with either A, U, C.

Question 30

operon definition

Answer 30

``` Operon: simply a transaction unit which is involved in the expression of multiple genes Incl promoter (P), operator, (O), and a set of structural genes ```

Question 31

lactose operon - structural genes - promoter

Answer 31

Gene z codes for beta-galactosidase, which hydrolyzes lactose to glucose and galactose; has a minor role in converting lactose to allolactose Gene y codes for galactosidase permease, which is a carrier molecule that transports lactose into the cell Gene a codes for thiogalactoside transacetylase, which is an enzyme that transfers an acetyl group from acetyl-CoA to galactosides, glucosides and lactosides Upstream from lactose promoter is the regulatory gene w its own promoter (Pi) -- Regulatory gene i codes for a repressor protein that can bind to the operator and prevent transcription of genes z, y, and a when lactose (the inducer) is not present in the cell’s medium

Question 32

lactose operon - when lactose is not present in the medium vs when it is

Answer 32

When lactose is not present in the medium: -- RNA polymerase codes regulatory gene that generates a repressor protein that binds to the operator, thus preventing RNA polymerase from transcribing the structural genes When lactose IS present in the medium: - - A small amount of it is converted into allolactose by the molecules of beta-galactosidase that are present in the cell - - Allolactose will bind to the repressor and decrease it’s affinity for the operator site → thus, allolactose is the inducer of the lactose operon - - Once the inducer is bound to the repressor, the complex dissociates from the operator and RNA polymerase can begin to transcribe the lactose operon genes - ---- The polycistronic mRNA that is transcribed (ie an mRNA which codes for two or more polypeptide chains) will eventually be translated into the desired enzymes

Question 33

tryptophan operon - genes - repressor

Answer 33

aka trp operon Required a polycistronic message composed of trpE/D/C/B/A that, when read by RNA polymerase, gave rise to the enzymes needed to convert the precursor molecule chorismate into tryptophan Also had a trpR gene that coded for a tryptophan repressor → but bc of the regulatory mutation, it was not effective in regulating the synthesis of tryptophan --- Instead, found that repressor must bind to end product in order to inhibit the entire pathway THUS: tryptophan acts as a corepressor for its own biosynthesis

Question 34

tryptophan operon - when levels are high - when levels are low

Answer 34

When tryptophan levels are high in the medium: - - Repressor binds to tryptophan, forming a complex that then binds to the operator region of the trp operon - - Binding of complex prevents RNA polymerase from initiating transcription of the structural genes * * EXAMPLE OF FEEDBACK REPRESSION at the transcriptional level When tryptophan levels are low in the medium: - - Complex will not form, thus operator is not bound to anything - - RNA polymerase allowed to transcribe the structural genes, thus generating tryptophan as an end product

Question 35

what can fix an error in DNA replication?

Answer 35

Recall that both DNA polymerase I and III possess a 3’ to 5’ exonuclease activity When they detect an error, that error is removed by this activity before continuing with the replication of the DNA template Cells with high mutation rates have a defective DNA polymerase (III) exonuclease activity

Question 36

how are mismatched base pairs fixed?

Answer 36

refers to imperfect base-pairing that creates a slight bulge in the DNA duplex that is fixed by the AP endonuclease depends on GATC box: signature of the parent strand that has a methylated adenine group, informing the AP endonuclease about which strand is the newly synthesized DNA strand Pathway: AP endonuclease observes a bulge in the duplex and begins searching for the GATC box → once found, the enzyme then removes the mispaired base and the intervening sequence of DNA up to the point of the unmethylated GATC box → DNA polymerase (I) will then resynthesize the DNA that has been removed by AP endonuclease and DNA ligase will seal it off → we now observe no bulge