Biochem MCAT

what stereochemistry are amino acids in eukaryotes?

L

What configuration do most chiral ammino acids have? what is the exception?

S ; except cystein (glycine is not chiral)

what amino acid interrupts 2ndary structure?

proline

what bonds are involved in primary structure?

peptide bonds

what bonds are involved in 2dry structure?

peptide, hydrogen

what bonds are involved in 3ry structure?

disulfide bonds, hydrophobic interactions, peptide, hydrogen

what are conjugated peptides?

addition of prosthetic group

what are the water soluble enzymes?

B complex & C (asorbic acid). Examples of B vitamins:

thiamine, riboflavin, niacin, pantothenic acid, pyridoxial phosphate, biotin, folic acid, cyanocbalamin

what are the fat soluble vitamins?

A,D, E, K

what is km?

enzymes affinity for substrate; the concentration of substate at half v max

How to calculate weight of amino acid? Ex: franeshift mutation from 591 to 626 bp

626-591 = 35 amino acid × (110 Da/amino acid) = 38500 Da = 3.85 kDa

110 Da/amino acid is avg weight of an amino aicd

What two amino acids disrupt 2ndry structure?

Glycine and proline.

What are histones and their functions?

DNA wraps around histones for support.

Strong interactions with histones means tighter wrapping, meaning it inhibits DNAs accessibility and prevents transcription

What is native page gels used for?

To preserve natural structure. Protein structure is preserved and binding interactions can occur

meant to analyize interactions with other molecules

differing net charges andd protein shapes impact migration

what is SDS Page used for ? features?

proteins are denatured and coated with negative charge

binding interactions CANNOT occur

separates proteins on the basis of mass only

can gel electrophorsesis (PAGE) separate protein domains?

No only subunits

what is protein cooperativity?

when binding affinity for one ligand increases or decreases uponf binding to another ligand. when a ligand binds, how it changes the proteins affinity for other ligands

what is the delta g for protein folding

negative since folding is spontaneous

G= - RTlnk

k Is the equilibrium ratio of products to reactants. folding favors products, so k is greater than 1. so ln k is positive, making delta G negative

what is the standard gibbs free energy equation?

G=-RTlnk

a decrease in pH would result in [decrease or increase] of protonation of amino acids?

decrease in pH means more protons floating around (cuz acidic), making it easier for amino acids to be come protonated. So there would be an increase in protonation

what is Kd?

dissociation constant

a low Kd means [high or low] affinity

a low dissociation constant means high affinity

what is Western blot used for?

to detect the presence of a specific protein and compare its relative abundance in one set of conditions compared to other conditions

what are the steps of western blot analysis?

1. load samples onto gel and undergo electrophoresis

2. proteins in the gel are transferred to a protein binding membrane where they become emobilized

3. the portions of the membrane to which protein was not transfered are blocked by protein rich mixtures. This prevents antibodies (proteins) from nonspecifically binding to the membrane (basically it makes sure that only the proteins bound stick and that everything else is empty. IT’S A WASH

4. the membrane is incubated with antibodies that specifically bind to the protein of interest (they basically mark the protein so it can be seen visually)

5. antibodies are detected (seen) through fluorescence.

what is the 1st step of citric acid cycle?

oxaoloacetate + acetyl coa → (citrate synthase) citrate

adol condensation followed by hydrolysis

What is the 2nd step of the citric acid cycle?

2. citrate → (aconitase) cis-aconitate →(aconitase) isocitrate

   dehydration then hydration

3rd step of citric acid cycle

3. isocitrate → (isocitrate dehydrogenase) alpha ketoglutarate + NADH & CO2

   OXIDATION, enol intermediate, then rearrangement

4th step of citric acid cycle

4. alpha-ketoglutarate →( alpha ketoglutarate dehydrogenase complex) succinyl-coA + NADH + CO2

oxidation

5th step of citric acid cycle

5. succinyl-coA + GDP → (succinyl-coA synthetase) succinate + GTP/ ATP

   CLEAVAGE couple with substrate level phosphorylation

6th step of citric acid cycle

6. succinate + FAD → (succinate dehydrogenase) Fumarate + FADH2

   oxidation

7th step fo citric acid cycle

7. fumarate +H2O → (fumarase) L-malate

HYDRATION

8th step of citric acid cycle

8. L-malate + NAD → (malate dehydrogenase) Oxaloacetate + NADH

Oxidation

each cycle of TCA produces what?

2 CO2, 3 NADH, 1 FADH2, and 1 ATP each cycle. 2 cycles cuz u have two pyruvate (which turn into acetyl coa)

STEPS OF GLYCOLYSIS

Produces 2 pyruvate, 2 atp, and 2 NADH

where are fatty acid chains activated and oxidized in the cell?

they are broken down in the mitochondria. Fatty acids are synthesized in the cytosol

what is the difference btwn ligand gated channels and g-protein coupled receptors

g-protein coupled receptors once bound to a ligand, activated 2nd messengers.

ligand gated ion channels once bound to ligand are immediately activated

what value of gibbs free energy is spontaneous?

negative delta G

features of enzymes

-stabilize transition state

-lower activation energy

-do NOT change the equilibrium of the rxn (Keq)

-saturation of enzyme actives sites by substrate molecules limits the maximum rxn velocity V max

-enzymes can be activated or deactivated by posttranslational modifications

true or false: substrates can covalently modify the enzyme to cause a permanent decrease in the enzymes turnover number k cat.

FALSE - they cannot be permanently changed when an enzyme acts on its substrate. kcat is not expected to permenantly change

which part of the cell does gluconeogenesis mainly occur?

cytosol

which part of the cell does the krebs cycle (citric acid cycle)

mitochondria

what are the steps of glycolysis?

1st step of glycolysis

1. glucose +ATP → (hexokinase) glucose 6 phosphate +ADP

phosphorylation

2. step of glycolysis

glucose-6-phosphate → (phosphoglucoisomerase) fructose 6 phosphate

isomerization

3rd step of glycolysis

3. fructose 6 phosphate + ATP→ (phosphofructokinase) fructose 1,6 bisphosphate +ADP

   phosphorylation

4th step of glycolysis

cleavage into g3p and DHAP

5th step of glycolysis

5. DHAP → ( triosephosphate isomerase) G3P

now we have two glyceraldehyde-3-phosphate

6th step of glycolysis

6 . two G3P → (glyceraldehyde dehydrogenase) 1,3 bisphosphoglycerate + 2 NADH

oxidation

7th step of glycolysis

1,3 bisphosphoglycerate → (phosphoglyerokinase) 3 phosphoglycerate + 2ATP

dephosphorylation

8. 3-phosphoglycerate → (phosphoglyceromutase) 2-phosphoglycerate

phosphate transfer/ISOMERIZATION

9. 2-phosphoglycerate → (enolase) phosphoenolpyruvate

dehydration +2 H2O

10th step of glycolysis

Phosphophenolpyruvate → (pyruvate kinase) 2 pyruvate + 2 ATP

dephosphorylation

where does glycolysis occur in the cell?

in the cytosol

what enzmes are different in gluconeogensis compared to glycolysis?

1. 2 pyruvate → (pyruvate carboxylase) 2 Oxaloacetate

2. 2 oxaloacetate → (PEP carboxykinase) phosphenolpyruvate

3. PEP → (enolase) 2-phosphoglycerate

4. 2-phosphoglycerate → (phosphoglycerate mutase) 3-phosphoglycerate

5. 3phosphoglycerate → (phosphoglycerate kinase) 1,2 bisphosphoglycerate

6. 1,2 bisphosphoglycerate → (G3P dehydrogenase)glyceraldehyde 3 phosphate

7. G3P → (triose phosphate isomerase) DHAP

8. DHAP → (aldolase) fuctose 1,6 bisphosphate

9. fructose 1,6 bisphosphate → (fructose 1,6 bisphosphatase) fructose 6 phosphate

10. fructose 6 phosphate → ( phosphohexose isomerase) glucose 6 phosphate

11. g6p → (glucose 6 phosphatase) 2 glucose

what assumptions does the Michaelis Menten equation rely on?

1. to ensure that ES formation does not significantly impact [S], the total concentration of enzyme should be much smaller than any substrate concentration

2. the concentration of ES remains constant over the course of the reaction, allowing the rate of product formation to remain constant. as [S] becomes significantly depleted, ES levels decrease and rxn slows

3. rxn proceeds only in the forward direction. product does not get converted back to substrate

what is Km?

the substrate concentration at which ½ vmax occurs.

what is needed for fatty acid synthesis?

ATP, NADPH, and acetly coa

if fatty acid synthesis is inhibited, what will build up?

NADPH will build up

when blood sugar is high, what hormone is used for homeostasis?

insulin reduces blood sugar level by increasing glucose uptake and storage

pyruvate dehydrogenase converts pyruvate into what?

to acetyl coa

CHECK OCHEM DECK FOR DYNEINS, KINESINS, CAMS (Integrins, Selectins, Cadherins)

what are the three types of G protein-coupled receptors?

Gs -(stimulate) stimulates adenylate cyclase → increases level of cAMP

Gi- (inihibit) → inhibits adenylate cyckase → decreasing levels of cAMP

Gq (activates phospholipase C), opening calcium channels in the ER → increases calcium levels in the cell

what is Native PAGE used for?

(Polyacrylamide Gel Electrophoresis)

Used to compare molecular size or the charge of SIMILAR size proteins

what is SDS PAGE used for?

Sodium dodecyl sulfate polyacrylamide gel electrophoresis

SDS binds to the proteins and creates large chains with net negative charges → NEUTRALIZES the protein’s original charge and DENATURES.

Used to find MASS without interference of charges

what charge are anodes and cathodes?

andoes are positively charged (oxidation) so anions are attracted to it

cathodes are negatively charged (reduction) so cations are attracted to it

What is chromatography?

use a solid medium (stationary phase) and run mobile phase through stationary phase. Sample runs (elutes) through the stationary phase. components with a high affinity for the stationary phase will barely migrate (long retention time), while those with high affinity for mobile phase will migrate fast (short retention time)

used to separate charge, pore size, and specific affinities of proteins

what is column chromatography used

USED TO SEPARATE POLARITY

the less polar the compound, the faster is can elute through the column (short retention time)

what is ion-exchange chromatography used for

beads in the column are coated with charged substances to bind compounds with an opposite charge. a salt gradient is then used to elute the charged molecules bound to column. Good for separating specific charged molecules

what is size-exclusion chromatography

beads in the column contain tiny pores of varying sizes. small compounds enter the beads and are slowed down. Large molecules pass through.

LARGE MOLECULES ELUTE FIRST, SMALL MOLECULES ARE SLOWED

How can protein structure be determined?

X-ray crytallography and NMR

What is Edman degradation used for?

Edman degradation removes N-terminal of amino acid of the protein, to cleave proteins and sequence them

what are some enzyme that cleave large proteins?

chymotrypsin, trypsin, cyanogen bromide

how to determine concentration of proteins

UV Spectroscopy, BCA assay, Lowry reagent assay, and BRADFORD PROTEIN ASSAY

Bradford protein assay- uses a color change from brownish green to blue. increased protein concentrations = larger concentration of blue dye

true or false: centrioles are involved in cell migration

false. centrioles (composed of microtubules) are only involved in mitosis

what type of receptors use a second messenger cascade system to amplify the signal by a lot?

g-protein coupled receptors and enzyme-linked receptors

true or false: calcium is usually protein bound

true - calcium is protein bound since it is used so much in the body

what type of channels provide MAINTENANCE of the resting membrane potential. Which channels causes DEVIATION from resting membrane potential?

maintenance : ungated “leak” channels permit limited free flow of ions

deviation: ligand-gated and voltage gated channels

what does the gel in isoelectric focusing use to separate by charge?

gel in isoelectric uses pH gradient. when a protein is in a region with a pH above its pI, it is negatively charged and moves to anode. when pH region is below its pI, it is positively charged and move to cathode

what does UV spec use to find protein concentration?

uses conjugated systems of double bonds (aka aromatic systems)

what is an aromatic compound?

alternating double bonds

What is most basic structural unit of carbohydrates?

monosaccharides

what does the simplest monosaccharid contain?

three carbon atoms. called trioses

what are aldoses and ketoses?

aldoses: carbohydrates with an aldehyde group as their most oxidized functional group

ketoses: with ketone

an aldohexose is a 6 carbon sugar with an aldehyde

what are stereoisomers?

compounds with same chemical formula but different arrangement

what is an enantiomer?

same chemical formula, mirror image of each other for spacial arrangement

ex: L and D ribose

how do u determine how many possible stereoisomers?

2^n n= number of chiral carbons

on a fisher projection, where are the wedges?

horizontal lines

how do you determine if sugars are L or D?

depends on where the highest numbered chiral center is

what are diastereomers?

same chemical formula, not mirror image

what are epimers?

diastereomer where the sugar only differs at on chiral center

how many carbons do pyranose and furanose rings have?

pyranose - 6

furanose - 5 Furanose Five

what are anomers?

sugars that differ by configuration on the anomeric carbon (carbon that’s attached to two Oxygens. one O, one OH)

makes alpha or beta

the Haworth projection vs fischer projection

haworth projection - 3D

what does hemiacetal look like?

when a hemiacetal ring is exposed to water, what is the name when they spontaneously cycle between the open and closed configuration?

they undergo mutarotation -? causes mixture to have both alpha and beta anomers

true or false: all monosaccharides are a reducing sugar

true

what to reagents are used to detect the presence of reducing sugars?

Tollens reagent- Produces silvery mirror AgNH3 when aldehydes are present

Benedicts reagent- precipitates red Cu2O when aldoses are present

what is a lactone?

a cyclic ester with a carbonyl (c=o) on anomeric carbon

vitamin C is a lactone

what is tautomerization?

rearrangement of bonds in a compound by moving a hydrogen and forming a double bond

resonance is just movement of electrons

what is the name when an alcohol and an acid (carboxylic acid) form an ester and water?

esterification

which enzyme catalyzes the phosphorylation of glucose (Glucose to G6P)

Hexokinase - forms a phosphate ester