Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MCAT > Biochemistry > Flashcards

Biochemistry Flashcards

You may prefer our related Brainscape-certified flashcards:
MCAT flashcards
1
Q

Which is the alpha-carbon for a carboxylic acids?

A

The carbon adjacent tot he carboxyl carbon.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

All chiral amino acids used in Eukaryotes are (L or D)-amino acids so the amino group is drawn on the (left or right) side of a Fischer projection.

A

L-Amino Acid
Amino Group on the LEFT

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

All amino acids are chiral and have a (R or S) absolute configuration. The TWO exceptions to this rule are the amino acids (1 and 2).

A

S absolute configuration

Glycine – not a chiral center
Cysteine – R absolute configuration

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Alanine

A

Alanine, Ala, A

R = CH3

Nonpolar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Glycine

A

Glycine, Gly,G

R = H

Nonpolar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Valine

A

Valine, Val, V

R = CH2 - (CH3)2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Arginine

A

Arginine, Arg, R

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Asparagine

A

Asparagine, Asn, N

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Aspartate

A

Aspartate, Asp, D

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Cysteine

A

Cysteine, Cys, C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Glutamate

A

Glutamate, Glu, E

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Glutamine

A

Glutamine, Gln, Q

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Histidine

A

Histidine, His, H

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Isoleucine

A

Isoleucine, Ile, I

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Leucine

A

Leucine, Leu, L

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Lysine

A

Lysine, Lys, K

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Methionine

A

Methionine, Met, M

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Phenylalanine

A

Phenylalanine, Phe, F

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Proline

A

Proline, Pro, P

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Serine

A

Serine, Ser, S

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Threonine

A

Threonine, Thr, T

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Tryptophan

A

Tryptophan, Trp, W

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Tyrosine

A

Tyrosine, Tyr, Y

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Positively Charged (Basic) Side Chains on Amino Acids

A

Lysine, Arginine, Histidine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What is the aromatic ring with two nitrogen atoms in histidine called?

A

Imidazole

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Negatively Charged (Acidic) Side Chains on Amino Acids

A

Aspartate and Glutamate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Polar Side Chains on Amino Acids

A

Serine, Threonine, Asparagine, Glutamine, Cysteine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Aromatic Side Chains on Amino Acids

A

Tryptophan, Phenylalanine, Tyrosine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Nonpolar, Nonaromatic Side Chains on Amino Acids

A

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, and Proline

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Amino acids are amphoteric species because…

A

they can either accept or donate a proton

carboxylic acid is acidic while amino in basic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

The pKa of a group is the pH at which…

A

on average, half of the molecules of that species are deprotonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

When the pH of a solution is equal to the pKa of an amino acid (or acid), then the solution will…

A

act as a buffer!

the titration curve will be FLAT

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

The isoelectric point (pI) of an amino acid is when…

A

the solute is entirely in its zwitterionic form (completely neutral)!!

the titration curve will increase rapidly (vertical) because it is not acting as a buffer anymore

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Explain the formation of a peptide bond.

A

CONDENSATION / DEHYDRATION REACTION

The electrophilic carbonyl carbon is attacked by the nucleophilic amino group. The hydroxyl group of the carboxylic acid is kicked off.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Why is the rotation of a protein backbone restricted in the peptide bond (C-N).

A

The amide group has delocalizable pi electrons in the carbonyl and amino nitrogen.
Exists as resonance (DOUBLE BOND ON PEPTIDE).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

How do hydrolytic enzymes (trypsin/chymotrypsin) hydrolyze peptide bonds?

A

break apart the amide bond by adding a hydrogen atom to the amide nitrogen and an OH to the carbonyl carbon.

HYDROLYSIS. Reverse reaction of dehydration peptide bond formation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Describe the bonds holding together an alpha helix.

A

Intramolecular hydrogen bonding between carbonyl oxygen atom and amide hydrogen atom 4 residues down.

The side chains point AWAY from the helix core.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Describe the bonds holding together a beta-pleated sheet.

A

Intramolecular hydrogen bonds between carbonyl oxygen and amide hydrogen atom on an adjacent chain.

R side chains lie ABOVE OR BELOW the plane of the sheet.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Proline relationship in secondary structure?

A

Introduces kinks due to its rigid structure. Found at the TURNS between beta-pleated sheets.
Sometimes the start of an alpha helix. NEVER in the middle.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

The tertiary structure of a protein primarily due to…

A

Result of hydrophobic interactions between amino acid side chains into the interior of the protein.

FOLDING

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

Important covalent bond in tertiary structure.

A

Disulfide bond between two cysteine to make cystine.

OXIDATION (loss of two protons and electrons).

S-S bonds create loops in the protein chain.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

A protein is denatured. What order of protein structure has been lost.

A

Tertiary

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Describe the entropic effects of a protein in water.

A

The entropy of the protein decreases while the entropy of the water increases.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

Oxidoreductase Enzymes

A

catalyze REDOX reactions

transfer of electrons

cofactors such as NAD+ or NADP+

dehydrogenase or reductase in the name

oxidase if oxygen is the final electron acceptor

electron donor is the reductant and the acceptor is the oxidant

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

Transferase Enzyme

A

catalyze the movement of functional group

straightforward named; kinases are also a form of transferase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

Hydrolase Enzyme

A

catalyze the breaking of a compound into two molecules by adding water

usually named only for their substrate

PHOSPHATASE

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

Lyase Enzyme

A

catalyzes the cleavage of a single molecule into two products

synthases when doing the opposite (synthesis of two molecules into one)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

Isomerase Enzyme

A

catalyze the rearrangement of bonds within a molecule

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

Ligase Enzyme

A

catalyze addition or synthesis reactions, generally between similar molecules, and often require ATP

NUCLEIC ACID SYNTHESIS

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

Endergonic vs Exergonic

A

Endergonic requires energy input (deltaG > 0)
Exergonic reaction in which energy is given off (deltaG < 0)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

Catalysts (enzymes) exert their effect by …

A

lowering the activation energy of a reaction

make it easier for the substrate to reach its transition state

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

Apoenzyme

A

an enzyme without its cofactor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

Holoenzyme

A

enzymes containing their cofactor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

Prosthetic Group

A

tightly bound cofactors that are necessary for enzyme function

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

Cofactor vs Coenzyme

A

Cofactors: inorganic molecules or metal ions; often ingested as dietary minerals

Coenzymes: small organic groups; vast majority are vitamins or vitamin derivatives

note:
vitamin B and vitamin C are WATER SOLUBLE
vitamin A, D, E, and K are FAT SOLUBLE

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

On the MCAT, the concentration of the enzyme will be constant. As a result, the Michaelis-Menten equation that will be used to determine reaction velocity is …

A

v = vmax * [S] / Km + [S]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

From the Michaelis-Menten equation, what happens when the reaction is running at half the velocity as its max velocity?

A

We derive that Km = [S]

Km then is the substrate concentration at which half of the enzyme’s active sites are full.

Michaelis Constant

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

Michaelis Constant (Km)

A

the measure of the affinity of the enzyme for its substrate

LOW Km = HIGH AFFINITY
HIGH Km = LOW AFFINITY

intrinsic to the substrate-enzyme system

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

Relationship between kcat and Vmax

A

Vmax = [E]*kcat

kcat represents the number of substrate molecules converted to product (per enzyme molecule per second)

Vmax represents maximum enzyme velocity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

Catalytic efficiency ratio

A

Kcat / Km

derived from low substrate concentrations (Km»[S]) where the Michaelis-Menten equation becomes:

v = (kcat/Km)[E][S]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

Lineweaver-Burk Plot x-axis and y-axis

A

x-axis = -1/Km
y-axis = 1/Vmax

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

Competitive Inhibition and effect to Lineweaver-Burk

How can it be overcome?

A

occupancy of the active site

NO CHANGE IN Vmax
INCREASE the measured Km

y-axis of plot stays the same
x-axis moves to the RIGHT

overcome by adding more substrate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

Noncompetitive inhibition and effect on the Lineweaver-Burk plot?

A

bind to an allosteric site rather than the active site, induces a change in enzyme conformation

MIXED - inhibitor binds equally well to the enzyme and enzyme-substrate complex

DECREASE in Vmax
NO CHANGE in Km

y-axis = moves UP
x-axis = no change

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

Uncompetitive Inhibition and effect on Lineweaver-Burl plot?

A

binds to enzyme-substrate complex only

LOWERS both Kmax nd Vmax

y-axis = goes UP
x-axis = goes LEFT

PARALLEL LINES because Km/Vmax (slope of line) UNCHANGED

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

Zymogen

A

enzyme in its inactive form (contain -ogen in name)

contain a catalytic and a regulatory domain

regulatory domain is removed or altered to expose active site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

Suicide Inhibition

A

Irreversible inhibition in which the enzyme is bound permanently to its inhibitor and rendered inactive.

IT IS NOT DEGRADED

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

Cadherins

A

type of CAM (cell adhesion molecule)

glycoprotein that mediate calcium-dependent cell adhesion

hold epithelial cells together

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

Integrins

A

type of CAM (cell adhesion molecule)

two membrane-spanning chains called alpha and beta

bind to and communicate with the ECM

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

Selectins

A

type of CAM (cell adhesion molecule)

bind to carbohydrates that project from other cell surfaces

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

Classic example of an enzyme-linked receptor

A

Receptor tyrosine kinases (RTK)

autophosphorylation

initiation of a second messenger cascade

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
71
Q

G Protein-Coupled Receptors

A

integral membrane proteins

binding of the ligand increases the affinity of the receptor for the G protein; affects the intracellular signaling pathway

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

Types of G Proteins

A

Gs = stimulates adenylate cyclase (increased cAMP)
Gi = inhibits adenylate cyclase (decreased cAMP)
Gq = activates phospholipase C (increased IP3; increased calcium levels)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

Which subunits are the G protein associated with when inactive?
What about active?

A

Inactive: alpha GDP associated with beta and gamma subunit

Active: alpha GTP dissociated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
74
Q

The migration velocity (v) of a protein moving in an electrophoresis separation can be calculated:

A

proportional to the electric field strength (E) and the net charge of the molecule (z)

inversely proportional to the frictional coefficient (f)

v = E*z / f

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
75
Q

What is special about PAGE (polyacrylamide gel electrophoresis)?

A

the functional native protein can be recovered after electrophoresis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
76
Q

How does SDS-PAGE (sodium dodecyl sulfate) work/separate proteins?

A

separates proteins on the basis of relative molecular mass alone

SDS disrupts all noncovalent interactions (NET NEGATIVE CHARGE)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
77
Q

How is protein atomic mass expressed? What is the molar mass of one amino acid?

A

expressed in Daltons (Da) aka g/mol

one amino acid is 100 Da

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
78
Q

How does isoelectric focusing work?

A

proteins are separated on the basis of their isoelectric point (pI)

proteins will stop on the gel when their pI = pH of the gel

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
79
Q

Describe Edman degredation

A

uses cleavage to sequence proteins of up to 50 to 70 amino acids

selectively and sequentially removes the N-terminal amino acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
80
Q

Carbohydrate nomenclature that contain aldehyde as most oxidized group? Ketone as most oxidized group?

A

Aldehyde: aldose
Ketone: ketose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
81
Q

What are the four monosaccharides that the MCAT tests structure and expects to know?

A

D-fructose (KLRR) [K = ketone on C-2]
D-glucose (RLRR)
D-galactose (RLLR)
D-mannose (LLRR)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
82
Q

Describe the absolute configuration of a Fischer projection of a carbohydrate (i.e. dashes and wedges)

A

The horizontal lines are WEDGES
the vertical lines are DASHES

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
83
Q

How does the D and L system work for carbohydrates?

A

D-sugars ALL have the hydroxide of their highest numbered chiral center on the RIGHT

L-sugars have the hydroxide of their highest numbered chiral center on the LEFT

84
Q

Describe the type of stereoisomer:
D-glucose to L-glucose?
glucose to mannose?
glucose to galactose?

A

D-glucose to L-glucose = enantiomer

glucose to mannose = diastereomer

glucose to galactose = epimer (subset of diastereomer that differ in configuration at exactly one chiral center!!)

85
Q

Pyranose vs furanose?

A

pyranose = six-membered ring
furanose = five-membered ring

86
Q

Why is oxygen a part of a ring in a hemiacetal and/or hemiketal?

A

the hydroxyl is a great nucleophile and attacks the great electrophile (the carbonyl carbon)

intramolecular ring-forming reaction

87
Q

What is an anomeric carbon?

A

the carbon that BECOMES CHIRAL in a sugar ring formation

the carbonyl carbon attacked by the hydroxyl group

88
Q

In glucose, which direction do the -OH groups point in the alpha and beta anomers?

A

alpha: -OH of C1 is trans (axial and down) to the CH2OH
beta: -OH of C1 is cis (equatorial and up) to the CH2OH

89
Q

Exposing hemiacetal rings to water will cause them to spontaneously cycle between the open and closed form. This is called …

A

mutarotation

bond between C-1 and C-2 can rotate freely and convert between alpha- and beta-anomers

occurs rapidly by acid or base catalyst

90
Q

Mutarotation equilibrium

A

occurs at the equilibrium constant of the individual carbohydrate

in glucose, beta-anomer dominates because there is LESS STRAIN

91
Q

Any monosaccharide with a hemiacetal ring is considered a …
hint: turns into a aldonic acid

A

reducing sugar

has the ability to be oxidized

92
Q

When an aldose in question is in its closed ring form, oxidation of the monosaccharide yields a …

A

lactone

93
Q

Tollens’ Reagent

A

detects the presence of a reducing sugar (ketose or aldehyde)

produces a SILVERY mirror when ALDEHYDES are present

94
Q

Benedict’s Reagent

A

detects the presence of a reducing sugar (ketose or aldehyde)

precipitates a red Cu2O when the aldehyde of an aldose is is oxidized

95
Q

Sucrose linkage?

A

glucose-alpha-1,2-fructose

96
Q

Lactose linkage?

A

galactose-beta-1,4-glucose

97
Q

Maltose linkage?

A

glucose-alpha-1,4-glucose

note: cellobiose is same link but beta; can’t be digested by humans

98
Q

Cellulose linkage?

A

polymer of 1,4-linked beta-D-glucose

beta-1,4-glycosidic bonds

99
Q

Amylose linkage?

A

plant storage from of starch

glucose polymer of alpha-1,4-glycosidic links

100
Q

Amylopectin linkage?

A

amylose with additional branching via alpha-1,6 glycosidic bonds

101
Q

Reagent for testing the presence of starch?

A

Iodine

102
Q

Glycogen linkage?

A

carbohydrate storage in animals

similar to starch but with more alpha-1,6 glycosidic bonds

103
Q

Glycogen phosphorylase?

A

cleaves glucose from the NONREDUCING end of a glycogen branch

104
Q

What fats form solids at room temperature? Which form liquids?

A

Saturated fats are SOLID
Unsaturated fats are LIQUID

105
Q

What is the major component in the plasma membrane of cells producing Myelin?

A

Sphingomyelin

no net charge on their heads

106
Q

Terpene structure?

A

class of lipids built from isoprene (C5H8)

a single terpene unit is comprised of 2 isoprene units

107
Q

Cholesterol in the cell membrane?

A

At low temperature: it keeps the cell at a constant fluidity (prevents from solidifying)
At high temperature: holds the membrane intact and prevents from becoming too permeable

108
Q

Vitamin in the retina important for vision?

A

Vitamin A

stored as retinol

109
Q

Lack of vitamin D results in …

A

rickets

underdeveloped, curved long bones

110
Q

What is a vitamin that serves as a biological antioxidant?

A

Vitamin E

111
Q

Which vitamin serves as an important precursor for blood clotting factors?

A

Vitamin K

112
Q

Soaps, formed by what process, acts as a surfactant. What is the process and what does a surfactant do?

A

The process is ester hydrolysis using a strong base to cleave the fatty acid.

Surfactants lower the surface tension at the surface of a liquid, serving as a detergent or emulsifier.

113
Q

Which receptors use secondary messenger systems?

A

Enzyme-linked receptors and G protein- coupled receptors

114
Q

Classically, which metal ions in the body are bound to protein rather than in their free state?

A

Calcium and magnesium

115
Q

Protein is in a region of an isoelectric gel at a pH above its pI. What will it do?
What about when the pH is lower?

A

pH higher: it is negatively charged and moves toward the ANODE

pH lower: it is positively charged and moves toward the CATHODE

116
Q

What happens when glucose reacts with ethanol under an acid catalyst?

A

the hemiacetal is converted to an acetal via replacement of the anomeric hydroxyl group with an alkoxy group

this is known as a GLYCOSIDE

117
Q

Beta-Amylose action?

A

cleaves amylose at the NONREDUCING END of the polymer to yield MALTOSE

118
Q

Fischer to Hawthorn projection?

A

groups pointing to the right go on BOTTOM and groups pointing to the left go ABOVE the projection

119
Q

Examples of glycolipids?

A

Cerebroside
Globoside
Ganglioside

all contain a sugar moiety; have a glycosidic bond

120
Q

Cholesterol mechanism of action?

A

Produced by endocrine glands and travel in the bloodstream to their target

Binds to DNA as part of the hormone-receptor complex to affect gene transcription (DOES NOT DIRECTLY BIND)

121
Q

Nucleoside structure?

A

five-carbon sugar (pentose) bonded to a nitrogenous base

covalent link to the C-1’ of the sugar

122
Q

Nucleotide structure?

A

formed when one or more phosphate groups attach to the C-5’ of the nucleoside

123
Q

Which carbon determines whether a nucleic acid is ribose or deoxyribose?

A

the 2’ carbon on the pentose sugar ring

124
Q

How are nucleotides joined together?

A

through a 3’-5’ phosphodiester bond

125
Q

Pyrimidines and purines

name them

A

Pyrimidines: cytosine, thymine, uracil (CUT)
Purines: adenine, guanine (AGs)

126
Q

Huckel’s Rule for aromaticity?

A

aromatic systems must have 4n + 2 pi electrons in the system

n = any integer

i.e. a cyclic butane with 2 double bonds is not aromatic because 4 pi electrons (must have either 2, 6 etc.

127
Q

What are the base-pairings in DNA?

A

adenine to thymine (2 hydrogen bonds)
guanine to cytosine (3 hydrogen bonds)

128
Q

What is commonly used to denature DNA?

A

heat, alkaline pH, formaldehyde and urea

129
Q

DNA is wound around histones. What structure did we just make?

A

chromatin

130
Q

Heterochromatin vs euchromatin?

A

Heterochromatin = stays compact during interphase (dark and silent // repetitive sequences)
Euchromatin = dispersed chromatin (light and genetically active)

131
Q

Telomere

A

caps the end of DNA to avoid genetic info from being lost

also, high GC-content creates strong strand attraction to prevent unraveling

part of telomere that is lost after each round of replication is replaced by telomerase

132
Q

How does DNA manage the large torsional strains created during DNA replication?

A

the enzyme DNA topoisomerase introduces negative supercoils to reduce the risk of strand breakage and alleviate torsional strain

work ahead of helicase, nicking one or both strands and resealing the cuts

133
Q

Why is DNA replication semiconservative?

A

ONE parental strand is retained in each of the two resulting identical double-stranded DNA molecules

134
Q

DNA polymerase

A

reads the parent strand in a 3’ to 5’ direction and synthesizes a daughter strand in the 5’ to 3’ direction

135
Q

Lagging strand

A

the strand that is copied in the opposite direction of the replication fork

daughter strands are synthesized in smaller fragments called Okazaki fragments

136
Q

Primase

A

enzyme that creates RNA fragments to act as a primer for DNA replication initiation (5’ to 3’ direction)

technically, only one primer needed for the leading strand

137
Q

What DNA polymerase is in prokaryotes? In eukaryotes?

A

Prokaryotes: DNA polymerase III
Eukaryotes: DNA polymerase alpha, delta, and epsilon

138
Q

What removes the RNA primer in prokaryotes and eukaryotes?

A

Prokaryotes: DNA polymerase I
Eukaryotes: RNase H

139
Q

What adds nucleotide sequences where the primer used to be in prokaryotes and eukaryotes?

A

Prokaryotes: DNA polymerase I
Eukaryotes: DNA polymerase delta

140
Q

What seals DNA back together after replication has occurred?

A

DNA ligase

141
Q

How do proofreading enzymes determine which is the parent strand and which is the daughter strand of DNA?

A

amount of methylation!

parent strands are more heavily methylated (been inside the body longer)

142
Q

MSH2 and MLH1 genes in eukaryotyes
MutS and MutL genes in prokaryotes

what are their roles??

A

mismatch repair in G2 phase of cell cycle

detect nd remove errors in DNA replication

143
Q

Effect of ultraviolet light on DNA? How is it fixed?

A

induces the formation of thymine dimers which disrupt shape and DNA replication

nucleotide excision repair (NER) mechanisms cut-and-patch DNA

endonucleases to the rescue

144
Q

Restriction enzyme?

A

cut DNA sequences at specific points

advantageously used in recombinant DNA technology

145
Q

How are cDNA libraries produced?

A

reverse transcribing mRNA (reverse transcriptase)

generates complementary DNA (lacks noncoding regions, such as introns)

146
Q

Which side of the chamber will DNA travel in electrophoresis on an agarose gel?

A

toward the anode (DNA is negatively charged)

147
Q

Southern Blot

A

used to detect the presence and quantity of various DNA strands

148
Q

mRNA

A

“messenger RNA”

only type of RNA carrying information translated into protein

monocistronic – 1 mRNA = 1 protein

149
Q

tRNA

A

“transfer RNA”

converts the language of nucleic acids to the language of amino acids/peptides

folded structure that contains a three-nucleotide anticodon

tRNA charged with an amino acid; activated by aminoacyl-tRNA-synthetase (required 2 ATP)

goes on to creates a peptide bond

150
Q

rRNA

A

“ribosomal RNA”

synthesized in the nucleolus; functions as integral part of the ribosomal machinery

ribozyme

151
Q

Which are the stop codons?

A

UAA
UAG
UGA

152
Q

Every protein begins with what protein?

A

Methionine

i.e. codon AUG

153
Q

Missense Mutation

A

a mutation where one amino acid substitutes for another

154
Q

Nonsense Mutation

A

premature stop codon mutation (truncation mutation)

155
Q

The template strand of DNA in RNA synthesis is also called the …

A

antisense strand

156
Q

How does the RNA polymerase II in eukaryotes know where to start transcription for RNA synthesis?

A

looks for a promotor region called the TATA box

157
Q

How is the coding strand (sense strand) of DNA compare to the processed mRNA?

A

coding strand is also complementary to the template strand, it is identical to the mRNA EXCEPT the thymine has been converted to uracil

158
Q

What is mRNA directly after synthesis and before posttranscriptional modifications?

A

heterogenous nuclear RNA (hnRNA)

159
Q

What are the three posttranscriptional processes that must occur after hnRNA synthesis?

A

Intron/Exon splicing
5’ cap
3’ poly-A tail

160
Q

Introns vs exons?

A

Introns = noncoding
Exons = coding and must be ligated together

161
Q

Intron/Exon Splicing?

A

accomplished by the spliceosome

small nuclear RNA (snRNA) couple with small nuclear ribonucleoproteins (snRNPs)

162
Q

What is alternative splicing?

A

multiple mRNAs from one hnRNA

more biodiversity from a
smaller genome

163
Q

In prokaryotes, translation is initiated by the small subunit (30S) binds to the … in the 5’ UTR of mRNA?

A

binds to the Shine-Dalgarno sequence

164
Q

Describe elongation in translation?

A

ribosome moves in the 5’ to 3’ direction and synthesizes protein from the N- amino to the C- carboxyl terminus

A site holds the incoming aminoacyl-tRNA complex; P site creates the peptide bond (peptidyl transferase; uses GTP); E site is where the now uncharged tRNA unbinds from mRNA

165
Q

What is the Jacob-Monod model of operons (gene expression)?

A

structural gene - codes for the protein of interest
operator site - upstream of structural gene; capable of binding a repressor protein
promotor site - upstream of structural gene - place for RNA polymerase to bind
regulator gene - furthest upstream; codes for proteins known as the repressor

operons can either be inducible systems or repressible systems

166
Q

Inducible Systems (operons)

A

repressor is bonded tightly to the operator system; acts as a roadblock

inducer must bind the repressor protein so that the RNA polymerase can start transcription

negative control (binding of a protein REDUCES transcriptional activity)

167
Q

Lac operon

A

INDUCIBLE SYSTEM

it is induced by the presence of lactose

assisted by the binding of catabolite activator protein (CAP)

glucose down = cAMP up, which binds to CAP

CAP binds to promotor to increase transcription (positive control)

168
Q

Repressible System (operon)

A

constant production of a protein product; repressor inactive until it binds to a corepressor

often negative feedback (final product acts as the corepressor)

169
Q

Trp Operon

A

repressible system (negative feedback)

when tryptophan is high, it acts as a corepressor and complex binds to operator site

170
Q

Transcription factor (TF) domains?

A

DNA-binding domain - binds to nucleotide sequence in the promotor region or to a DNA response element

Activation domain – binds to other TFs and other regulatory proteins

171
Q

Histone aceylation

A

histone acetylases acetylate the lysine residue found in the amino terminal tail

acetylation of the histone DECREASES the positive charge on lysine resulting in a OPEN chromatin conformation (transcription increases)

172
Q

DNA methylation

A

DNA methylases add methyl groups to cytosine and adenine nucleotides

methylaton linked with GENE SILENCING

173
Q

What creates a coat around the plasma membrane of eukaryotes?
What can be seen moving rapidly in the plane of the membrane through simple diffusion?

A

glycoprotein (carbohydrates) coat

phospholipids (lipid rafts) move through the membrane

174
Q

Unsaturated fats are consumed in the form of essential fatty acids that are ingested in the diet. These are transported in the form of … from the intestine inside of …?

A

Transported as triacylglycerols inside of chylomicrons

175
Q

What are two important ESSENTIAL fatty acids for humans?

A

alpha-linolenic acid
linoleic acid

176
Q

We take a triacylglycerol and replace one of the esterified fatty acid heads with a phosphate group. What did we just form?

A

a glycerophospholipid more commonly known as a PHOSPHOLIPID

this is the primary component of the cell membrane

177
Q

What is a ceramide?

A

type of sphingolipid

sphingosine backbone

single hydrogen atom as its head group

178
Q

What is sphingomyelin?

A

sphingolipid AND a phospholipid

either a phosphocholine OR a phosphoethanolamine as a head group (phosphodiester bond)

NO NET CHARGE

179
Q

What is a cerebroside?

A

type of sphingolipid

head group composed of sugars bonded by glycosidic linkages

only a SINGLE SUGAR to be considered a cerebroside

NOT a phospholipid

180
Q

What is a ganglioside?

A

type of sphingosine

polar head composed of oligosaccharide with one or more N-acetylneuraminic acid (NANA; aka sialic acid) molecules

NEGATIVE terminus

181
Q

Desmosomes

A

bind adjacent cells together via INTERMEDIATE FILAMENTS

182
Q

Equation for osmotic pressure?

A

pi = iMRT

pi = osmotic pressure
i = van’t Hoff factor (number of particles obtained from the molecule when in solution)
M = molarity of the solution
R = ideal gas constant
T = absolute temperature in Kelvin

think as the “sucking pressure”, drawing water INTO the cell in proportion to the concentration of the solution

183
Q

Primary active transport vs secondary active transport?

A

Primary = uses ATP to directly power the transport of molecules

Secondary = uses energy but no direct coupling of to ATP hydrolysis (one particle does down its gradient to drive a different particle up its gradient)

184
Q

Endocytosis

A

cell invaginates and brings material INTO the cell

initiated and carried out by vesicle-coating protein such as clathrin

185
Q

Pinocytosis vs Phagocytosis

A

BOTH endocytosis

pinocytosis - endocytosis of fluids and dissolved particles
phagocytosis - endocytosis of large solids

186
Q

Exocytosis

A

secretory vesicle fuses with membrane to RELEASE material from the cell

187
Q

What is normal glucose concentration in the body?

A

4-5 mM OR 100 mg/dL

188
Q

GLUT 2 glucose transporter

A

low affinity on hepatocytes and pancreatic cells

captures the excess glucose (really high Km)

189
Q

GLUT 4 glucose transporter

A

adipose tissue and muscle

rate of transport increased by insulin

Km is close to the normal glucose level in blood

190
Q

Broad glycolysis overview

i.e. location, substrate, product

A

cytoplasmic process

start with one glucose and get two pyruvate

2 phosphorylation and one oxidation

191
Q

Hexokinase / Glucokinase

A

phosphorylates glucose once it enters the cell to glucose 6-phosphate

prevents glucose from leaving the cell

GLUCOKINASE only found in liver cells and pancreatic beta-islet cells (induced by insulin)

192
Q

Phosphofructokinases (PFK-1 and PFK-2)

A

rate-limiting enzyme (MAIN CONTROL POINT in glycolysis)

fructose 6-phosphate converted to fructose 1,6-bisphosphate using ATP

193
Q

PFK-1 is inhibited by …
activated by …

A

inhibited by ATP and citrate

activated by AMP

194
Q

PFK-2 is activated by …
inhibited by …

A

activated by insulin
inhibited by glucagon

195
Q

What does PFK-2 do?
Where is it found?

A

converts a tiny amount of fructose 6-phosphate into fructose 2,6-bisphosphate (F2,6-BP)

F2,6-BP ACTIVATES PFK-1 and is found in the LIVER

196
Q

Glyceraldehyde-3-Phosphate Dehydrogenase

A

converts glyceraldehyde 3-phosphate into 1,3-bisphosphoglycerate

oxidation and Pi addition

reduction of NAD+ to NADH

197
Q

3-Phosphoglycerate Kinase

A

transfers high-energy phosphate from 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate

substrate-level phosphorylation (O2 independent)

198
Q

Pyruvate Kinase

A

catalyzes a substrate-level phosphorylation of ADP using phosphoenolpyruvate (PEP)

199
Q

What is the key fermentation enzyme in mammalian cells?

A

lactase dehydrogenase

oxidizes NADH to NAD+ (replenishes oxidized coenzyme for glyceraldehyde 3-phosphate dehydrogenase

200
Q

Dihydroxyacetone phosphate (DHAP)

A

hepatic and adipose tissue for triacylglycerol synthesis

intermediate of glycolysis

formed from fructose 1,6-bisphosphate (isomerized to glycerol 3-phosphate)

201
Q

What is special about 1,3-Bisphosphateglycerate (1,3-BPG) and phosphoenolpyruvate (PEP)?

A

generate ATP via substrate-level phosphorylation

202
Q

What are the irreversible enzymes in glycolsis?

A

Glucokinase / Hexokinase
PFK-1
Pyruvate kinase

203
Q

2,3-bisphosphate glycerate (2,3-BPG)

A

found in erythrocytes

converted from 1,3-BPG via biphosphoglycerate mutase

binds allosterically to the beta-chain of hemoglobin A (HbA) and DECREASES affinity for O2

204
Q

Glycogenesis is triggered when glucose 6-phosphate is converted into … ?

A

glucose 1-phosphate

205
Q

What does branching enzyme do?

A

Hydrolyzes a alpha-1,4 bond and forms a alpha-1,6 bond in glycogen

206
Q

What are the two major functions of the pentose phosphate pathway (PPP)?

A

production of NADPH and ribose 5-phosphate (nucleotide synthesis)

MCAT (6 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions