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biochem > full review - biochem mcat > Flashcards

full review - biochem mcat Flashcards

1
Q

four groups on AAs

A

carboxylic acid

R group

H atom

amino group

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2
Q

R group on AA determines

A

functions

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3
Q

amino acids with long alkyl chains are

A

hydrophobic

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4
Q

AAs with charges are

A

hydrophilic

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5
Q

stereochemistry of alpha-carbon is (answer) for all chiral AAs

A

L configuration

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6
Q

carbohydrates are (answer) configuration

A

D config

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7
Q

all chiral AAs except (what) have S configuration

A

cysteine

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8
Q

all amino acids are chiral except

A

glycine

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9
Q

lower pH means

A

AA is FULLY protonated

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10
Q

when the pH is around the same value of the pI, that means the AA is a

A

neutral zwitterion

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11
Q

increased pH means that the AA is

A

FULLY deprotonated

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12
Q

what is pI?

A

pH at which AA is in zwitterion form

charges cancel out to make a neutral molecule

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13
Q

titration midpoint

A

pH = pKa

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14
Q

equivalence pt for a titration

A

pH = pI

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15
Q

dipeptide = how many residues

A

2

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16
Q

tripeptide =

A

3 residues

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17
Q

oligopeptides has less than

A

20 residues

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18
Q

polypeptides have greater than

A

20 residues

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19
Q

how to form a peptide bond

A

dehydration rxn

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20
Q

in a dehydration rxn, nucleophilic amino group of one AA attacks the

A

electrophilic carbonyl group of another AA

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21
Q

amide bonds

A

C-N bond of a peptide bond

RIGID due to resonance

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22
Q

breaking a peptide bond is a

A

hydrolysis rxn

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23
Q

primary structure of a protein

A

linear sequence of an AA in a peptide

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24
Q

what stabilizes primary structure

A

peptide bonds

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25
Q

AA sequence in primary structure is written

A

N-terminus to C-terminus

N-terminus is POSITIVELY charged due to -NH3+

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26
Q

secondary structure is the local structure of

A

neighboring AA

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27
Q

what stabilizes secondary structure

A

H-bonding between amino groups and nonadjacent carboxyl groups

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28
Q

alpha helices are found in what protein structure

A

secondary structure

clockwise coils around a central axis

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29
Q

beta-plated sheets are found in

A

2ndary structure

rippled strand that can be parallel or antiparallel

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30
Q

which AA can interrupt 2ndary structure

A

proline b/c of its rigid cyclic structure

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31
Q

what is denaturing

A

protein (or nucleic acid) loses quarternary/tertiary/2ndary structures

non-covalent interactions break

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32
Q

what non-covalent interactions break during denaturing

A

h-bonds

hydrophobic interactions

dipole-dipole interactions

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33
Q

tertiary structure is the

A

3d shape of a single polypeptide chain

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34
Q

what stabilizes tertiary structure

A

hydrophobic interactions

acid-base interactions

h bonds

disulfide bonds

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35
Q

hydrophobic interactions push r groups to the

A

interior of a protein

increases entropy of surrounding water molecules

negative gibbs free E created

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36
Q

disulfide bonds occur when two cystein molecules…

A

oxidize and create a covalent bond b/w thiol groups

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37
Q

when two cystein molecules are oxidized and create a covalet bond b/w thiol groups, what is formed

A

cystine

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38
Q

quarternary structure is the interaction between

A

peptides in proteins that contain multiple subunits

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39
Q

conjugated proteins are proteins with

A

covalently attached molecules

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40
Q

what is the attached molecule in a conjugated protein?

A

prosthetic group

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41
Q

what can a prosthetic group be?

A

metal ion

vitamin

lipid

carbohydrate

nucleic acid

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42
Q

what can cause denaturation

A

heat or solute concentration

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43
Q

monosaccharides are single carbohydrate units with…

A

glucose as the most commonly observed monomer

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44
Q

monosaccharides can undergo

A

oxidation/reduction

esterification

glycoside formation

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45
Q

aldoses oxidized into

A

aldonic acids

reduced to alditols

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46
Q

sugar that can be oxidized are

A

reducing agents

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47
Q

sugar that are reducing agents can be detected by

A

reacting with Tollen’s or Benedict’s reagents

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48
Q

in deoxy sugars, what replaces what

A

-H replaces -OH

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49
Q

in esterification, sugars react with…

A

carboxylic acids and their derivatives

forming esters

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50
Q

phosphorylation is a phosphate ester formed by….

A

transferring a phosphate group from ATP onto sugar

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51
Q

glycoside formation is the basis for building….

A

complex carbohydrates and requires anomeric carbon to link to another sugar

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52
Q

cyclization describes ring formation of

A

carbohydrates from straight-chain forms

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53
Q

anomeric carbon is the new chiral center formed in

A

ring closure

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54
Q

alpha-anomers have the -OH on the

A

anomeric carbon trans to the free -CH2OH group

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55
Q

beta-anomers have the –OH on the

A

anomeric carbon cis to the free CH2OH group

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56
Q

what represents 3D structure of a monosaccharide?

A

hawthorn projections

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57
Q

mutarotation is the spontaneous shift from one

A

anomeric form to another w/ the straight-chain form as an intermediate

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58
Q

disaccharides form as a result of

A

glycosidic bonding b/w two monosaccharide subunits

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59
Q

dissacharide examples

A

sucrose, lactose, maltose

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60
Q

polysaccharides are formed by repeated…

A

monosaccharide or polysaccharide glycosidic bonding

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61
Q

cellulose is the main structure component for

A

plant cell walls

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62
Q

cellulose is the main source of

A

fiber in a human diet

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63
Q

starches are the main energy storage form for

A

plants

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64
Q

amylose is unbranched or branched?

A

unbranched

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65
Q

amylopectin is branched or unbranched?

A

branched

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66
Q

lipids are insolube in

A

water

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67
Q

lipids are soluble in

A

nonpolar organic solvents

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68
Q

phospholipids are

A

amphipathic and form the bilayer of membranes

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69
Q

phospholipids contain a

A

polar head and nonpolar tails

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70
Q

polar head is attached by

A

phosphodiester linkage which determines the phospholipid function

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71
Q

saturation of the fatty acid tails determines

A

membrane fluidity

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72
Q

saturated fatty acid is less or more fluid than unsaturated

A

less

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73
Q

glycerophospholipids contain a

A

glycerol backbone

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74
Q

spingolopids contain a

A

spingosine backbone

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75
Q

many spingolipids are also phospholipids with a

A

phosphodiester bond

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76
Q

spingomyelines are the major class of

A

spingophospholipids

part of myelin sheath

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77
Q

glycosphingolipids are attached to sugar moieties instead of

A

a phosphate group

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78
Q

cerebrodies have how many sugars connected to the spingosine

A

1 sugar

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79
Q

globosides have how many sugars

A

2 connected to spingosine

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80
Q

gangliosides contain oligosaccharides with….

A

at least 1 terminal acetylneuraminic acid

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81
Q

waxes contain long-chain fatty acids…

A

esterified to long chain alcohols

protection against evaporation/parasites in plants and animals

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82
Q

terpenes are

A

steroid precursors

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83
Q

terpenoids are derived from terpenes via

A

oxygenation or backbone rearrangement

odorous characteristics

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84
Q

steroids contain…

A

3 cyclohexane rings

1 cyclopentane

3 rooms and 1 basement

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85
Q

steroid hormones have high-affinity receptors, work at low…

A

concentrations

affect gene expression/metabolism

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86
Q

cholesterol is a steroid important to

A

membrane fluidity and stability

serves as a precursor to many other molecules

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87
Q

prostaglandins are what kind of signalling molecules

A

autocrine and paracrine signalling molecules

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88
Q

prostaglandins regulate

A

cAMP levels

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89
Q

prostaglandins affect

A

smooth muscle contraction

body temp

sleep-wake cycle

fever

pain

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90
Q

fat soluble vitamins

A

vitamins A, D, E, K

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91
Q

vitamin A

A

carotene

vision

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92
Q

vit D

A

cholecalciferol

bone formation

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93
Q

vit E

A

tocopherols

antioxidants

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94
Q

vit K

A

forms prothrombin (clotting factor)

phylloquinone and menaquinone

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95
Q

triacylglycerols are a storage form of

A

fatty acids

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96
Q

1 glycerol attached to 3 fatty acids by ester bonds is

A

triacylglycerols (very hydrophobic!)

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97
Q

adipocytes are animals cells used for

A

triacyglycerol storage

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98
Q

free fatty acids are unesterified fatty acids that

A

travel in bloodstream

salts of free fatty acids = soaps

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99
Q

saponification is the ester hydrolysis of

A

triacylglycerols using a strong base like sodium or KOH

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100
Q

micelle can dissolve a lipid-solube molecule in

A

its fatty acid core

washes away with water b/c of shell with carboxylate head groups

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101
Q

cerebroside is a type of

A

glycolipids

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102
Q

a glycolipid is a

A

lipid linked to any sugar

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103
Q

2ndary structure are interactions between bases within

A

the same molecule

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104
Q

2ndary structure in DNA, bases are held together by

A

h bonds

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105
Q

2ndary structure is responsible for the

A

shape of nucleic acid

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106
Q

quarternary structure is the interactions of

A

nucleic acids with other molecules

e.g. chromatin interacting w/ histones

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107
Q

nucleic acids are

A

polymers of nucleotides

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108
Q

DNA replication is the process of producing an

A

identical replica of a DNA molecule

occurs during S phase of cell cycle

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109
Q

oncogenes develop from mutations of

A

proto-oncogenes and promote cell cycling

may lead to cancer

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110
Q

oncogenes =

A

stepping on gas pedal

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111
Q

tumor suppressor genes code for

A

proteins that REDUCE cell cycling

promote DNA repair

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112
Q

mutated tumor suppressor genes =

A

cutting the brakes

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113
Q

proofreading is when DNA polymerase

A

proofreads its work and excises incorrectly matched bases

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114
Q

daughter strand is identified by its

A

lack of methylation and corrected accordingly

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115
Q

mismatch repair occurs during

A

G2 phase using MSH2 and MLH1 genes

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116
Q

nucleotide excision repair fixes helix-deforming lesions of

A

DNA such a thymine dimers

cut-and-patch process

excision endonuclease

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117
Q

base excision fixes nondeforming lesions of the

A

DNA helix such as the cytosine deamination by removing base

leaving AP site

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118
Q

AP endonuclease removes the

A

damaged sequence which can be filled in with the correct bases

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119
Q

what is DNA

A

macromolecule that stores genetic info in all living organisms

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120
Q

nucleoside is a 5-carbon sugar and

A

nitrogenous base

NO PHOSPHATE groups

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121
Q

nucleotides are

A

a nucleoside with 1 to 3 phosphate groups added

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122
Q

nucleotides in DNA contain

A

deoxyribose

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123
Q

nucleotides in RNA contain

A

ribose

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124
Q

name the nucleotides

A

adenine (A)

thymine (T)

guanine (G)

cytosine (C)

uracil (U)

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125
Q

in RNA, what replaces T

A

U replaces T

A paired with U via 2 H-bonds

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126
Q

watson-crick model is the backbone of

A

alternating sugar/phosphate groups

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127
Q

watson-crick model is always read

A

5’ to 3’

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128
Q

two strands with antiparallel polarity wind into a

A

double helix

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129
Q

nitrogenous bases

A

purines: adenine and guanine (2 rings)

pyrimidines: cytosine, thymine, uracil (1 ring)

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130
Q

chargaff’s rule states that

A

number of purines = number of pyrimidines

A = T

C = G

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131
Q

B-DNA means

A

a right-handed helix is formed

DNA is B-DNA

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132
Q

low concentrations of Z-DNA has what shape

A

zigzag shape

has a high GC content or high salt concentration

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133
Q

denatured DNA gets

A

pulled aparted

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134
Q

reannealed DNA gets

A

brought back together

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135
Q

how many chromosomes in human cells

A

46

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136
Q

DNA is wound around (what) to form…

A

histones to form nucleosomes

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137
Q

nucleosomes can be stabilized by

A

another histone protein

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138
Q

as a whole, DNA and its associated histones make up

A

chromatin in the nucleus

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139
Q

chromatin types

A

heterochromatin

euchromatin

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140
Q

heterochromatin is

A

dark, dense, silent

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141
Q

euchromatin is

A

light, uncondensed, expressed

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142
Q

where are telomeres

A

end of chromosomes

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143
Q

telomeres contain high GC-content to prevent

A

DNA unravelling

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144
Q

during replication, telomeres are

A

shortened

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145
Q

telomeres shortening can be partially…

A

reversed by telomerase

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146
Q

where are centromeres

A

middle of chromosomes

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147
Q

centromeres hold

A

sister chromatids together until separation during anaphase in mitosis

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148
Q

high GC-content maintains what between chromatids

A

a strong bond

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149
Q

acrocentric chromosomes is located near one end of the

A

chromosome and not in the middle

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150
Q

recombinant DNA is DNA composed of

A

nucleotides from 2 different sources

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151
Q

hybridization is the joining of

A

complementary base pair sequences

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152
Q

what is the central dogma

A

statement that DNA is transcribed to DNA which is translated to protein

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153
Q

degenerate code allows for multiple codons to

A

encode for the same AA

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154
Q

start and stop codons

A

start codon: AUG

stop codons: UAA, UGA, UAG

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155
Q

start codon

A

AUG

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156
Q

stop codons

A

UAA

UGA

UAG

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157
Q

wobble is the

A

3rd base in the codon

allows for mutations to occur w/o effects in protein

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158
Q

wobble base pairings are less

A

stable

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159
Q

silent point mutations are…

A

mutations with no effect on protein synthesis

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160
Q

silent point mutations are usually found in the

A

3rd base of a codon

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161
Q

nonsense point mutations are…

A

mutations that produce a premature STOP codon

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162
Q

missense point mutations produce a codon that…

A

codes for a different AA

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163
Q

frameshift mutations result from a

A

nucleotide addition or deletion

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164
Q

frameshift mutations change the

A

reading frame of subsequent codons

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165
Q

RNA is similar to DNA except that

A

ribose sugar instead of deoxyribose

uracil instead of thymine

single stranded not double

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166
Q

3 types of RNA

A

mRNA

tRNA

rRNA

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167
Q

mRNA is transcribed from

A

DNA in nucleus

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168
Q

mRNA travels into

A

cytoplasm for translation

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169
Q

tRNA brings in AAs and…

A

recognizes the codon on mRNA using its anticodon

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170
Q

rRNA makes up the

A

ribosome and is enzymatically active

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171
Q

tRNA translates the…

A

codon into the correct AA

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172
Q

ribosomes are factories where

A

translation (protein synthesis) occurs

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173
Q

eukaryotes have which ribosomes

A

80s

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174
Q

prokaryotes have which ribosomes

A

70s

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175
Q

initiation in prokaryotes is when the

A

30S ribosome attaches to the Shine-Delgarno sequences

scans for a start codon

lays down N-formylmethionine in P side of ribosome

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176
Q

eukaryote initiation

A

when 40S ribosome attaches to 5’ cap

scans for start codon

lays down methionine in P site of ribosome

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177
Q

elongation is the addition of a new

A

aminoacyl-tRNA into the A site of ribosome

transfer of growing polypeptide chain from tRNA in P site –> tRNA in A site

uncharged tRNA pauses in E site before exiting ribosome

A site tRNA moves to P site

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178
Q

termination occurs when the codon in the

A

A site is a stop codon

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179
Q

release factors places a water molecule on the

A

polypeptide chain and thus releases the protein during termination

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180
Q

posttranslation modifications:

A

folding by chaperones

quarternary structure formation

cleavage of protein/signal sequences

covalent addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)

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181
Q

DNA ligase fuses what together to create…

A

fuses DNA strands to create one strand

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182
Q

helicase function

A

unwinds DNA double helix

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183
Q

RNA polymerase II function

A

binds to TATA box within promoter region of gene

25 base pairs upstream from first transcribed base

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184
Q

hnRNA is the collective term for

A

the unprocessed mRNA in nucleus

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185
Q

posttranscriptional modification is the process in which the

A

eukaryotic cells where primary transcript RNA is converted into mature RNA

introns cut out

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186
Q

exons exit the

A

nucleus and form mRNA

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187
Q

introns spliced out so they

A

stay in nucleus

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188
Q

introns also enable

A

alternative splicing

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189
Q

alternative splicing is when

A

introns cut away and exons remain

but in alternative splicing, a certain exon may be cut out or an intro may stay

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190
Q

alternative splicing allows for the

A

RNA segment to code for more than one gene

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191
Q

what are added to the mRNA

A

5’ cap and poly-A tail

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192
Q

what do the 5’ cap and poly-A tail do

A

stabilizes mRNA for translation

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193
Q

prokaryotic cells can increase variability of gene products from

A

one transcript through polycistronic genes

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194
Q

multiple translation sites within the gene which leads to

A

different gene products

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195
Q

jacob-monod model explains how

A

operons work

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196
Q

operons are inducible or repressible

A

clusters of genes transcribed as a single mRNA

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197
Q

inducible systems

A

under normal condition, IS bonded to a repressor

turned on when an inducer pulls the repressor off

e.g. Lac operon

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198
Q

repressible systems

A

transcribed under normal conditions

can be turned off by a corepressor coupling w/ the repressor

binding of complex to operator site

e.g. Trp operon

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199
Q

transcription factors search for promoter and enhancer

A

regions in DNA

bind to DNA and recruit RNA polymerase

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200
Q

promoters are within

A

25 base pairs of transcription start site

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201
Q

enhancers are more than

A

25 base pairs away from the transcription start site

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202
Q

modification of chromatin structure affects the ability of transcriptional enzymes to….

A

access the DNA thru histone acetylation (+ access)

or DNA methylation (- access)

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203
Q

what does the fluid mosaic model account for?

A

presence of lipids, proteins and carbohydrates in a dynamic, semisolid plasma membrane that surrounds cells

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204
Q

in the phospholipid bilayer, each phosphlipid has a

A

hydrophilic head + hydrophobic tail

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205
Q

heads of phospholipids are arranged so that they are

A

facing outward and the tails make up in the inside of the membrane

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206
Q

proteins are embedded in the

A

phospholipid bilayer

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207
Q

lipid rafts are made of

A

lipids moving freely in the plane of the membrane

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208
Q

flippases are specific membrane proteins that maintain the…

A

bidirectional transport of lipids b/w layers of the phospholipid bilayer in cells

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209
Q

proteins and carbohydrates may also move within the

A

membrane but are slowed by their large size

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210
Q

all transmembrane movement is based on

A

concentration gradients

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211
Q

concentration gradient tells us whether the process is

A

passive or active

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212
Q

osmotic pressure is what kind of property

A

colligative

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213
Q

osmotic pressure is the pressure applied to a

A

pure solvent to prevent osmosis

used to express solution’s concentration

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214
Q

what characterizes osmotic pressure

A

“sucking” pressure in which a solution is drawing water in

proportional to its concentration

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215
Q

passive transport does not require

A

energy b/c the molecule is moving down its concentration gradient

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216
Q

simple diffusion is a type of

A

passive transport

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217
Q

in simple diffusion, small nonpolar molecules move…

A

passively from an area of high to low concentration until equilibrium is achieved

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218
Q

osmosis is a type of

A

passive transport

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219
Q

osmosis describes diffusion of water across

A

a selectively permeable membrane

220
Q

facilitated diffusion is a form of

A

passive transport

221
Q

facilitated diffusion uses what to move…

A

transport proteins to move impermeable solute across the cell membrane

222
Q

active transport requires

A

energy (ATP)

223
Q

primary active transport uses what to…

A

ATP to power transport of molecules across a membrane

224
Q

secondary active transport is known as

A

coupled transport

225
Q

2ndary active transport harnesses energy released by

A

one particle going down electrochemical gradient to drive a different particle up its gradient

226
Q

symport is when

A

both particles flow in same direction

part of 2ndary active transport

227
Q

antiport is when

A

particles flow in opp direction

part of secondary active transport

228
Q

endocytosis and exocytosis are the methods of

A

engulfing material into the cells or releasing material out of the cell

229
Q

pinocytosis is the ingestion of

A

liquids aka vesicles

230
Q

phagocytosis is the ingestion of

A

larger solid materials

231
Q

lipids are the primary…

A

membrane component

both by mass and mole fraction

232
Q

triaglycerols and fatty acids act as

A

phospholipid precursors and are found in low levels in the membrane

233
Q

glycerophospholipids replace one fatty acid with a

A

phosphate group (often linked to other hydrophilic groups)

234
Q

cholesterol is present in

A

large amounts in the membrane

235
Q

cholesterol contributes to

A

membrane fluidity and stability

lower temp = decrease fluidity
increase temp = increase fluidity

236
Q

waxes are present in very

A

small amounts

237
Q

what are waxes most prevalent in?

A

in plants

function: waterproofing and defense

238
Q

transmembrane proteins are a type of integral protein that…

A

spans the entire membrane

often glycoproteins

239
Q

embedded proteins are most likely part of

A

catalytic complex or involved in cellular communication

240
Q

membrane-associated proteins may act as

A

recognition molecules or enzymes

241
Q

carbohydrates can form a

A

protective glycoprotein and also function in cell recognition

242
Q

extracellular ligands can bind to

A

membrane receptors which function as channels/enzymes in second messenger pathways

243
Q

gap functions allow for rapid exchange of

A

ions and other small molecules b/w adjacent cells

244
Q

tight junctions prevent solutes from leaking into

A

the space b/w cells via a paracellular route

do NOT provide intercellular transport

245
Q

desmosomes bind adjacent cells by

A

anchoring to cytoskeletons

246
Q

hemidesmosomes are similar to desmosomes but

A

their main function is to attach epithelial cells to underlying structures

247
Q

GLUT-2 is found in

A

liver for glucose storage and pancretic b-islet cells (as a part of the glucose sensor)

INCREASED Km

248
Q

GLUT-4 is found in

A

adipose tissue and muscle

stimulated by insulin

LOWERED Km

249
Q

mechanical digestion of lipids occurs…

A

primarily in the mouth and stomach

250
Q

chemical digestion of lipids occurs in the

A

small intenstine

251
Q

chemical digestion is facilitated by

A

bile, pancreatic lipase, colipase, cholesterol esterase

252
Q

upon entry into the duodenum, what occurs

A

emulsification which is the mixing two liquids don’t mix usually (fat + water)

253
Q

emulsification increases the

A

surface area of the lipid

254
Q

increasing surface of the lipid via emulsification permits

A

greater enzymatic interaction and processing

255
Q

what aids emulsification?

A

bile salts

256
Q

micelles are

A

water-soluble spheres w/ a lipid soluble interior

257
Q

digested lipids may form micelles to be carried to

A

the intestinal epithelium where they are absorbed across the PM

258
Q

short chain fatty acids are absorbed across

A

the intestine into the blood

259
Q

long chain fatty acids are absorbed as

A

micelles and assembled into CHYLOMICRONS for release into lymphatic system

260
Q

fatty acids are

A

carboxylic acids w/ a long chain

261
Q

saturated fatty acids have

A

NO double bonds

262
Q

unsaturated fatty acids have

A

one or more double bonds

263
Q

five steps of fatty acid synthesis

A

activation

bond formation

reduction

dehydration

second reduction

264
Q

where are fatty acids formed

A

cytoplasm from acetyl-COA that is transported out of the mitochondria

265
Q

arachidonate is the precursor to

A

eicosanoid signalling mollecules

leukotrienes

266
Q

eicosanoid signalling molecules:

A

prostaglandins

prostacyclins

thromboxanes

267
Q

fatty acid oxidation occurs in the

A

mitochondria following transport by the carnitine shuttle

268
Q

beta-oxidation uses cycle of

A

oxidation, hydration, thiolysis cleavage

269
Q

fatty acid chain is shortened by

A

two carbon atoms in fatty acid oxidation

270
Q

in fatty acid oxidation, what is generated

A

FADH2

NADH

acetyl CoA

271
Q

ketogenesis is the process by which

A

ketone bodies form due to excess acetyl-CoA in liver (during prolonged starvation)

272
Q

ketolysis regenerated

A

acetyl-CoA for energy use in peripheral tissues

273
Q

brain can derive up to

A

2/3 of its energy from ketone bodies during starvation

274
Q

where does protein digestion usually occur

A

small intestine

275
Q

catabolism of cellular proteins occurs ONLY under

A

conditions of starvation

276
Q

amino acids released from proteins usually…

A

lose their amino group through deamination

277
Q

in protein catabolism, remaining carbon skeleton can be used for

A

energy

278
Q

glucogenic AAs can be converted into

A

glucose through gluconeogenesis

279
Q

all amino acids except (which ones) can be converted into glucose via gluconeogenesis

A

leucine and lysine

280
Q

ketogenic can be converted into

A

acetyl-CoA and ketone bodies

281
Q

which AAs are the only ones that are solely ketogenic?

A

leucine and lysine

282
Q

cholesterol may be obtained through

A

dietary sources or through de novo synthesis in liver

283
Q

HMG-CoA reductase synthesizes

A

mevalonate

rate limiting step of cholesterol synthesis

284
Q

LCAT catalyzes formation of

A

cholesteryl esters for transport with HDL

285
Q

CETP catalyzes transition of LDL by

A

transferring cholesteryl esters from HDL

286
Q

open system is where matter and E can be

A

exchanged with the environment

287
Q

closed system is where

A

ONLY energy can be exchanged w/ the environment

288
Q

no work is performed during a closed system because

A

pressure and volume remain constant

289
Q

entropy is the measure of

A

energy dispersion in a system

290
Q

chain in free energy

A

delta G that occurs at 1 M concentration, 1 atm, 25 C

291
Q

ATP is a

A

mid level energy molecules

292
Q

ATP contains high energy phosphate bonds that are

A

stabilized via hydrolysis by resonance, ionization, loss of charge repulsion

293
Q

ATP provides energy through

A

hydrolysis and coupling to energetically unfavorable reactions

294
Q

ATP can donate a

A

phosphate group to other molecules

295
Q

in glycolysis, ATP donates a

A

phosphate group to glucose = G6P

296
Q

bio oxidation and reduction reactions can be broken down into

A

component half-reactions

297
Q

half-reactions provide useful info about

A

stoichiometry and thermodynamics

298
Q

high energy electron carriers may be

A

soluble or membrane-bound

299
Q

high energy electron carriers include

A

NADH2

NADPH

FADH2

ubiquinone

cytochromes

glutathione

300
Q

flavoproteins is a subclass of electrons carriers…

A

dervied from riboflavin (vit B2)

e.g. FAD and FMN

301
Q

insulin is secreted by

A

pancreatic b-cells

302
Q

insulin is regulated by

A

glucose

303
Q

insulin decreases

A

blood glucose by increasing cellular uptake

304
Q

insulin increases rate of

A

anabolic metabolism

305
Q

what secretes glucagon

A

pancreate a-cells

306
Q

glucagon is stimulated by

A

low glucose and high AA levels

307
Q

glucose increases

A

blood glucose by promoting gluconeogensis and glycogenolysis in liver

308
Q

glucocorticoids increase blood glucose in response to…

A

stress by mobilizing fat stores and inhibiting glucose uptake

309
Q

glucocorticoids increase impact of…

A

glucagon and catecholamines

e.g. cortisol

310
Q

catecholamines promote glycogenolysis and….

A

increases basal metabolic rate through sympathetic NS activity

“adrenaline rush”

e.g. epinephrine and noriepinephine

311
Q

thyroid hormones increase

A

basal metabolic rate

due to increased oxygen consumption and heat production when thyroid hormones are secreted

312
Q

T3 is more potent than

A

T4 b/c i.t. has a shorter half-life

t3 is available in lower concentrations in the blood

313
Q

T4 is converted to

A

t3 at tissues

314
Q

thyroid hormones are what-based

A

tyrosine

315
Q

equilibrium is a (what) state for most biochemical rxns

A

undesirable state for biochemicals rxns b/c organisms need free energy to survive

316
Q

postprandial state is when body is

A

well-fed + absorptive

insulin increases

anabolism prevails

317
Q

postabsorptive state is when body is

A

fasting

lowered insulin

increased glucagon and catecholamine

transition to catabolism

318
Q

starvation leads to increased

A

glucagon and catecholamine

319
Q

most tissues rely on

A

fatty acids

320
Q

calorimetry measures

A

metabolic rates

321
Q

respiratory quotient estimates

A

composition of fuel actively consumed by body

322
Q

RQ =

A

Co2 produced / O2 consumed

323
Q

ghrelin increases

A

appetite

regulatory hormone

324
Q

orexin increases

A

appetite

regulatory hormone

325
Q

leptin decreases

A

appetite by suppressing orexin production

326
Q

BMI =

A

mass / height^2

327
Q

liver is the most

A

metabolically diverse tissue

328
Q

hepatocytes are responsible for the maintenance of blood glucose levels…

A

by glycogenolysis and gluconeogenesis to pancreatic hormone stimulation

329
Q

liver process what materials

A

lipids, cholesterol, bile, urea, toxins

330
Q

adipose tissue stores lipids under the influences of…

A

insulin and releases them under the influence of epinephrine

331
Q

skeletal muscle metabolism will differ depending on

A

current activity level and fiber type

332
Q

resting muscle conserve carbohydrates in…

A

glycogen stores and uses free fatty acids from bloodstream

333
Q

active muscle may use anaerobic metabolism and…

A

glucose phosphorylation

direct phosphorylation from creatine phosphate

or

fatty acid oxidation

depending on fiber type + exercise duration

334
Q

cardiac muscle uses fatty acid oxidation in…

A

both the well-fed and fasting states

335
Q

brain and nervous tissue consume only glucose in

A

all metabolic states except for prolonged fasts (where 2/3 of brain’s fuel will come from ketone bodies)

336
Q

name the branched alkyl side chains

A

leucine

isoleucine

valine

337
Q

protein domains are

A

distinct regions in a polypeptide chain that fold independently

338
Q

each protein domain carries out

A

a separate function (may assist another domain in performing its function)

339
Q

one of the most common functions of a protein domain is to

A

bind a ligand (small molecule)

340
Q

what does Kd measure

A

Kd = dissociation constant / affinity of a protein

341
Q

small Kd =

A

high binding affinity (low tendency of complex to dissociate)

342
Q

what does DNA determine?

A

sequence of AA in proteins

blueprint for living organisms passed from one gen to the next

343
Q

main difference b/w prok or euk cells?

A

NUCLEUS

344
Q

which of the following is found in prokaryotes:

mitochondria

nucleus

chloroplasts

ribosomes

more than 1 of these

A

ribosomes

345
Q

where are ribosomes found?

A

rough ER

346
Q

smooth ER does what?

A

makes lipids

347
Q

rough ER does what?

A

makes ribosomes from mRNA

348
Q

what can capture light energy and turn it to sugar?

A

chloroplast

349
Q

what does the golgi apparatus involved in

A

sorting and modifying

350
Q

spontaneous reaction is exer or endergonic?

A

exergonic

351
Q

speed of spontaneous process?

A

FAST

352
Q

heat of reaction at constant pressure is marked by

A

its change in enthalpy

353
Q

hydrolysis of ATP involves

A

release of energy

354
Q

monomers of proteins are

A

amino acids

355
Q

what kind of compounds are more likely to dissolve in nonpolar solvents?

A

covalent compounds

356
Q

ionic compounds and polar covalent compounds tend to dissolve in water because of

A

on-dipole and dipole-dipole interactions

357
Q

hydrogen bonds can only form within a single molecule. T or F?

A

false

358
Q

max number of H bonds a single water molecule can form?

A

4

359
Q

what makes for a good H bond acceptor?

A

high electronegativity

nonbonding pair of electrons

360
Q

h bonds explain which of the following properties of water?

A

water is a good solvent for ionic/polar molecules

water has a high melting pt and boiling pts for its small size

ice expands when frozen

361
Q

bases are

A

proton acceptors

362
Q

what has a greater Ka: weak or strong acid?

A

strong acid

363
Q

small pkA means

A

strong acid

364
Q

dissociation cosntant (Ka) for an acid with a pKa value of 6.0 is

A

1 x 10^-6

365
Q

how to calculate pH from H+ ion concentration

A

pH = -log[H+|

366
Q

how to calculate H+ concentration

A

[H+] = 10^ -pH

367
Q

buffering capacity refers to the

A

extent to which a buffer solution can counteract the effect of added base or acid

368
Q

main intracellular buffer system

A

H2PO4- / HPO4

369
Q

stereoisomers are

A

nonsuperimposable mirror-image molecules

370
Q

which AA takes on a negative charge when the R group loses a proton?

A

glutamic acid

371
Q

true or false: Thr and Ser have hydroxyls as side chains

A

true

372
Q

Asn has a polar or nonpolar side chain?

A

polar

373
Q

pKa values of the amino groups of common AAs are around

A

pH 9

374
Q

alpha-helices only use

A

intrachain H bonds

375
Q

beta-sheets can use

A

intrachain or interchain H bonds

376
Q

in the alpha-helix, there are

A

h bonds parallel to the helix axis

377
Q

which forces are important in tertiary structure

A

disulfide bonds

h bonds

hydrophobic interactions

378
Q

bonds involved in disulfide bonding

A

covalent bonds w/ R groups

379
Q

what can cause protein denaturation?

A

heat

extreme pH

detergents

380
Q

what maintains quarternary structure of a protein?

A

h bonds

ionic interactions

hydrophobic interactions

381
Q

what does catalyst do to deltaG?

A

catalyst lowers deltaG

382
Q

what does increased temperature do to enzyme-catalyzed reactions?

A

rate of enzyme rxns increases until heat denatures enzymes

383
Q

true or false: all catalysts work by lowering the activation energy for a rxn

A

TRUE

384
Q

active sit of an enzyme

A

substrate binds via noncovalent forces

substrate binding site

reactive group catalyze rxn here

385
Q

sigmoidal curve suggests that

A

the characteristics of a multi-subunit enzyme

386
Q

what type of enzyme display sigmoidal kinetics

A

ALLOSTERIC

387
Q

allosteric enzymes have what curve shape

A

sigmoidal

e.g. hemoglobin

388
Q

mechanism of an enzyme-catalyzed reaction makes which assumption about the conversion of production into substrate

A

product is not converted to substrate to any appreciable extent

389
Q

lineweaver burk plot is useful for

A

seeing whether points deviate from a straight line than from a curve

390
Q

lineweaver burk plot is not affected by

A

presence of inhibitors

391
Q

lineweaver-burk plot can be used whether or not

A

the enzyme displays michaelis-menten kinetics

392
Q

what does the michaelis constant determine

A

Km

393
Q

michaelis constant describes the

A

affinity between enzyme and substrate

394
Q

dimension (units) for the michaelis constant is

A

concentration such as molarity

395
Q

Km is the substrate concentration necessary to

A

reach 1/2 vmax

396
Q

lower Km =

A

HIGHER affinity

397
Q

which inhibitor binds to the enzyme at a site other than the active site?

A

noncompetitive inhibitor

398
Q

what inhibitor has an unchanged Vmax?

A

competitive inhibitor

399
Q

what happens to the vmax with noncompetitive inhibitor?

A

vmax is altered

400
Q

behavior of allosteric enzymes depends on

A

changes in quaternary structure upon binding of substrate or effectors

401
Q

according to the concerted model of allosteric behavior, an allosteric activator favors the

A

relaxed form of the enzyme

402
Q

main distinguishing feature of the concerted model for the behavior of allosteric enzyme is the

A

conformation of all subunits changes simultaneously

403
Q

phosphorylation and allosteric control of enzymes can be combined to

A

afford a high degree of control over enzymatic reactions

404
Q

in zymogen activation, an inactive protein is converted to

A

an active one by bond cleavage

405
Q

how are cofactors bound to their enzymes

A

either covalently or non-covalently

406
Q

examples of coenzymes

A

NAD+

FAD

biotin

407
Q

what often functions as coenzymes in redox reactions?

A

NAD+ and FAD (nicotinamide adenine dinucleotides)

408
Q

what does amphipathic mean?

A

there are hydrophilic and hydrophobic regions

409
Q

fatty acids in both (x and y) vary

A

triacylglycerols and phospoacylglycerols

410
Q

cholesterol has some degree of what nature

A

amphipathic

411
Q

true or false: lipids differ from most biomolecules b/c they are defined on basis of solubility rather than chemical structure

A

TRUE

412
Q

what does cholesterol do for membrane fluidity?

A

prevents extremes (too fluid or too firm)

413
Q

association of integral membrane proteins w/ lipids in the membrane bilayer always involves

A

hydrophobic interactions

414
Q

plants oils have more unsaturated or saturated fats?

A

UNSATURATED (less cholesterol)

415
Q

distribution of lipids in membrane is

A

uneven w/ bulkier molecules on exterior

416
Q

where can membrane proteins be located?

A

entirely within membrane

on surface of membrane

417
Q

properties of membrane proteins

A

transport of substances into and out of cell

catalysis (enzymatic activity)

acting as a receptor

418
Q

is energy storage part of the functions for membrane proteins?

A

no

419
Q

lipid vitamins found in membranes

A

vitamins A and E

420
Q

vitamin needed for blood coagulation

A

vitamin K

421
Q

if a single strand of DNA contains 2100 A residues and 1800 T residues, what will be on the complementary strand?

A

2100 T (threonine) residues and 1800 A residues (alanine)

422
Q

supercoiled helix can be untwisted by

A

helicase

423
Q

production RNA from a DNA template is

A

transcription

424
Q

mRNA base sequence directs AA sequence of a protein is called

A

translation

425
Q

DNA replication in a prokaryote begins at a

A

unique site and proceeds in one direction all the way around a typically circular chromosome

426
Q

when the synthesis of new DNA is directed by an original template DNA molecule…

A

two DNA molecules are formed

each w/ one new strand and the other from original DNA

427
Q

functions of DNA polymerase III

A

polymerization

clamping on to the DNA template

proofreading

428
Q

what activity of DNA polymerase I is most important in removing the primer?

A

3’ to 5’ exonuclease activity

429
Q

strands in double helix are

A

anti-parallel

have their 3’ to 5’ directions opposed

430
Q

DNA synthesis direction

A

5’ to 3’ end on one strand and 3’ to 5’ end on the other strand

431
Q

which enzyme is responsible for bulk of DNA synthesis during replication

A

DNA polymerase I

432
Q

okazaki fragments are

A

short DNA pieces that explain how DNA is synthesized on lagging strand

433
Q

why is a primer strand needed in DNA replication

A

DNA polymerases require a preexisting strand w/ a nucleotide having a 3’-OH

434
Q

why is telomerase needed

A

one major difficulty in replicating linear DNA molecules is replacing DNA segment that is occupied by the RNA primer on telomeres at DNA ends

435
Q

hydrolysis of a nucleoside triphosphate drives the

A

reaction

436
Q

direction of RNA synthesis

A

5’ to 3’ end

437
Q

RNA base pairing includes

A

A to U

G to C

438
Q

promote site is

A

site on DNA at which RNA polymerase bind to start transcription

439
Q

which RNA has a cloverleaf structure

A

tRNA

440
Q

ends of eukaryotic mRNA protected from degradation

A

3’ end only (polyA tail)

441
Q

5’ end of mRNA is the

A

5’ cap

442
Q

which ends of prokaryotic mRNA are protected from degradation

A

neither end

443
Q

TRUE OR FALSE: single codon can coded for more than one AA

A

false

444
Q

best linkage describes covalent bond b/w an AA and its tRNA

A

carboxyl group fo AA linked to 3’ –OH of tRNA

445
Q

codons known for each AA?

A

depends on AA

446
Q

TRUE OR FALSE: in bacterial, each mRNA will bind to only one ribosome at a time?

A

TRUE

447
Q

necessary step after peptide bond formation takes place to continue protein synthesis

A

dissociation of ribosomal subunits

448
Q

in protein synthesis formation of new peptide bonds is catalyzed by

A

peptidyl transferase

449
Q

translation of mRNA in bacteria begins

A

during transcription of mRNA

450
Q

first tRNA (bearing fmet) binds to

A

“P” site on the ribosome

451
Q

production of larger to smaller molecules is called

A

catabolism

452
Q

what kind of process is catabolism

A

oxidative

453
Q

what kind of process is anabolism

A

reduction

454
Q

smaller to larger molecules is

A

anabolism

455
Q

oxidation refers to the

A

loss of electrons

456
Q

reduction refers to the

A

gain of electrons

457
Q

TRUE OR FALSE: molecular oxygen is always the substrate in oxidation rxns

A

true

458
Q

TRUE OR FALSE: oxidation of food molecules supplies energy used to separate ATP

A

TRUE

459
Q

to drive the synthesis of ATP, hydrolysis of an organic phosphate substrate must

A

have a HIGHER free energy than ADP + Pi –> ATP

460
Q

TRUE OR FALSE: in order to initiate a metabolic pathway it is sometimes necessary to activate the starting materials

A

TRUE

461
Q

mechanisms used to activate substrates for further metabolism

A

making an isomer that is more reactive

addition of a phosphate group

combination with a vitamin (i.e. coenzyme A)

462
Q

metabolism takes place in stages to:

A
  • allow for efficient production and use of E and regulation of process
  • b/c large free energy changes cannot occur in living organisms
463
Q

in the absence of oxygen, pyruvate can be converted to

A

lactate IN HUMANS

464
Q

in glycolysis, how many actual steps involve electron transfer

A

1 step

465
Q

enzyme glucokinase does what?

A

phosphorylates a number of different sugars:

glucose, fructose, mannose

466
Q

which molecule allosterically control the enzyme phosphofructokinase?

A

ATP

467
Q

isomerization of dihydroxyacetone phosphate (DHAP) to G3P is favored because

A

G3P is being continuously drained off subsequent rxn in glycolytic pathway

468
Q

ATP is synthesize by what in glycolysis

A

both substrate-level and oxidative phosphorylation

469
Q

can the citric acid cycle be used as both an anabolic and catabolic pathway?

A

NO

470
Q

which enzyme uses coenzyme FAD as an e- acceptor?

A

succinate dehydrogenase

471
Q

conversion of malate to oxaloacetate has a high/pos gibbs free E yet it can take place b/c

A

the oxaloacetate product is used up in the subsequent rxn

472
Q

when mitochondria are actively carrying out aerobic respiration…

A

the pH of the matrix is greater than the pH of the intermembrane space

473
Q

TRUE OR FALSE: synthesis of ATP in mitochondria is driven by a proton/pH gradient

A

true

474
Q

ultimate electron acceptor in ETC is

A

oxygen

475
Q

what is an advantage of the multiple steps in electron transport?

A

more E can be captured to synthesize ATP by using small steps

476
Q

ATP is more efficiently generated through

A

substrate level phosrylation than oxphos

477
Q

main purpose of TCA

A

generate reduced coenzymes NADH and FADH2 to be used in ETC = ATP

478
Q

net yield of ATP per glucose molecule during aerobic respiration

A

max 28

479
Q

reduction of pyruvate to lactate

A

allows for recycling of NAD+

lactate fermentation

480
Q

alcohol dehydrogenase resembles lactate dehydrogenase in that it

A

uses NADH as a coenzyme

481
Q

does fermentation make any ATP?

A

no - it uses NAD+ when oxygen is not present

482
Q

an uncompetitive inhibitor binds only with the

A

enzyme-substrate complex

483
Q

allosteric effector binds at (where) and does what

A

allosteric site

induces a chance in enzyme shape so substrate can no longer bind to the active site

484
Q

what happens with positive effectors

A

activity goes up

485
Q

negative effectors

A

activity goes down

486
Q

secondary structure of nucleic acids is made up of

A

interactions between bases within same molecule

487
Q

secondary structure is responsible for the

A

shape that the nucleic acid assumes

488
Q

RNA secondary structure has 4 basic elemetns

A

loops

helices

bulges

junctions

489
Q

what fixes helix-deforming lesions of DNA such as thymine dimers

A

nucleotide excision repair

cut and patch process

490
Q

oncogenes develop from

A

mutations of proto-oncogenes and promote cell cycling

may lead to cancer

491
Q

DNA ligase function

A

joins DNA strands by catalyzing formation of phosphodiester bonds

492
Q

pyrimidines

A

C, T, U

493
Q

purines

A

A and G

494
Q

during replication, telomeres are shortened and this can

A

be partially reversed by telomerase

495
Q

recombinant DNA is composed of

A

nucleotides from two different sources

created only in labs

496
Q

base excision repair fixes

A

nondeforming lesions of DNA helix by removing base and leaving an AP site

497
Q

AP endonuclease then removes the

A

damaged sequence which can be filled in w/ the correct bases

498
Q

bonds between nucleotide bases

A

h bonds

499
Q

DNA backbone is held together by

A

phosphodiester bonds

form b/w sugar and phosphate groups

500
Q

saturated fatty acid has how many double bonds in its tail and is more/less fluid

A

NO double bonds

less fluid

501
Q

prostaglandins are

A

lipid compounds that are signalling molecules and regulae cAMP levels

502
Q

prostaglandins affect the following functions

A

smooth muscle contraction

body temp

sleep-wake cycle

fever

pain

503
Q

3 parts of a nucleotide

A

phosphate group, nitrogenous base, pentose sugar

504
Q

irreversible inhibitor is any inhibitor that

A

covalently binds to the active site of some enzyme (eliminates any activity)

505
Q

vmax and Km in noncompetitive inhibition

A

vmax goes down

Km has no change

506
Q

vmax and Km in uncompetitive inhibition

A

vmax and Km go down

507
Q

vmax and Km in competitive inhibition

A

vmax - no change

Km goes up

508
Q

feedback inhibition of an enzyme is when

A

an enzyme is inhibited by high levels of a production from later in the same pathway

509
Q

translation occurs in the

A

cytoplasm at the ribosomes

510
Q

translation steps

A

initiation

elongation

termination

511
Q

in prokaryotic translation, the 30S ribosome subunit attaches to the

A

Shine-Delgarno sequence and scans for a start codon

512
Q

in translation elongation, the new tRNA enters ribosome at

A

A site

513
Q

in elogation, the polypeptide chain is transferred from the

A

P site to A site to meet the new tRNA

514
Q

in elogation, before leaving the ribosome, the tRNA stops in the

A

E site

515
Q

order of sites for tRNA is

A

A P E

516
Q

in translation, termination will occur when the

A

codon in the A site is a stop codon

517
Q

release factor places a water molecule on the

A

polypeptide chain and thus releases the protein

518
Q

post-translational modification can happen at

A

any time of protein’s lifespan

commonly phosphorylation

519
Q

what are operons

A

found in prok DNA

contain groups of genes regulated together

520
Q

operons contain

A

activators

inducers

repressors

521
Q

advantage of operons

A

group of genes whose products are all needed for a common function can be transcribed together

522
Q

operon promoter is the

A

binding site for RNA polymerase (enzyme that performs transcription)

523
Q

operon operation is a

A

short region of DNA that lies partially within the promoter

interacts w/ a repressor that controls transcription of the operon

524
Q

operation repressor does what

A

turns operon off

525
Q

repressor binds to the

A

operator

blocks movement of RNA polymerase down DNA

526
Q

when lactose is absent, the lac repressor

A

binds tightly to the operator

gets in RNA polymerase’s way

prevents transcription

527
Q

with lactose, the lac repressor

A

is bound to allolactose and operator is released

RNA polymerase can now transcribe operon

528
Q

operon activator does what

A

turns operon on

529
Q

lac operon uses

A

catabolite activation protein (CAP)

530
Q

when glucose levels are low, what is produced

A

cAMP

cAMP attaches to CAP –> binding DNA

RNA polymerase binds to promoter –> high levels of transcription

531
Q

when glucose levels are high,

A

no cAMP is made

CAP cannot bind DNA w/o cAMP –> low levels of transcription

532
Q

operon inducer

A

small molecule that triggers gene or operon expression

533
Q

lac operon is considered an

A

inducible operon b/c its default state is to be turned off/repressed

but can be turned on w/ allolactose

534
Q

inducible operon under normal conditions is

A

bonded to a repressor

535
Q

inducible operons are turned on when an inducer

A

pulls the repressor from the operator site

e.g. lac operon is an inducible operon

536
Q

repressible operon under normal conditions will

A

proceed w/ transcription

537
Q

repressible operons can be turned off by a

A

corepressor coupling w/ the repressor and

the binding of this complex to the operator site

e.g. Trp operon

538
Q

in the absence of tryptophan, the trp repressor

A

dissociated from operator and RNA synthesis proceeds

539
Q

when trp is present, the trp repressor binds the operator and

A

RNA synthesis is blocked

540
Q

transcription factors are proteins that

A

help turn specific genes “on” or “off” by binding to nearby DNA

541
Q

enhancers are sequences of DNA that function

A

to enhance transcription

more than 25 base pairs away from transcription start site

542
Q

histone acetylation increases accessibility of chromatin and allows

A

DNA binding proteins to interact

activates transcription

543
Q

DNA methylation decreases the

A

accessibility of chromatin and stops DNA binding proteins from interacting

inhibits transcription

544
Q

lac operon contains genes that code for proteins in

A

charge of transporting lactose into the cytosol and digesting into glucose

glucose used to make energy

INDUCIBLE operon

545
Q

genes in the lac operon will be expressed if

A

lactose is available

glucose is low

546
Q

when lactose is available, the inducer

A

binds to the repressor and the repressor detaches from the DNA

547
Q
A

biochem (11 decks)

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