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MCAT Prep > U6: F1 Biomolecules > Flashcards

U6: F1 Biomolecules Flashcards

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1
Q

globular protein

A

finely tuned 3D structures that determine function in biomolecules

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2
Q

primary structure driving force

A

attractions between left and right sides of neighboring amino acids

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3
Q

secondary structure driving force

A

attractive and repulsive forces generated by interactions between main chain atoms of neighboring amino acids

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4
Q

tertiary structure driving force

A

interactions between side chain atoms of amino acids and water molecules of the environment

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5
Q

basic amino acid structure

A
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6
Q

how are peptide bonds formed

A

nucleophilic addition elimination reaction between carboxyl group of one amino acid and amino group of another amino acid

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7
Q

peptide bond reaction nucleophile and electrophile

A

nucleophile: amino group
electrophile: carboxyl carbon

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8
Q

what type of bond is a peptide bond

A

amide bond formed between two amino acids
rigid and planar stabilized by resonance delocalization

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9
Q

peptide bond side product

A

water molecule

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10
Q

basic pattern for polypeptide chain

A

nitrogen atom, alpha carbon, carboxyl carbon repeat

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11
Q

terminals present on amino acid

A

N terminal (nitrogen atom side)
C terminal (Carboxyl atom side)

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12
Q

individual amino acids in a polypeptide chain are called

A

residue

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13
Q

how are peptide bonds broken

A

acid hydrolysis (using strong acid)
proteolytic enzymes

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14
Q

acid hydrolysis

A

non specific, cleaves peptide bonds using strong acid

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15
Q

proteolysis

A

specific cleavage of peptide bond using protease
ex: trypsin only cleaves on C term of basic amino acids like Arg & Lys

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16
Q

four amino acids with special side chains

A

Histidine, Proline, Glycine, Cysteine

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17
Q

pH < pKa
amino acid exists as

A

protonated form

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18
Q

pH > pKa
amino acid exists as

A

deprotonated form

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19
Q

pH ~ pKa

A

both protonated and deprotonated form (very helpful)

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20
Q

histidine side chain pKa

A

~ 6.5 ~ physiological pH 7

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21
Q

histidine is most helpful when located at

A

the active site of the protein
(can stabilize or destabilize)

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22
Q

what is unique about proline’s side chain

A

2˚ alpha amino group

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23
Q

glycine side chain

A

simplest side chain - H atom
NO CHIRAL ALPHA CARBON! (very flexible)

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24
Q

what amino acid has an achiral alpha carbon

A

Gly

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25
Q

glycine and proline are known as

A

alpha helix breakers (introduces kinks to 2˚ structures)

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26
Q

what happens when 2 cysteines come into close proximity

A

disulfide bridge forms between thiol groups of Cys

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27
Q

how are disulfide bridges formed between cysteines

A

reducing –> oxidizing environment
(thiol loses H, thiols interact)

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28
Q

extracellular space is

A

oxidizing

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29
Q

intracellular space is

A

reducing

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30
Q

disulfide bridge formation is favored in

A

oxidizing environment (extracellular)

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31
Q

antioxidants make the intracellular environment

A

reducing (enforces it)

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32
Q

cystine

A

cysteine in oxidized form

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33
Q

hemoglobin

A

responsible for transporting oxygen in RBCs to tissues

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34
Q

chiral meaning

A

under plane polarized light it will rotate towards that light

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35
Q

L amino acid vs D amino acid fischer projections

A

L = Amine group left
d = dextro = right amino group

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36
Q

what form of amino acids are found in the human body

A

L amino acids

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37
Q

isoelectric point

A

point on the pH scale at which the molecule exists as neutral

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38
Q

amino group on amino acids are

A

H+ acceptors, basic

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39
Q

carboxylic acid group on amino acids are

A

H+ donors, acidic

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39
Q

zwitterion

A

having both a positively charged group and a negatively charged group

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40
Q

in acidic solutions (H+), amino acids exist as

A

protonated

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41
Q

in basic solutions (OH-), amino acids exist as

A

deprotonated

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42
Q

how do you find the pH at which a zwitterion exists

A

take the average of the pKa’s of the functional groups

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43
Q

pKa of amino group (average)

A

9

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44
Q

pKa of carboxylic group (average)

A

2

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45
Q

for GENERIC amino acid, what is the isoelectric point

A

9+2/2 = 11/2 = 5.5

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46
Q

nonpolar amino acids side chain categorization

A

alkyl or aromatic

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47
Q

polar amino acids side chain categorization

A

neutral, acidic, basic

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48
Q

nonpolar is ____
polar is _____

A

hydrophobic
hydrophilic

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49
Q

alkyl side chain amino acids (nonpolar)

A

glycine, alanine, valine, methionine, leucine, isoleucine, proline

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50
Q

aromatic side chain amino acids (nonpolar)

A

phenylalanine, tryptophan

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51
Q

neutral side chain amino acids (polar)

A

serine, threonine, asparagine, glutamine, cysteine, tyrosine

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52
Q

acidic side chain amino acids (polar)

A

aspartic acid, glutamic acid
(COOH in side chain)

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53
Q

deprotonated name for apartic acid and glutamic acid

A

aspartate and glutamate

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54
Q

basic side chain amino acids (polar)

A

histidine, lysine, arginine
(lots of N in side chains)

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55
Q

protein folding levels and causes

A

1˚ = peptide bonds
2˚ = backbone interactions (H-bonding stabilized) - alpha helix and beta sheet
3˚ = distant group interactions (H-bonding, VDW, hydrophobic, disulfide bridge stabilized)

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56
Q

parallel vs antiparallel beta sheets

A

parallel: N terminals together and C terminals together opposite ends
anti-parallel: C terminal and N terminal on both ends

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57
Q

hydrophobic packing of 3˚ proteins

A

water on the exterior of the protein = polar groups hang on the outside to interact with water, hydrophobic center

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58
Q

4˚ structure

A

bonding between multiple polypeptides
described by interactions between polypeptides (subunits determine nomenclature - dimer, trimer, tetramer)

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59
Q

what is necessary to achieve conformation

A

correct 1˚, 2˚, 3˚, 4˚ structures

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60
Q

solvation shell

A

layer of water outside a protein molecule (electronegative oxygen of water stabilized positive charges of polar groups in protein)

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61
Q

how can proteins be denatured

A

temperature, pH, chemicals, enzymes

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62
Q

temperature denaturation

A

breaks 2˚, 3˚, 4˚ structure of proteins

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63
Q

pH denaturation

A

breaks ionic bonds = 3˚ and 4˚

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64
Q

chemical denaturation

A

disrupt h bonding, destroy 2˚, 3˚, 4˚

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65
Q

enzyme denaturation

A

alters 1˚structure

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66
Q

acid/base catalysis

A

enzyme acts as an acid (proton donor) or base (proton acceptor)

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67
Q

covalent catalysis

A

enzymes form covalent bond with target molecule

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68
Q

electrostatic catalysis

A

charge stabilization
(metal cation stabilizing negative phosphate charges in DNA)

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69
Q

proximity and orientation effects

A

enzyme brings molecules closer together so they collide and react
(increases frequency of successful collisions)

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70
Q

for a molecule to achieve a higher energy transition state (unstable), there must be

A

an input of energy

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71
Q

transition state of reaction

A

highest energy point on conversion from A to B (most instability)

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72
Q

free energy of activation of reaction

A

energy from starting point to transition state

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73
Q

standard free energy of whole reaction

A

net change in energy level between reactants and products

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74
Q

what does it mean for a reaction to be spontaneous

A

more energy in the reactants than the products (high to low)

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75
Q

what determines how quickly a reaction will go

A

free energy of activation

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76
Q

enzymes lower a reaction’s

A

free energy of activation

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77
Q

T/F: enzymes are not used up in a reaction

A

TRUE

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78
Q

enzymes are specific to

A

certain substrates and reactions

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79
Q

induced fit

A

after the enzyme and substrate change shape to bind tightly (full force catalysis)

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80
Q

general enzyme formula

A

E + S –> ES –> [E-X] transition –> EP1P2 –> E + p1 + p2
X = diff form of S

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81
Q

binding between enzyme and substrate is strongest at

A

the transition state

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82
Q

allosteric binding

A

regulating molecule (like an inhibitor) binds away from active site to change the active site shape

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83
Q

categories of enzymes

A

transferase (A + BX –> AX + B)
ligase (A + B –> AB)
oxidoreductase (transfer electrons from A to B or B to A, changes oxidation state)
isomerase (A to B)
hydrolase (A + H2O –> B + C)
lyase (A –> B + C)

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84
Q

co-enzyme

A

co-enzymes are organic carrier molecules (hold onto certain things for an enzyme)
ex: NADH carries electrons

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85
Q

co-factor

A

directly participate in catalysis
ex: DNA polymerase recruits Mg2+ to stabilize DNA

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86
Q

vitamins and minerals

A

can serve as cofactors or coenzymes
must be obtained from diet

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87
Q

vitamins

A

organic cofactors and coenzymes
b3 - niacin –> NAD
B5 –> CoA

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88
Q

minerals

A

inorganic cofactors
Mg2+ –> DNA polymerase
Ca2+ –> bone structure

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89
Q

what enzyme breaks protein into peptides in the human body

A

pepsin

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90
Q
A
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91
Q

effects of pH change on enzyme function

A

protonating/deprotonating groups affects whether they can be cofactors or coenzymes

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91
Q

effects of temperature change on enzyme function

A

temperature can disrupt protein geometry hence function

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92
Q

A –> B
rate of reaction formula

A

rate = k [A]

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93
Q

rate of reaction

A

how fast a reaction occurs
V

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94
Q

Rate (V) = ?
generic formula

A

V = d[P]/dt OR ∆[P]/∆t

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95
Q

how could you increase the rate of a reaction?

A

increase substrate concentration
increase enzyme concentration

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96
Q

in enzyme kinetics, what is the assumption?

A

total [E] is constant

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97
Q

vmax

A

maximum rate of a reaction

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98
Q

at high [S], the enzymes are

A

saturated
(full with substrate)

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99
Q

2 steps of enzyme catalysis

A
  1. binding of enzyme to substrate
  2. formation of product
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100
Q

steady-state assumption

A

[ES] is constant so
formation of ES = loss of ES
rate1 + rate-2 = rate-1 + rate2
rate1 = rate-1 + rate2 (rate -2 is negligible bc product rarely reverts to reactant)

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101
Q

Km =

A

k-1 + k2 / k1

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102
Q

Michaelis Menten Equation

A

Vo = Vmax[S] / Km + [S]

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103
Q

If Km = [S] then

A

Vo = Vmax/2

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104
Q

kcat =

A

vmax/ [E]t
how many substrates an enzyme can turn into product at its maximum speed (rxns/sec)

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105
Q

catalytic efficiency

A

Kcat / Km
higher Kcat, lower Km makes for the most efficient

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106
Q

substrate binding changes

A

substrate affinity
(cooperativity)

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107
Q

positively cooperative binding

A

substrate binding increases enzymes affinity for subsequent substrate

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108
Q

negatively cooperative binding

A

substrate binding decrease enzymes affinity for subsequent substrate

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109
Q

non-cooperative binding

A

substrate binding does not affect affinity for subsequent substrate

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110
Q

positive cooperativity on a graph

A

sigmoidal shape

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111
Q

non-cooperative binding on a graph

A

hyperbolic shape

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112
Q

negative cooperativity on a graph

A

flatter curve than non-cooperative

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113
Q

allosteric activator

A

increase enzymatic activity

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114
Q

allosteric inhibitory

A

decrease enzymatic activity

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115
Q

how would a cooperativity graph look if the allosteric regulators altered Km

A

lines are closer together and Vmax is similar

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116
Q

how would a cooperativity graph look if the allosteric regulators altered Vmax

A

more spaced out lines with different Vmaxes

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117
Q

what is the basis of a feedback loop

A

downstream products regulate upstream reactions

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118
Q

ATP is a _____ of phosphofructokinase

A

allosteric inhibitor
(more ATP = less phosphofructokinase activity)

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119
Q

homotropic inhibitor

A

substrate and regulator are the same

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120
Q

what are some examples of non-enzymatic proteins

A

proteins that serve as receptors/ion channels, transport, motor, or antibodies

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121
Q

receptor/ion channel proteins

A

proteins that receive or bind a signal cell (in the membrane)
- ex: insulin receptor that binds insulin

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122
Q

transport proteins

A

at high concentration of a ligand - high affinity
at low concentration of a ligand - low affinity
- ex: Hemoglobin

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123
Q

motor proteins

A

myosin (muscle), kinesin, dynein (intracellular)

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124
Q

antibodies

A

protein components of adaptive immune system (target foreign antigens for destruction) - strong affinity

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125
Q

small post-translational modifications

A

adding or removing small functional groups after translation
- methylation (add CH3), acetylation (add CH3CO), glycosylation (add sugar)
- ex: acetylation of lysine to dampen effects of positive charge on side chain

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126
Q

zymogens

A

inactive form of an enzyme that requires covalent modification
- ex: trypsinogen is covalently modified in the intestine to trypsin (prevents trypsin from breaking down proteins in pancreas)

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127
Q

suicide inhibition

A

covalently bind the enzyme to prevent use
rarely unbind

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128
Q

central dogma of life (and molecular biology)

simplified version

A

DNA –> RNA –> protein

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129
Q

nucleic acids are made of

A

nucleotides

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130
Q

replication

A

DNA copies itself

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131
Q

transcription

A

DNA to RNA

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132
Q

translation

A

RNA to protein

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133
Q

reverse transcription

A

RNA to DNA
reverse transciptase (produce cDNA)

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134
Q

how are retroviruses, like HIV, created?

A

reverse transcription (their rna genome turns into dna and inserted into host)

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135
Q

RNA viruses

A

viruses whose RNA genome can be directly translated into protein or self replicated into more RNA
COVID-19

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136
Q

non-coding RNA (ncRNA)

A

functional RNA that functions as an RNA molecule without being translated into protein
like tRNA or rRNA

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137
Q

DNA methylation and histone modification are examples of

A

epigenetic mechanisms (allow transcription of only certain genes in the genome)

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138
Q

describe the structure of DNA

A

antiparallel strands, sugar = deoxyribose, nitrogenous base, and a phosphate group (backbone)
put together, units are called nucleotides

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139
Q

difference between ribose and deoxyribose

A

ribose is has an extra oxygen whereas deoxyribose has a hydrogen off the carbon, not an OH

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140
Q

nitrogenous bases can be

A

pyrimidines (1 ring) or purines (2 rings)

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141
Q

is the phosphate backbone of DNA protonated or deprotonated

A

deprotonated in neutral solution and in nucleus (acid)

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142
Q

describe the antiparallel nature of DNA

A

one strand runs 5’ to 3’ and the other runs 3’ to 5’
this is due to the orientation of the sugar molecules

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143
Q

purpose of telomeres

A

protect ends of chromosomes from deterioration
(act as a buffer zone because they do not contain any important genes)
prevents chromosomes from sticking to each other

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144
Q

what is the purpose of telomerase

A

rebuild the telomeres because they progressively get shorter as chromosomes are replicated

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145
Q

single copy DNA vs repetitive DNA

A

single copy does not repeat itself
repetitive DNA does repeat itself (varying degrees)

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146
Q

most of the important genes in eukaryotes are what kind of DNA?

A

single copy DNA

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147
Q

repetitive DNA is found near what part of the chromatid/chromosome?

A

centromere

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148
Q

which is more susceptible to mutation - repetitive DNA or single copy DNA

A

repetitive DNA

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149
Q

DNA is replicated in which direction?

A

5’ to 3’ (adding on 3’ end)

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150
Q

topoisomerase

A

breaks DNA backbone to unwind DNA for replication

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151
Q

helicase

A

breaks hydrogen bonds between nitrogenous bases of DNA for replication

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152
Q

DNA primase

A

adds the RNA primer for DNA replication of lagging strand

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153
Q

what enzyme adds nucleotides to DNA?

A

DNA polymerase

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154
Q

okazaki fragments

A

fragmented DNA during DNA replication in the lagging strand

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155
Q

DNA ligase

A

glues okazaki fragments together and replaces RNA with DNA

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156
Q

where does transcription occur in eukaryotic cells?

A

the nucleus

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157
Q

where does RNA polymerase attach?

A

promoters

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158
Q

transcription occurs in which direction?

A

5’ to 3’ (can only add to 3’)

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159
Q

DNA is transcripted to ? then to ?

A

pre-mRNA
mRNA

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160
Q

how are the ends of mRNA protected?

A

poly-A tail and 5’ cap (methylated guanine)

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161
Q

introns vs exons

A

introns = nonsense coding that is spliced
exons = important coding that stays

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162
Q

how many codons are there?

A

61 codons code for amino acids
3 are stop codons

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163
Q

how do antibiotics work in the context of DNA vs RNA (translation)?

A

antibiotics can target the prokaryotic ribosome (bacteria) and essentially mess it up to kill the bacteria while not effecting the eukaryotic ribosome

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164
Q

where does the prokaryotic ribosome bind on prokaryotic mRNA?

A

shine-delgarno sequence

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165
Q

what is the ribosomal binding site in eukaryotes?

A

5’ cap (methylated guanine)

166
Q

first amino acid read in eukaryotes vs prokaryotes

A

eukaryotes = methionine
prokaryotes = formyl methionine

167
Q

exonuclease vs endonuclease

A

exonuclease - fixes errors at the end of the strand
endonuclease - fixes errors in the middle of the strand

168
Q

mutation vs DNA damage

A

mutation - error in DNA sequence
damage - damage to DNA structure

169
Q

types of protein modifications

A

co-translational (during translation)
post-translational (after translation)

170
Q

examples of co-translational modifications

A

acetylation

171
Q

examples of post-translational modifications

A

glycosylation, lipidation, phosphorylation, methylation, proteolysis, ubiquination

172
Q

glycosylation

A

adds carbohydrates to proteins (usually proteins embedded in cell membrane)

173
Q

example of how glycosylation can help identify different types of cells

A

ABO blood groups
A blood type has specific carbohydrate group
B Blood type has specific carbohydrate group
AB blood type has both
O has no carbohydrate groups

174
Q

lipidation

A

adds lipid to protein

175
Q

example of lipidation

A

GPI anchors - lipids that attach or tether proteins to the cell membrane by attaching to hydrophobic interior of cell membrane (lipid is hydrophobic too)

176
Q

phosphorylation

A

adds phosphate groups to protein or enzyme

177
Q

example of phosphorylation

A

sodium potassium pump
phosphorylation causes the channel of the pump to change shape so that 3 sodium can exit then 2 K can come in

178
Q

methylation

A

adds methyl group to proteins or enzyme

179
Q

examples of methylation

A

histones (proteins that DNA wraps itself around in chromosomes)
helps turn certain genes on and off

180
Q

proteolysis (as modification)

A

cuts proteins to activate it
zymogens are inactive forms of enzymes - can be done vis proteolysis

181
Q

ubiquitination

A

adding ubiquitin to protein marks it for breakdown

182
Q

gene regulation at protein level

A

all DNA is transcribed to RNA, then all RNA translated into proteins, but only specific proteins are activated for expression

183
Q

gene regulation at translation level

A

all DNA is transcribed to RNA, then only some RNA is translated into proteins

184
Q

gene regulation at transcription level

A

only DNA that codes for proteins for specific cell gets transcribed into RNA

185
Q

what level is the most effective gene regulation?

A

transcription level

186
Q

Jacob-Monod Lac Operon

A

describes how only specific genes are expressed at the transcriptional level in E. Coli

187
Q

lactose is broken down into

A

glucose and galactose

188
Q

lacZ codes for

A

B-galactosidase
enzyme that breaks lactose into glycose and galactose

189
Q

lacY codes for

A

lactose permease
helps cell bring lactose into the cell

190
Q

lacA codes for

A

enzyme that helps in lactose metabolism

191
Q

how does the repressor of the Jacob-Monod lac operon function?

A

if there is a lot of lactose, allolactose will bind to the repressor to make it fall off so that transcription occurs (RNA polymerase can now go through)
if there is minimal lactose, it will not bind to the repressor and the repressor will continue to repress the gene expression until there is a need for breakdown (more lactose present)

192
Q

order of lac operon units on the non-coding/template strand

A

promoter, operator, start, lacZ, lacY, lacA, stop

193
Q

structural vs regulatory genes

A

structural genes are the lacZ, lacY, lacA
regulatory genes are repressor promotor, repressor protein, promoter, and operator

194
Q

nucleosomes

A

repeating units of chromatin that are made of 146 base pairs of DNA wrapped around a core of 8 histones

195
Q

chromatin histones

A

H2A, H2B, H3, H4

196
Q

histone acetyltransferase

A

reversible modification that acetylates histones on the amino terminal end in chromatin to uncoil DNA and increase transcription

197
Q

histone deacetylase

A

deacetylates and condenses dNA to decrease transcription

198
Q

what are the 2 forms of chromatin?

A

euchromatin (open to transcription)
heterochromatin (not open to transcription)

199
Q

methylation of DNA

A

methyltransferase methylates Cytosine in DNA as a form of gene silencing

200
Q

CpG islands

A

cytosine rich sequences of DNA

201
Q

DNA methylation can affect transcription by

A
  1. physically impede binding of transcriptional proteins ot gene
  2. methylated dna may be bound by methyl-CpG binding domain proteins, which can recruit additional proteins to modify histones and make them transcriptionally silent
202
Q

general transcription factors (GTFs)

A

class of protein transcription factors that bind to specific sites (promoter) on DNA to activate transcription of genetic information from DNA to messenger RNA.

203
Q

activators

A

enhance the interaction between RNA polymerase and a particular promoter (through interactions with RNA polymerase subunits)

204
Q

enhancers

A

bound by activators to loop the DNA in a certain way that brings a specific promoter to the initiation complex to enhances transcription
bound by activator proteins that interact with mediator complex (doesnt interact with promoter)

205
Q

repressors

A

bind to operator to impede RNA polymerase

206
Q

silencers

A

regions of dna bound by repressor proteins in order to silence gene expression
repressor protein binds to silencer, rna polymerase is prevented from binding to promoter region

207
Q

prokaryotic vs eukaryotic transcriptional regulation

A

prokaryotes - needed for cell to be able to quickly adapt (activators, repressors, enhancers determine whether gene is transcribed)
eukaryotes - more sophisticated response (nuclear envelope - prevents simultaneous transcription)

208
Q

spliceosome

A

binds on either side of intron, loops intron, and cleaves it off, and ligates the existing ends of exons (exons exit the nucleus)

209
Q

before exiting the nucleus, mRNA must grab

A

poly-A tail and 5’ cap

210
Q

5’ cap purposes

A

protects from exonuclease degegradation
promotes ribosomal binding for transcription
regulates nuclear export of mRNA

211
Q

poly-A tail

A

protects, regulates, and promotes (like 5’ cap)
helps with transcription termination for RNA polymerase

211
Q

How long is the poly-A tail?

A

250ish nucleotides long

211
Q

micro-RNA (miRNA)

A

function in transcriptional and post-transcriptional regulation by base pairing with mRNA to silence genes through translational repression or target degradation

212
Q

non-coding RNA

A

go directly from transcription to molecule that can skip translation and function as RNA

213
Q

rRNA

A

ribosomal RNA
makes up ribosomes

214
Q

tRNA

A

transfer RNA
links codons in mRNA strand to amino acids

215
Q

Small nucleolar RNA (snoRNA)

A

guide covalent modifications of rRNA, tRNA, and miRNA by methylation or pseudouridylation

216
Q

small nuclear RNA (snRNA)

A

150 nucleotides
process pre-mRNA
maintain telomeres
snRNPs = small nuclear ribonucleic proteins

217
Q

spliceosomes are what type of RNA

A

snRNA + snRNP

218
Q

oncogene

A

tumor-inducing agent

219
Q

how does a proto-oncogene become an oncogene

A

deletion or point mutation - hyperactive protein or overexpressed protein
gene amplification - increases mRNA stability, overexpressed protein
chromosomal arrangement - overexpressed protein or fusion protein (leads to overexpression)

220
Q

two hit hypothesis

A

both alleles must mutate for cancer to manifest

221
Q

what is the cause of sickle cell disease?

A

hemoglobin protein has one glutamine mutated into a valine, resulting in aggregated hemoglobin cells making them less effective in carrying oxygen to tissues

222
Q

mutations arise at

A

the dna level

223
Q

point mutations

A

one base is mutated to another, changing one nucleotide and one amino acid

224
Q

frame-shift mutations

A

extra base shifts the reading frame of the RNA (more significant effects)

225
Q

non-sense mutations

A

genetic mutation leading to RNA sequence reading stop codon (cuts it off early, very bad)

226
Q

missense mutation

A

genetic mutation that changes an amino acid to another

227
Q

silent mutations

A

changing the base does not affect what amino acid is produced

228
Q

conservative mutation

A

mutation leads to different amino acid of the same characteristics (glutamate and aspartate)

229
Q

non-conservative mutation

A

mutation leads to different amino acid in different category

230
Q

mutations originate at _____ level
mutations show their effects at ____ level

A

DNA
protein

231
Q

causes of point mutations

A

base substitution
transition: within purines or pyrimidines
transversion: cross category (purine to pyrimidine)
mispairing (mismatch): A and C pair or G and T pair

232
Q

causes of frame-shift mutations

A

insertion or deletion

233
Q

causes of large scale mutations

A

large scale mutations = chromosome level
translocation - genes on chromosomes are swapped on non-homologous chromosomes
chromosomal inversion = 2 genes on same chromosome switch places

234
Q

mutagen

A

chemical substance or physical event that can cause a mutation
endogenous or exogenous

235
Q

endogenous mutagen

A

sourcing from inside the body

236
Q

exogenous mutagen

A

sourcing from outside the body
intercalators (EtBr inserts into DNA)
base analogues (5-bromouracil can switch between keto and enol)

237
Q

examples of endogenous mutagens

A

reactive oxygen species (ROS)
byproduct of oxidative phosphorylation

238
Q

why are reactive oxygen species dangerous to human cells?

A

they cause double strand breaks and base modifications

239
Q

oxidative stress

A

increase reactive oxygen species in your body

240
Q

examples of good mutations

A

antibiotic resistance is beneficial for bacteria

241
Q

examples of bad mutations

A

CFTR gene mutation that causes thick mucus to lead to cystic fibrosis

242
Q

how many alleles do humans have per gene (on average)?

A

2 because one maternal and one paternal

243
Q

homozygous vs heterozygous

A

homozygous = similar alleles
heterozygous = different alleles

244
Q

genotype

A

alleles in human chromosomes

245
Q

phenotype

A

physical characteristics

246
Q

3 patterns of dominance

A

complete dominance (heterozygote takes dominant allele)
co-dominance (when 2 alleles are dominant together so both traits show up)
incomplete dominance (neither allele is dominant over the other so theres a mix)

247
Q

Hardy-Weinberg principle

A

p + q = 1
p^2 + 2pq + q^2 = 1
p = probability of getting one dominant allele
q = probability of getting one recessive allele
p^2 = both dominant
q^2 = both recessive

248
Q

how is a DNA library made?

A

amino acid sequence –> mRNA strand + reverse transcriptase –> cDNA (single stranded) + DNA polymerase –> double stranded DNA
(mRNA can be inferred from DNA only)
DNA into cloning vector then use amplification to get sequence and enter into database

249
Q

what do restriction enzymes do

A

cuts genes out of DNA for cloning

250
Q

plasmid

A

piece of genetic material that sits outside of chromosomes but can reproduce with genetic machinery or express itself as a gene

251
Q

purpose of plasmid

A

insert a gene into it, DNA ligase glues it together, and it is injected into something else that will replicate it for us
heat shock causes bacteria to accept plasmid

252
Q

how can you tell what bacteria took up the plasmid in the cloning experiment?

A

place gene for antibiotic resistance in plasmid so antibiotics kill off bacteria that does not have the resistance (and target gene) in them

253
Q

DNA hybridization and microarray technology

A

allows us to identify upregulated and downregulated genes to compare gene expression in normal vs cancerous cells
marking Gene A, Gene B, Gene C, then putting it in a microarray chip with their marked mRNA templates to see what aggregates form

254
Q

steps of gene cloning

A
  1. isolate mRNA strand (using reverse transciptase) to make cDNA (only exons)
  2. put cDNA into a plasmid with antibiotic resistant genes
  3. insert into bacteria cell so it will replicate it and add antibiotics into it so that everything but the DNA of interest is killed
255
Q

southern blot

A

identifis specific DNA sequences in a mixture by cutting the DNA into fragments, separating them by gel electrophoresis (size), transferring them to a filter, then eposing them to radio-labeled DNA probe

256
Q

steps of southern blot

A
  1. cleave DNA using enzymes (making small fragments of DNA)
  2. gel electrophoresis to separate by size
  3. denature DNA by making pH basic (to make it single stranded)
  4. transfer gel to filter
  5. expose filter to radio-labeled DNA (complementary sequence of target gene) - radiolabeled DNA will anneal to the target gene and give a signal where the probe bound to the target gene
257
Q

steps of DNA sequencing

A
  1. use PCR to amplify DNA fragment sample
  2. add dideoxynucleotides (without an oxygen so elongation of the DNA will not occur) - able to label nucleotides with fluorescent labels
  3. gel electrophoresis to separate strands by size and have computer analyze fluorescent labels (overlap fragments to see sequence)
258
Q

knock out experiments

A

the use of genetic engineering to inactivate or remove one or more specific genes from an organism

259
Q

reverse genetics

A

start with a gene, sequence it, then look for other gene sequences that are homologous

260
Q

applications of DNA technology

A

medicine - insulin, HGH (can grow them in E. Coli then isolate), vaccines
forensics - short tandem repeats can be sequenced to compare DNA sequences, mtDNA to identify suspect, y chromosome typing
agriculture - plants that are resistant to insects and herbicides, can delay ripening of crops to transport them

261
Q

genetic material in the nucleus in made of

A

proteins and nucleic acids

262
Q

how did Roux determine that the material in the nucleus was genetic material ?

A

chromosomes were divided and passed on in an orderly fashion whereas other components of the cell were not

263
Q

Hershey-Chase experiment

A

determined that nucleic acid is the genetic material in cells
used sulfur to label all amino acids so they can track protein since it is in protein but not DNA. when injected into bacteria, the labeled protein coats stayed outside the cell, whereas the phages in the cell are not labeled. so genetic material was in the cell as passed from the phages into the cell
labeled nucleotides with radioactive phosphorus (found in DNA but not protein coat) and found that since DNA entered the cell, that was genetic material

264
Q

chromosomes are based on

A

the number of centromeres (chromatid and chromosome are both chromosomes because they have 1 centromere each)

265
Q

synapsis

A

homologous chromosomes get closer to each other, and potentially overlap or cross (chaisma when crossed)

266
Q

synaptonemal complex

A

complex of chromatids that are crossed over where they switch some genetic material at the bottom of the chromosome (crossing over)

267
Q

crossing over is known as

A

genetic recombination

268
Q

how many gametes and what type of gametes result from crossing over?

A

4 gametes
2 are recombinant, 2 are purely one or the other

269
Q

genetic recombination increases

A

genetic variability

270
Q

the distance between genes determines the likelihood that

A

they will recombine

271
Q

genes on chromatids that are farther apart are

A

more likely to recombine / separate

272
Q

centimorgen

A

distance between genes for which one product of meiosis in 100 is recombinant (2 genes are 1 centimorgen apart, 1/100 times it will recombine)
genetic map unit (distance between chromosomes) (m.u.)

273
Q

25 map units apart produces what likelihood of recombination happening?

A

25%

274
Q

extranuclear inheritane

A

the ability of certain organelles (mitochondria and chloroplasts) to replicate independently outside of the nucleus

275
Q

organelles of a zygote come from

A

maternal egg cell

276
Q

maternal inheritance is contrary to

A

mendelian genetics (assumes half of the DNA from egg, half from sperm)
but chloroplasts and mitochondria exhibit maternal inheritance

277
Q

endosymbiotic theory

A

mitochondria and chloroplasts were once independent prokaryotes, but at some point they shared an ancestral eukaryotic cell and lived together in symbiosis

278
Q

evolution is

A

small changes in a population over time (not individuals)

279
Q

natural selection

A

natural = probability of surviving, no individual is choosing
selection = one trait is more advantageous or disadvantageous

280
Q

natural selection does not apply to

A

acquired characteristics

281
Q

fitness

A

organisms total ability to pass traits onto offspring

282
Q

fecundity

A

how easily and how often an organism can produce offspring
asexual reproduction: how quickly they can reproduce
sexual reproduction: how well they can procreate and carry a child

283
Q

fecundity is related to natural selection because

A

fecundity is selected for

284
Q

group selection

A

genetic traits that benefit the population will stil be selected for even if they dont directly increase the fitness
ex: survival after reproduction (like surviving through menopause)

285
Q

artificial selection

A

outside being determines desirable traits
ex: farmer picking seeds of 3 biggest tomatoes to plant for next year

286
Q

genetic drift

A

random changes in heritable traits
more likely to happen in smaller populations

287
Q

bottleneck effect

A

major disaster or event wipes a lot of the population so the population left to reproduce is bottlenecked

288
Q

founder effect

A

founders of a new population by random chance (like settlers finding a mountain valley or something to populate)

288
Q

inbreeding

A

people in a population selectively have offspring witha. certain smaller group with the larger population

289
Q

geography is the main driver for

A

animal inbreeding

290
Q

why is inbreeding a problem?

A

example of tay sachs (homozygous recessive) increases the chance that the children will be affected because of the limited selection of partners

291
Q

pre-zygotic

A

all the different forces that stop offspring from having offspring before the zygote is formed

291
Q

asexual reproduction vs sexual reproduction genetic diversity

A

asexual = low genetic diversity
sexual = high genetic diversity

291
Q

reproductive isolation

A

there are many forces that stop 2 different organisms from having offspring

292
Q

types of pre-zygotic reproductive isolation

A
  1. temporal/habitat isolation (organisms do not mate at the same time of year or in the same habitat)
  2. behavioral isolation (mate selection and methods of attracting a mate like singing or dancing)
  3. mechanical isolation - physical inability of 2 organisms to mate like an elephant and a mouse
  4. gametic isolation - fertilization between gametes is impossible
293
Q
A
293
Q
A
293
Q
A
294
Q

types of post-zygotic reproductive isolation

A
  1. zygote mortality - two gametes fuse successfully, but the zygote has a high mortality rate
  2. hybrid inviability - zygote matures into offspring, but offspring has a high mortality rate
  3. hybdrid sterility - zygote matures into offspring then an adult, but the adult is unable to reproduct
295
Q

Gibbs free energy (∆G)

A

free energy of products compared to free energy of reactants and determines spontaneity in J/mol

296
Q

state function

A

total gibbs free energy of a multi-step reaction is the total of the gibbs free energy of each steps

297
Q

∆G =

A

∆H - T(∆S)
H = enthalpy
S = entropy

298
Q

∆G < 0 means
∆G > 0 means

A

negative = spontaneous reaction (no input of energy)
positive = requires gain of energy to occur

299
Q

heat vs temperature

A

heat = amount of energy transferred to a change in temperature
temperature = average kinetic energy of molecules

300
Q

heat transfer variable

A

q
(-q = loss of heat)
(+q = gain of heat)

301
Q

q of system =

A

q of surroundings

302
Q

enthalpy

A

term to describe heat transfer for chemical reactions
referred to as ∆H because it is heat lost or gained from the system (products - reactants)
J/mol of reactant

303
Q

enthalpy of endothermic rxn vs exothermic

A

positive for endothermic (absorbing heat)
negative for exothermic (releasing heat)

304
Q

∆G refers to
Ea refers to

A

thermodynamics
kinetics

305
Q

kinetics refers to
thermodynamics refers to

A

the reaction rate or speed (activation energy)
relative energy between reactions and products

306
Q

kinetically unfavorable means

A

lots of energy is required to get from reactants to transition state

307
Q

metabolism

A

ability for the body to use proteins, fats, carbohydrates, and nucleic acids to sustain life

308
Q

catabolism

A

breaking down macromolecules

309
Q

anabolism

A

building macromolecules back up

310
Q

anabolism requires

A

energy

311
Q

where does the energy for anabolism to occur come from?

A

hydrolysis of ATP into ADP and Pi

312
Q

ATP

A

Adenosine Triphosphate
adenine and ribose with 3 phosphate groups

313
Q

How can you “produce” energy from ATP?

A

hydrolysis releases a phosphate group and releases energy

314
Q

what are some of the processes that ATP fuels?

A

biosynthesis
muscle contraction
ion movement

315
Q

why is ATP a good energy source for cells?

A

because the gibbs free energy of the hydrolysis of ATP to ADP and P is very negative and favorable

316
Q

example of ATP usefulness in coupling

A

ATP hydrolysis has a negative ∆G
monomer to polymer reactions have positive ∆G
coupling the reactions allows us to add the ∆G and get an overall negative ∆G (making unfavorable reaction favorable)

317
Q

how does ATP actually donate energy to polymers when going from monomer to polymer, like in amino acids?

A

ATP donates 2 phosphates to the nucleotides then the amino acid chain displaces 1/3 of the phosphates, then the other diphosphates are hydrolyzed and thermodynamically favorable to drive the reaction

318
Q

oxidation is

A

losing hydrogen atoms

319
Q

reduction is

A

gaining hydrogen atoms

320
Q

electrochemistry allows us to

A

track electron flow in redox reactions and form an electrochemical “cell”

321
Q

overall cellular respiration equation

A

C6H12O2 + 6O2 –> 6H2O + 6CO2

322
Q

what is being reduced and oxidized in cellular respiration?

A

reduced: oxygen going to H2O
oxidized: glucose going to CO2
***electrons flow from glucose to the oxygen and co2 is the oxidized product of this

323
Q

what does the harnessing of electrons in cellular respiration allow for?

A

ADP to ATP conversion

324
Q

as glucose breaks down, the metabolites are

A

more and more oxidized (have less and less electron density)

325
Q

where do electron carrier molecules bring their electrons?

A

electron transport chain (which brings it to O2)

326
Q

benefit of enzymes in glucose metabolism

A

produce a large amount of metabolites to use in other reactions
slow and controlled oxidation of glucose, allowing for the harnessing of energy

327
Q

electron carrier molecules are also known as

A

coenzymes

328
Q

what class of enzymes take hydrogens (electrons) from reactants?

A

dehydrogenases

329
Q

NAD+ + 2H+ + 2e- =

A

NADH + H+

330
Q

FAD + 2H+ + 2e- =

A

FADH2

331
Q

what form of electron carrier molecules shuttle electrons to the ETC?

A

reduced form (NADH and FADH2)

332
Q

carbohydrates

A

chemical compound made of carbon molecules that are fully hydrated
general formula: Cn(H2O)n
1:2:1 ratio of Carbon, Hydrogen, Water

333
Q

monosaccharide

A

one carbohydrate molecule (saccharide = sugar)
ex: glucose or fructose

334
Q

cellulose is a

A

polysaccharide

335
Q

how are carbohydrates named?

A

based on number of carbons and functional groups present (aldehyde or ketone)
(highest number carbon determines stereochemistry)

336
Q

glucose is a _____
fructose is a ______

A

aldohexose (aldehyde)
ketohexose (ketone)

337
Q

D-Glucose and L-glucose are

A

enantiomers (differ at every chiral carbon)

338
Q

all D-aldohexoses are

A

diastereomers of each other

339
Q

epimer

A

molecules whose stereochemistry differs at ONE chiral carbon

340
Q

how do we know there are 8 D-Aldohexoses?

A

there are 4 chiral carbons in glucose so 2^4 = 16 stereoisomers and half of them would have OH on the right at the bottom, so there are 8 D-Aldohexoses

341
Q

D-Ribose structure

A

all right - all OH on the right

342
Q

D-Glucose structure

A

F#@! Glucose (middle finger pointing left)

343
Q

D-Mannose structure

A

like a man holding a gun

344
Q

D-Galactose structure

A

C4 Epimer of Glucose

345
Q

D-Fructose structure

A

ketose form of glucose

346
Q

how does glucose become cyclical?

A

C5 Oxygen attacks carbonyl carbon
becomes pyranose

347
Q

how to remember which substituents go up vs down in the haworth diagram of D-glucose

A

“downright, uplefting” in reference to OH groups
groups on the right point down
groups on the left point up

348
Q

alpha vs beta form of glucose

A

alpha - OH on anomeric carbon is axial
beta - OH on anomeric carbon is equatorial

349
Q

glycosidic linkage

A

a covalent bond that connects a carbohydrate (sugar) molecule to another group to make a disaccharide

350
Q

what bond between what molecules creates lactose?

A

1,4 B-glycosidic linkage between glucose and galactose

351
Q

what bond between what molecules creates maltose?

A

1,4 alpha-glycosidic linkage between two glucoses

352
Q

how many ATPs does cellular respiration form? (ideally)

A

38 ATPs

353
Q

stages of cellular respiration

A

glycolysis - (6C –> 3C) - 2 net ATP (2 needed, 4 produced), anaerobic
Krebs cycle (aerobic) - generates 2 ATP
electron transport chain (aerobic) - 34 ATPs made

354
Q

if oxygen isnt in supply for cellular respiration to continue, what happens?

A

glycolysis byproducts go into lactic acid fermentation

355
Q

in the fasted state, what are the 2 ways the body regulates its blood glucose?

A

glycogen stores
gluconeogenesis (amino acids, lactate, etc to glucose)

356
Q

of the 3 steps of glycolysis that are irreversible, how are those steps bypassed for gluconeogenesis?

A
  1. pyruvate to oxaloacetate then catalyzed to phosphoenolpyruvate
  2. fructose 1,6-bisphosphate to fructose-6-phosphate using fructose 1,6-bisphosphotase
  3. glucose-6-phosphate to glucose using glucose-6-phosphotase
357
Q

what enzyme is considered the opposite of a kinase?

A

phosphatase

358
Q

fast acting forms of glucose regulation

A

Le Chatlier’s principle (influx of glucose shifts equilibrium to the products for glycolysis and amino acids to oxaloacetate for gluconeogenesis to shift towards reactants)
allosteric regulation - allosteric inhibitors or promoters - ATP is a big allosteric regulator of both processes

359
Q

slow acting forms of glucose regulation

A

upregulate transcription mechanisms to promote gluconeogenesis to dump glucose in the blood

360
Q

other forms of glucose regulation

A

hormonal regulation
- insulin (at high BG) - glycolysis
- glucagon (at low BG) - glucooneogenesis

361
Q

what is the energy production of the pentose phosphate pathway?

A

0 ATP (no ATP produced or consumed)

362
Q

what are the products of the pentose phosphate pathway?

A
  1. ribose-5-phosphate
  2. NADPH (reduced form has H)
363
Q

Of NAD+/NADH and NADP+/NADPH, which are found more in the body?

A

NAD+ and NADPH

364
Q

the biggest role of NADPH is to

A

donate electrons - anabolic rxns
***it is not used in glycolysis since glycolysis also donates electrons

365
Q

phases of pentose phosphate pathway

A

oxidative and nonoxidative

366
Q

oxidative phase of pentose phosphate pathway

A

start: Glucose-6-Phosphate
end: NADPH

367
Q

non-oxidative phase of pentose phosphate pathway

A

start: ribulose-5-phosphate
end: ribose-5-phosphate, interconverted sugars that are part of glycolysis

368
Q

pyruvate oxidation

A

occurs after glycolysis to convert pyruvate (3C) to Acetyl CoA (2C) and oxidizes NAD+ to NADH
side product: CO2

369
Q

acetyl CoA reacts with _______ before entering the citric acid cycle forming _______

A

oxaloacetic acid (4C)
citric acid (6C)

370
Q

how many CO2 are produced in citric acid cycle?

A

2 CO2 per cycle
2 cycles occur

371
Q

for each pyruvate, how many NADH, ATP, and FADH2 are produced? (not including pyruvate oxidation, just krebs cycle)

A

3 NADH
1 ATP
1 FADH2
(all doubled because there are two pyruvates)

372
Q

regulation often occurs on what kind of step?

A

irreversible steps

373
Q

when ATP levels are high, what else can Acetyl CoA produce?

A

fatty acids

374
Q

how is pyruvate oxidation regulated?

A

allosteric regulation of pyruvate dehydrogenase
- activators: CoA, NAD+, pyruvate, AMP, Calcium
- inhibitors: Acetyl CoA, NADH, ATP, Fatty Acids

375
Q

how is the citric acid cycle regulated?

A

** no hormonal regulation **
allosteric regulation
substrate availability

376
Q

oxidation of NADH equation

A

NADH –> NAD+ + H+ + 2e-

377
Q

first and last steps of the electron transport chain

A

first: NADH –> NAD+ + H+ + 2e- (oxidation of NADH)
last: 2e- + 2H+ + 1/2O2 –> H2O (reduction of oxygen to water)

378
Q

when the intermembrane space becomes acidic and full of H+, what happens?

A

ATP synthase utilizes the proton gradient to shuttle H+ into the matrix, thus producing energy
similar to a turbine (ADP on matrix side, H+ pumps through, ATP is created and pushed out)

379
Q

chemiosmosis

A

the movement of ions across a semipermeable membrane bound structure, down their electrochemical gradient

380
Q

what is an example of when apoptosis may be useful?

A

in embryonic development, our hands start as paws and programmed cell death allows for the development of our individual digits

381
Q

purpose of increasing permeability of mitochondrial membrane

A

allows cytochrome C (transports electrons between 3rd and 4th complex) to exit into the cell, activates C-ASP-ASEs which are proteases that break down proteins after the aspartate residue using a cystine residue

382
Q

what are the bodies forms of fuel storage and where are they found?

A

glycogen - liver/muscle (4 kcal/g)
protein - muscle (4 kcal/g)
fats - adipose (9 kcal/g) - usually the largest store

383
Q

why are fats so useful for energy storage?

A
  1. energy rich - it is stored in a reduced form so we can oxidize it to get energy, there are lots of saturated (–) and unsaturated (=) bonds
  2. Inert (wont react with other things like glucose)
  3. no large functional role inside the body
  4. very hydrophobic -
384
Q

what kind of cells line the small intestine?

A

epithelial cells

385
Q

what enzyme is responsible for digesting fats in the small intestine?

A

lipases

386
Q

if lipases require an aqueous environment to function, but fats are hydrophobic, how is this problem bypassed?

A

bile “emulsifies” the fat droplets that accumulate and increase the surface area / break them apart so that lipase is able to function properly

387
Q

lipases break triacylglycerides into

A

glycerol backbone
carboxylic acid groups (FATTY ACIDS)

388
Q

once triacylglycerides become fatty acids, what happens?

A

they are transported into the cell to be turned into TAGs again by reforming the ester linkages and packaged for transport

389
Q

what is responsible for packaging TAGs? why is this done?

A

lipoprotein
allows the fats to stay in the core, which is surrounded by proteins so that the outside of the molecule is no longer hydrophobic and can be transported
called a chylomicron

390
Q

lacteal

A

lymphatic capillary that surrounds the cell and take up chylomicrons to travel to the the thoracic ducts located in the shoulders/chest area to enter the veins

391
Q

pathway of fatty acids for absorption

A

chylomicron –> lacteal –> veins –> arteries –> capillary beds

392
Q

lipoprotein lipase

A

the enzyme responsible for breaking down the chylomicron into triacylglycerides into fatty acids and glycerol backbones
also activated by insulin

393
Q

adipose stores fat as

A

triacylglycerides

394
Q

what absorbs chylomicron remnants?

A

liver (contains specific receptors for the remnants)

395
Q

all roads of digestion lead to

A

the liver

396
Q

decrease in ____ and increase in ______ can lead to the release of triacylglycerides from the adipose cells

A

insulin
glucagon

397
Q

how do free fatty acids travel in the blood?

A

along the protein albumin

398
Q

the liver can convert excess ______ into fatty acids

A

glucose

399
Q

the enzymes for fatty acid synthesis are located in the ________. this is a problem because ?

A

cytoplasm
acetyl CoA is only in the mitochondria

400
Q

how can Acetyl CoA reach the cytoplasm?

A

by being transported into the cytoplasm as citrate, then broken down into oxaloacetate and acetyl CoA

401
Q

the oxaloacetate that comes from citrate for fatty acid synthesis becomes

A

pyruvate again

402
Q

the main fatty acid chain in our bodies is

A

palmitic acid

403
Q

ketogenic

A

carbon backbone of AA feeds into precursor molecules of fatty acid synthesis (acetyl-CoA or acetoacetyl CoA)

404
Q

glucogenic

A

carbon backbone of AA feeds into precursor molecules of glucose synthesis (pyruvate, oxaloacetate, or intermediates of the krebs cycle)

405
Q

exclusively ketogenic amino acids

A

lysine + leucine

406
Q

what is the first reaction that occurs in amino acid degradation?

A

transamination (removing amine group to be excreted) to become an alpha keto acid

407
Q

molecule used in transamination

A

alpha-ketoglutarate which accepts amine group to become glutamate (then donates it as ammonia to urea cycle)

MCAT Prep (5 decks)

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