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MCAT Prep > General Biochemistry > Flashcards

General Biochemistry Flashcards

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1
Q

What powers ATP synthase?

A

charge difference between inner membrane (high concentration of +) and mitochondrial matrix

think of it like a battery

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2
Q

What type of reactions does the ETC use?

A

redox reactions

move electrons across the chain

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3
Q

What are FAD and NAD?

A

coenzymes that interact with the ETC enzymes

also they are oxidizing/reducing agents depending

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4
Q

NADH

A

reduced form of NAD+

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5
Q

FADH2

A

reduced form of FAD

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6
Q

If you add double bonds to a hydrocarbon, does this make the hydrocarbon more or less oxidized?

A

this makes the hydrocarbon more oxidized

some of its electrons are pulled away from the carbons through double bonds

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7
Q

What is more oxidized a carboxylic acid or an alcohol?

A

carboxylic acid

has more oxygen pulling electrons away from the carbon

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8
Q

Where will H-bonding occur?

A

-OH -FH and -SH bonds

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9
Q

Amphipathic molecules

A

polar and nonpolar regions

ex: cholesterol and phospholipids

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10
Q

Is CO2 polar or nonpolar?

A

nonpolar by symmetry

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11
Q

Where does the polarity of amino acids make a big impact?

A

the active site of enzymes

transmembrane proteins

protein folding

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12
Q

What does plasma membrane keep out?

A

hydrophillic / polar molecules

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13
Q

Peptide hormones

A

composed of amino acids

large and polar

must use extracellular receptors

they quickly trigger a signal pathway to make short-term changes

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14
Q

Steroid hormones

A

derivatives of cholesterol

small and nonpolar

cross the plasma membrane and interact with nuclear receptors

trigger long-term changes more slowly

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15
Q

How do histones work generally?

A

histones are positively charged so they can attract negatively charged DNA

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16
Q

What do modifications like acetylation, phosphorylation and methylation do to histones?

A

normally replace the positively charged lysine with either neutral or negatively charged groups

this weakens the interaction between DNA and histones and the DNA loosens

when the DNA loosens, more gene expression can happen

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17
Q

What are the stereochemical configurations of most of our amino acids?

A

L and S configurations

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18
Q

Exceptions to configurations of amino acids

A

cysteine is R and glycine is not chiral

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19
Q

How can proline affect a protein?

A

can introduce kinks and make the protein more rigid

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20
Q

How can glycine affect a protein?

A

can decrease steric hindrance and make the protein more fluid

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21
Q

Which amino acid can form disulfide bridges?

A

cysteine

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22
Q

Which two amino acids have sulfur?

A

cysteine and met

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23
Q

Which amino acids are negatively charged / acidic?

A

D (aspartate)
E (glutamate)

both have carboxylic acids on their ends

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24
Q

Which amino acids are positively charged / basic?

A

lysine, arginine, and histidine

histidine is neutral in physiological conditions

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25
Q

Why are positively charged amino acids basic?

A

because they already ACCEPTED a proton

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26
Q

Why are negatively charged amino acids acidic?

A

because they already DONATED a proton

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27
Q

What are two ways to artificially synthesis amino acids?

A

Strecker and Gabriel synthesis

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28
Q

Proteases

A

catalyze breaking down proteins / peptides

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29
Q

Is formation or hydroylsis of peptide bonds energetically favorable?

A

hydrolysis

but it is so slow that it doesn’t occur

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30
Q

What increases the stability of peptide bonds?

A

resonance between the carbonyl carbon and amide nitrogen

creates a rigid planar configuration

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31
Q

How are peptide bonds formed?

A

dehydration / condensation through the nitrogen’s nucleophilic attack on the carbonyl carbon

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32
Q

Key points of Strecker synthesis

A

Start with: aldehyde
End with: amino acid

Process: use nitrogen reagents to form an intermediate, then go through multiple protonation and deprotonation steps to form an amino acid

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33
Q

Key points of Gabriel synthesis

A

Start with: highly protected nitrogen, phtalimide
End with: amino acid

Process: use MALONIC ESTER to attach amide to carboxylic acid. then, add R-group and remove unwanted groups

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34
Q

Pepsin

A

a protease that breaks down peptide bonds in the stomach

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35
Q

Around how much does 1 Amino acid weight?

A

100 Da

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36
Q

What levels of protein folding would changes in temperature or pH influence?

A

mostly 3º and 4º

also affects 2º

1º is very strong due to covalent peptide bond

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37
Q

What terminus is a new amino acid added to?

A

C-terminus

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38
Q

What stabilizes the 2º structure of amino acids?

A

H-bonds on the backbone!

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39
Q

Where are alpha helices commonly found?

A

transmembrane proteins and DNA binding proteins

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40
Q

Where do R-groups face in alpha helices?

A

outwards

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41
Q

What can cause amyloid diseases?

A

misfolded B-pleated sheets

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42
Q

If there is a large amount of proline, what secondary protein structure would we expect?

A

B-pleated sheets because it introduces a kink

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43
Q

What creates the 3º and 4º structure of proteins?

A

interactions between side chains, mostly noncovalent

ex: h-bonding, salt bridges, disulfide bonds, hydrophobic interactions

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44
Q

Salt bridges

A

seen in protein folding

ionic interaction between oppositely charged side chains

ex: K and D

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45
Q

Disulfide bonds

A

formed by oxidation of two cysteine side chains

covalent

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46
Q

How to break disulfide bonds?

A

introduce a reducing agent

reduce the sulfur-sulfur bond back to two sulfur-H bonds

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47
Q

Is protein folding spontaneous?

A

yes, due to decrease in entropy and thermodynamics

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48
Q

How do misfolded proteins aggregate together?

A

exposed nonpolar regions attach to each other

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49
Q

Where is activation energy on a graph?

A

difference between the maximum energy (transition state) and reactants’ energy

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50
Q

What do the two subunits of the active site do?

A

binding site is where intermolecular interactions occur

catalytic site is where catalysis happens

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51
Q

Orthosteric regulation

A

regulation of enzymes at the active site

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52
Q

What supports the induced fit model?

A

stabilization of the transition state

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53
Q

lyases

A

cleave bonds through mechanisms other than hydrolysis

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54
Q

ligases

A

join molecules together with covalent bonds

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55
Q

kinases versus phosphatases

A

kinases add phosphate groups

phosphatases remove phosphate groups

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56
Q

What are the respective pKas of the carbonyl and amino groups in an amino acid?

A

2.2 and 9

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57
Q

amphipathic versus amphoteric

A

amphoteric: molecule can act as acid or base
amphipathic: molecule has nonpolar and polar regions

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58
Q

example of negative feedback in glycolysis

A

rate limiting step is fructose 6-phosphate to fructose 1,6-bisphophate

catalyzed by PFK (phosphofructokinase)

ATP (end product of glycolysis) limits PFK’s activity

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59
Q

feed forward regulation

A

intermediates upstream make downstream enzymes better

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60
Q

What type of feedback is insulin an example of?

A

insulin is an example of negative feedback

when blood glucose levels are high, insulin is produced and tells body to uptake glucose

glucose levels go from high to low

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61
Q

What type of curve do we see for cooperativity?

A

sigmodial (S) curve

stronger cooperativity = more of an S shape

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62
Q

What is the Hill Coefficient? What do its values mean?

A

Hill Coefficient is measure of cooperativity

> 1 is positive cooperativity (like hemoglobin)
=1 is no cooperativity
<1 is negative cooperativity (rare)

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63
Q

how does a substrate bind to an enzyme?

A

through noncovalent, temporary interactions

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64
Q

where does phosphorylation of an enzyme happen?

A

at serine, threonine, and tyrosine residues

places where there is an -OH group

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65
Q

What type of enzyme dephosphorylates?

A

phosphatases

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66
Q

how can cleavage modify enzymes?

A

can make an inactive zymogen active

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67
Q

example of cleavage of enzymes to activate

A

trypsinogen being cut to trypsin in the stomach

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68
Q

zymogens

A

inactive, non-cleaved form of enzymes

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69
Q

How do allosteric enzyme regulators work?

A

interact at site outside of active site

noncovalent

change the 3º structure of an enzyme

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70
Q

Cofactors versus coenzymes

A

coenzymes are an organic form of a cofactor

all coenzymes are cofactors, but not all cofactors are coenzymes

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71
Q

prosthetic groups

A

coenzymes tightly/covalently bound to their enzymes

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72
Q

example of a prosthetic group

A

Heme group with the covalently bound Fe

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73
Q

Holoenzyme versus apoenzyme

A

holoenzyme: WHOLE set of coenzymes/cofactors needed are present
apoenzyme: missing certain needed coenzymes/cofactors

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74
Q

What are FAD and NAD+ examples of?

A

coenzymes needed for redox reactions

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75
Q

Do enzyme inhibitors normally bind covalently or noncovalently?

A

noncovalently

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76
Q

Vmax

A

maximum rate of enzyme catalyzed reaction

relianet on enzyme concentration

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77
Q

Km

A

concentration of substrate needed to reach 1/2Vmax

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78
Q

What does Km tell us?

A

the affinity of an enzyme for a particular substrate

high Km = low affinity

low Km = high affinity

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79
Q

What are the x and y intercepts in a Lineweaver-Burke plot?

A

x-intercept: -1/Km

y-intercept: 1/Vmax

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80
Q

If x-intercept of Lineweaver Burke plot moves to the left was does this indicate?

A

more negative x-intercept

means that -1/Km is greater, so Km is smaller

Km is lower means that affinity is higher

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81
Q

If If x-intercept of Lineweaver Burke plot moves closer to the origin what does this indicate?

A

less negative x-intercept

means that -1/Km is smaller, so Km is higher

Km is higher means that affinity is lower

would see this with competitive inhibition

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82
Q

competitive inhibitors effect on kinetic parameters

A

Vmax stays the same (can flood system with substrate to overcome inhibit)

Km increase (less affinity, need more substrate to reach 1/2Vmax)

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83
Q

noncompetitive inhibitors effect on kinetic parameters

A

Vmax decreases (can’t overcome inhibitor by flooding system)

Km stays the same

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84
Q

noncompetitive versus uncompetitive inhibitors

A

noncompetitive inhibitors bind to the empty enzyme

uncompetitive inhibitors bind to the ES complex

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85
Q

uncompetitive inhibitors effect of kinetic parameters

A

Vmax decreases (can’t overcome inhibitor by flooding the system)

Km decreases (in uncompetitive inhibition, the ES complex doesn’t release product. there is a higher affinity for the substrate)

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86
Q

Mixed inhibitors

A

always decrease Vmax

can increase or decrease Km depending on when and where the inhibitor binds

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87
Q

In general, how can we reduce a molecule?

A

make more constituents bound to hydrogen

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88
Q

pI

A

isoelectric point

where net charge is equal to 0

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89
Q

When a protein is denatured what levels of folding are affected?

A

2º, 3º and 4º

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90
Q

Does water flow to higher or lower osmotic pressure?

A

higher osmotic pressure

osmotic pressure = solute concentration

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91
Q

Does cholesterol always increase fluidity?

A

no

at temperatures greater than the physiological temp (37ºC), cholesterol makes membrane more rigid

92
Q

What is the physiological temperature?

A

37ºC

93
Q

How are phospholipids formed?

A

attach fatty acids to glycerol through esterfication

94
Q

amphipathic

A

polar and nonpolar regions on same molecule

95
Q

glycolypids

A

a carbohydrate group is attached to two fatty acids through either glycerol or sphingosine

96
Q

sphingomyelin

A

a type of glycolipid, amphipathic

clusters with cholesterol to form lipid rafts

signaling and adhesion

97
Q

integral proteins

A

also called transmembrane proteins

nonpolar amino acids inside and polar outside

98
Q

examples of integral proteins

A

proton pumps, ion channels, G-protein receptors

99
Q

example of a lipid anchored protein

A

G-protein complexes attached to intracellular side of membrane through a lipid

100
Q

peripheral protein

A

temporarily attached to the membrane in the cytoplasmic side

ex: enzymes

101
Q

surfactants

A

can reduce surface tension of a solution

amphipathic molecules like phospholipids and glycerolipids

102
Q

flippase

A

move phospholipids from outer to inner surface

103
Q

floppase

A

move phospholipids from inner to outer surface

104
Q

scramblases

A

move phospholipids in both directions

105
Q

what happens at lower temperatures?

A

decreased membrane fluidity

106
Q

at higher temperatures, do we want more or less unsaturated phospholipids?

A

less

want to reduce fluidity and have the membrane be more tightly packed

107
Q

What molecules can always freely diffuse across the cell membrane?

A

gases

O2 and CO2

(water normally can)

108
Q

hypotonic

A

extracellular solution is low in solutes and water moves into cell

109
Q

hypertonic

A

extracellular solution is high in solutes and water moves out of cell

110
Q

osmotic pressure

A

minimum amount of pressure that prevents further osmosis

111
Q

equation for osmotic pressure

A

pi = iMRT

i= number of molecules a solute can dissociate into
M= total concentration of solutes
112
Q

relationship between osmotic pressure and solutes

A

higher osmotic pressure = higher solutes

113
Q

something to be careful of when doing calculations with osmotic pressure

A

need to consider the number of molecules a solute can dissolve into

114
Q

osmolarity

A

molarity of all solute particles

115
Q

Why is diffusion thermodynamically favorable?

A

increase in entropy

116
Q

sodium potassium pump

A

moves 3 Na+ out and 2 K+ in

creates net negative charge

think of salty bannana

example of primary active transport

117
Q

Voltage gated ion channels and ligand gated ion channels are examples of?

A

facilitated diffusion

118
Q

What type of channels do neurotransmitters act on?

A

ligand gated ion channels

119
Q

Is facilitated diffusion active or passive?

A

passive

diffuse down concentration gradient

120
Q

primary active transport

A

couples ATP/energy source hydrolysis to directly move solutes

121
Q

secondary active transport

A

active transport generates concentration gradient where passive transport then occurs

122
Q

antiporter

A

type of secondary active transport

moves two solutes in opposite directions

123
Q

symporter

A

type of secondary active transport

moves two solutes in the same direction

124
Q

endocytosis

A

engulfment of particles by the cell membrane

125
Q

receptor-mediated endocytosis

A

takes up very specific molecules into the cell through endocytosis

126
Q

do you need ATP for primary active transport?

A

no. can use light or other sources of energy

127
Q

endosomes

A

organelles that sort products of endocytosis

128
Q

what organelle is responsible for digesting and repurposing materials ingested during endocytosis?

A

lysosome

129
Q

what type of endosomes are used for pinocytosis?

A

early and late endosomes

130
Q

what type of endosomes are used for phagocytosis?

A

phagosomes

131
Q

how can exocytosis be regulated?

A

through Ca2+

ex: in neurons, more Ca2+ triggers the release of neurotransmitters through exocytosis

132
Q

How is ATP used for energy?

A

add water (hydrolysis) to cleave the gamma phosphate

gamma phosphate becomes an inorganic phosphate group (Pi)

133
Q

What are two types of ATP hydrolysis?

A

substrate level phosphorylation

oxidative phosphorylation

134
Q

substrate level phosphorylation

A

transfer a phosphate group directly to ADP

use an enzyme to catalyze this transfer

ex: glycolysis

135
Q

oxidative phosphorylation

A

use the ETC to generate ATP

requires oxygen

136
Q

why does the ETC require oxygen?

A

diatomic oxygen serves as the last electron acceptor in the ETC due to it’s high reduction potential

137
Q

What happens to FADH2 and NADH in the ETC? Why?

A

they are oxidized as the enzymes in the chain have higher reduction potentials

138
Q

Reduction potential

A

ºE

measures how energetically favorable reduction (gain) is

139
Q

What does a more positive ºE indicate?

A

more favorable to reduce

140
Q

What happens when electrons move to higher ºE?

A

energy is released as it is more favorable to go to a higher ºE

141
Q

Glycogen

A

hydrolyzed to glucose which releases energy

142
Q

What is the first step the body makes regarding how to use glucose?

A

determines what type of glucose membrane receptor to display

143
Q

GLUT1

A

glucose transporter found on nearly all tissues to serve as baseline glucose uptake

144
Q

What happens to receptors when glucose levels are low?

A

more GLUT1 is expressed to uptake more glucose for energy

145
Q

GLUT2

A

glucose transporter found on kidney, liver and pancreas cells as it allows for 2 way transport of glucose

146
Q

GLUT3

A

glucose transporter found on neurons and placenta

has a high affinity for glucose so these cells have glucose even when food is scarce

147
Q

GLUT4

A

glucose transporter found on muscles + adipose tissues

takes up glucose for energy and storage

148
Q

Which glucose receptor does insulin work on?

A

GLUT4

149
Q

Ka

A

the association constant

greater Ka = greater affinity

units M-1

150
Q

Kd

A

the dissociation constant

lower Kd = greater affinity

unit M

the inverse of the association constant, Ka

151
Q

Km

A

halfway substrate concentration to Vmax

152
Q

Kt

A

equivalent to Km

is affinity for transport and is independent of solute concentrations

153
Q

What denaturants can break disulfide bonds?

A

strong reducing agent or strong bases

154
Q

How can you denature hydrophobic interactions?

A

with a detergent

155
Q

Majority of fibrous proteins

A

are hydrophobic and used for structure

156
Q

Majority of globular proteins

A

are hydrophilic and often perform enzymatic roles

157
Q

How does SDS work?

A

it breaks up hydrophobic interactions

SDS is an amphipathic molecule

158
Q

How can you disrupt salt bridges?

A

change the pH of the solution

pH will make different amino acids charged and ionic interactions are what constitute salt bridges

159
Q

Triglycerides

A

three fatty acids connected through ester bonds to a glyceride backbone

160
Q

Saponification

A

use a strong base to break triglycerides into soap and glycerol

161
Q

Phosphatidyl

A

prefix that indicates a phospholipid

162
Q

Sphingolipids

A

fatty acids connected to a sphingosine head that has a nitrogen atom

163
Q

Sphingomyelin

A

type of sphingolipid that clusters in lipid rafts in the plasma membrane

plays a role in biosignalling

164
Q

What are two types of eicosanoids?

A

thromboxanes and prostaglandins

165
Q

prostaglandins

A

lipid that mediates pain and inflammation

type of eicosanoid

166
Q

thromboxanes

A

found in platelets and mediate clotting

type of eicosanoid

167
Q

terpenes

A

derived from isoprenes

make up cholesterol

168
Q

vitamin D

A

cholesterol derivative

169
Q

Which vitamins are water soluble?

A

B and C

170
Q

What type of lipid makes up steroid hormones?

A

cholesterol NOT fatty acids

171
Q

omega notation for fatty acids

A

starts counting carbons on the non-carbonyl end

omega - (double bond location)

172
Q

lipid numbering notation

A

only gives the total number of carbons and the number of double bond

ex: 16:1

173
Q

delta notation

A

starts counting at the carbonyl end

ex: ∆9

174
Q

Which type of unsaturated fatty acid is typically more solid at room temperature?

A

trans - fatty acids because they can pack together more tightly

175
Q

Why are trans-fats considered more unhealthy than cis-fats?

A

trans-fats can increase the number of LDL to HDL

176
Q

lipoproteins

A

made of proteins and lipids

transport fats into the bloostream

177
Q

chylomicrons

A

can transport lipids through aqueous bloodstream

chylomicrons are similar to VLDL

178
Q

Order how a newly synthesized chylomicron would move through the body

A 
intestinal epithelium 
lacteals
lymphatic vessels
adipose tissue
liver
179
Q

Where are lipoproteins made?

A

the liver

180
Q

Do more or less lipids make a lipoprotein less dense?

A

more lipids = less dense

181
Q

LDL

A

low-density lipoprotein (has lots of lipids)

delivers cholesterol to cells

182
Q

HDL

A

high-density lipoproteinn (doesn’t have many lipids)

can pick up cholesterol and take it back to the liver

183
Q

What do higher LDL levels indicate?

A

higher risk of cardiovascular disease and atherosclerosis

184
Q

What triggers the release of fatty acids from adipose cells?

A

epinephrine and glucagon

185
Q

Lipase

A

breaks down triglycerides to free fatty acids

186
Q

catabolism

A

refers to breaking molecules down

187
Q

lipolysis

A

fatty acid molecules are mobilized from storage and made available to cells that need energy

occurs in adipose cytosol

188
Q

Beta oxidation

A

fatty acids are oxidized to produce intermediates that can be used to make energy

189
Q

How can lipids enter the mitochondria for beta-oxidation?

A

tagged with a CoA tail

190
Q

Where does beta-oxidation primarily occur?

A

the mitochondria

191
Q

carnitine shuttle

A

acts as a control point for regulating fat metabolism

allows larger CoA tagged lipids to enter mitochondria

192
Q

What does each round of B-oxidation include?

A

1) oxidation
2) hydration
3) oxidation
4) thiolysis cleavage

193
Q

What do odd-numbered unsaturated fatty acids need to do before beta-oxidation?

A

use an isomerase to move the double bond between the alpha and beta carbons

194
Q

What do even-numbered saturated fatty acids need to do before beta-oxidation?

A

2 double bonds will occur

so, first need to reduce one double bond and then, isomerase the other to between the alpha and beta carbons

195
Q

Calculation for how many ATP molecules produced per lipid

A

a little less than 7 * the number of carbons

196
Q

Calculation for how many round of Beta-oxidation needed?

A

number of carbons/2 minus 1

197
Q

Ketone bodies

A

made from acetyl-CoA in the liver in times of low glucose

198
Q

What can ketone bodies be used for?

A

can be used to transport acetyl-CoA to heart and brain tissues for energy production during times of low glucose

199
Q

Where are ketone bodies made?

A

the liver

200
Q

hepatocytes

A

liver cells

201
Q

3 common ketone bodies

A

acetoacetate
acetone
D-B-hydroxybutyrate

202
Q

when does ketoacidosis occur?

A

occurs when insulin does not work so glucose is not being used for energy and this leads to a reliance on ketogenesis for energy

203
Q

Why are lipids used for energy storage?

A

they are more reduced than carbs/proteins

they carry less water than carbs/proteins so they are lighter

204
Q

Where does fatty acid synthesis occur?

A

cytoplasm of adipocytes

205
Q

What lipid can the body naturally produce?

A

palmitic acid

206
Q

Where is cholesterol synthesized?

A

in the smooth ER of heptacytes (liver cells)

207
Q

What transports cholesterol from the liver to the tissues?

A

LDL

208
Q

G-actin

A

the monomer form of actin

209
Q

F-actin

A

the polymer form of actin

210
Q

How is F-actin created?

A

actin hydrolyzes ATP to catalyze its own reaction

211
Q

What are microfilaments made of?

A

actin

212
Q

Treadmilling

A

when actin is being added to + end while being simultaneously removed from - end

can also happen with microtubules

213
Q

Keratin

A

an example of an intermediate filament

214
Q

What is needed for microtubule creation?

A

GTP and tubulin dimers

215
Q

Kinesin

A

a motor protein that walks from the center of the cell to the periphery down microtubules

transports cargo

require ATP to walk

216
Q

Dyneins

A

walk from periphery to center of cell down microtubules

transports cargo

requires ATP to walk

217
Q

Myosins

A

attach to actin filaments during muscle contraction

requires ATP

218
Q

Selectins

A

a type of cell adhesion molecule that mediate the inflammatory response

selectins help slow down leukocytes when they come to an infected area

219
Q

Cadherins

A

a type of cell adhesion molecule involved in growth and development

Ca2+ dependent adhesion

Formation of cell to cell connections

220
Q

Integrins

A

a type of cell adhesion molecule that helps cells adhere to the extracellular matrix and also act as signaling molecules

221
Q

Anchoring junctions

A

stabilize cells and tissues

222
Q

Gap junctions

A

bring 2 cytoplasms into contact with each other

seen in tissues that conduct chemical and electrical signals to coordinate function

223
Q

Tight junctions

A

found in epithelial cells

link cells together without allowing transport

ex: BBB

224
Q

Antibody abbreviation

A

Ig for immunoglobulin

225
Q

Class switching

A

changes the type of antibody by modifying the constant domain of the heavy chain

keeps hypervariable region

226
Q

IgG

A

the most abundant class of antibody

does most work during the humoral immune response

only antibodies that can get passed to fetus

MCAT Prep (22 decks)

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