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MCAT - Kaplan > Biochem > Flashcards

Biochem Flashcards

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1
Q

Aromatic Amino Acids

A

WYF (Tryptophan, Phenylalanine and Tyrosine)

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2
Q

Basic (+) Amino Acids

A

His Lies Are basic (Arginine, Histidine, Lysine)

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3
Q

Nonpolar Amino Acids

A

LIMP VAG (Leucine, Isoleucine, Methionine, Proline and Valine, Alanine, Glycine)

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4
Q

Polar Amino Acids

A

STQNC (Serine, Threonine, Glutamine, Asparagine, Cysteine)

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5
Q

Acidic (-) Amino Acids

A

Aspartic Acid and Glutamic Acid

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6
Q

All amino acids are chiral except for __

A

glycine

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7
Q

All amino acids are S configuration except for __

A

cysteine

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8
Q

Thiols are prone to __.

A

oxidation

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9
Q

Amides (Asp and Glu) do not become charged with __ changes.

A

pH

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10
Q

Serine and Threonine are often found __ bonding.

A

hydrogen

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11
Q

All proteinogenic amino acids are __.

A

L

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12
Q

Peptide bonds are formed via ___ which involves removing H2O.

A

condensation / dehydrogenation

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13
Q

Hydrolysis of peptide bonds breaks the __ bond by adding H to the amide nitrogen and OH to the carbonyl carbon.

A

C-N

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14
Q

Primary protein structure consists of the __ . It is stabilized by __ bonds.

A

order of amino acids ; peptide

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15
Q

Secondary protein structure consists of the __ . It is stabilized by __ bonds.

A

alpha helices and beta pleated sheets ; hydrogen (proline introduces kinks and usually is not in the middle)

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16
Q

Tertiary protein structure consists of the __ . It is stabilized by __ bonds.

A

folded protein; disulfide

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17
Q

Quaternary protein structure consists of the __ .

A

more than one polypeptide chain (subunits)

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18
Q

If you lose tertiary structure than the protein is said to be __. Heat can cause hydrophobic interactions to break with increased kinetic energy. Solutes like urea can break cystine, H bonds and SDS solubilizes the protein.

A

denatured

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19
Q

GLUT2

A

1) hepatocytes and pancreatic
2) high Km
3) liver picks up excess glucose and stores it preferentially post meal when high glucose
4) Beta cells: glut 2 and glucokinase –> glucose sensors
5) 1st order kinetics

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20
Q

GLUT4

A

1) adipose tissue, muscle
2) incr. insulin incr. GLUT4
3) saturated when higher than normal blood glucose levels because close to normal glucose levels
4) 0 order kinetics

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21
Q

Glycolysis is necessary for RBC because they lack __

A

mitochondria

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22
Q

Glycolysis overall can be defined as glucose –> __

A

2 pyruvate

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23
Q

Glycolysis : Hexokinase

1) irreversible or reversible
2) inhibited by _
3) forms _

A

IRREVERSIBLE
Glucose-6-Phosphate
Forms glucose-6-phosphate

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24
Q

Glycolysis : Glucokinase (RATE LIMITING STEP)

1) irreversible or reversible
2) works with __
3) induced by __

A

1) Irreversible
2) works with Glut 2
3) insulin, senses glucose

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25
Q

Glycolysis : PFK-1

1) irreversible or reversible
2) inhibited __
3) activated __

A

1) Irreversible
2) ATP, citrate, glucagon
3) activated by AMP , f-2,6 bisphosphate, insulin

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26
Q

Glycolysis : Glyceraldehyde-3- Phosphate Dehydrogenase

1) irreversible or reversible
2) generates _

A

1) reversible

2) generates NADH

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27
Q

Glycolysis : 3 Phosphoglycerate Kinase

1) irreversible or reversible
2) forms __

A

1) reversible

2) ATP and 3-phosphoglycerate

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28
Q

Glycolysis : Pyruvate Kinase

1) irreversible or reversible
2) activated by_
3) forms _

A

1) irreversible
2) 1,6 bisphosphate
3) forms ATP and pyruvate

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29
Q

Monosaccharides can under glycolysis instead of glucose. This happens through __ and __.

A

trapping ; linking

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30
Q

Galactose is trapped by __ and linked by __

A

galactokinase ; galactose-1 p uridyltransferase

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31
Q

Fructose is trapped by __ and linked by aldolase B –> DHAP –> Glyceraldehyde –> Glyc-3-Phosph.

A

fructokinase

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32
Q

Pyruvate dehydrogenase is activated by __ in the liver. It Causes pyruvate to become Acetyl-CoA and releases CO2 and converts NAD+ to NADH.

A

insulin

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33
Q

Pyruvate dehydrogenase is inhibited by __.

A

Acetyl-CoA

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34
Q

Pyruvate has three potential fates 1) Acetyl CoA by pyruvate dehydrogenase 2) lactate by __ 3) oxaloacetate by __.

A

lactate dehydrogenase ; pyruvate carboxylase

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35
Q

Glycogenesis is the synthesis of _ .

A

glycogen

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36
Q

Glycogenesis is inhibited by __ and __ via a protein kinase cascade.

A

epinephrine, glucagon

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37
Q

(Glycogenesis) a alpha 1,4 linkage attaches to glucose because of __

A

glycogen synthase

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38
Q

(Glycogenesis) a alpha 1,6 linkage breaks _ and moves block of __.

A

alpha 1,4 linkage ; oligoglucose

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39
Q

Glycogenolysis results in the breaking down of __

A

glycogen

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40
Q

What breaks down alpha 1,4 linkages and creates glucose-1-phosphate (Glycogenolysis)

A

glycogen phosphorylase

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41
Q

The break down of alpha 1,6 linkages forms __(Glycogenolysis)

A

free glucose

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42
Q

Glycogenolysis is activated by AMP and epinephrine but inhibited by __.

A

ATP

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43
Q

(Gluconeogenesis) occurs when fasting glycogen levels __

A

decrease

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44
Q

Gluconeogenesis Pyruvate Carboxylase replaces __.

A

pyruvate kinase

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45
Q

Gluconeogenesis PEPCK replaces __.

A

pyruvate kinase

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46
Q

Gluconeogenesis F-1,6 bisphosphatase replaces __.

A

PFK-1

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47
Q

Gluconeogenesis 6-6-phosphatase replaces __.

A

glucokinase

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48
Q

Gluconeogenesis occurs as it reverses the steps of glycolysis including bypassing the 3 irreversible steps. It depends upon __.

A

beta oxidation for acetyl-coA and ketone bodies

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49
Q

The Pentose Phosphate Pathway has two major products. What are they?

A

1) Ribose -5- Phosphate 2) NADPH

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50
Q

The Pentose Phosphate Pathway NADPH Product has what functions?

A

1) biosynthesis of fatty acid + cholesterol
2) cellular bleach production
3) maintain supply of reduced glutathione against ROS

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51
Q

Acetyl-CoA is comprised of thioester bonds which are __ in energy.

A

high

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52
Q

Acetyl-CoA is inhibited by __ and __.

A

acetyl CoA and NADH

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53
Q

Acetyl-CoA is activated by __ then PDH and then dihydrolipoyl x2

A

pyruvate dehydrogenase phosphatase

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54
Q

The Citric Acid Cycle generates __

A

NADH, FADH2, GTP

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55
Q

The Citric Acid Cycle oxidizes __

A

carbons, intermediates to CO2

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56
Q

The Citric Acid Cycle begins with 1) citrate synthase 2) __ 3) __ 4) __ 5)__ 6)__ 7)__ 8) malate dehydrogenase

A

2) aconitase
3) isocitrate dehydrogenase
4) alpha ketoglutarate dehydrogenase
5) succinyl- coA- synthetase
6) succinate dehydrogenase
7) fumarase

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57
Q

The Electron Transport chain takes place in the __

A

inner mitochondrial membrane , facing the matrix

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58
Q

The Citric Acid cycle is a part of __

A

mitochondrial matrix

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59
Q

Electron Transport Chain (Complex I) translocates __ protons. NADH to FMN to CoQ results in __. The key components are iron-sulfur

A

4 ; CoQH2

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60
Q

Electron Transport Chain (Complex II) translocates __ protons. Succinate to FAT to CoQ results in __ . The key components are iron-sulfur

A

0 ; CoQH2

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61
Q

Electron Transport Chain (Complex III) translocates __ protons. CoQH2 to heme leading to __. The key components are iron-sulfur

A

4 ; cytochrome C

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62
Q

Electron Transport Chain (Complex IV) translocates __ protons. H+ ions lead to cytochrome C to oxygen making __. The key components are cytochrome and Cu2+

A

2; H2O

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63
Q

ETC NADH cannot cross and needs a shuttle. One path leads to glycerol-3-phosphate and one leads to malate.

A

1) gly-3-phosphate NADH to DHAP to glycerol-3-phosphate

2) malate aspartate NADH to oxaloacetate to malate

64
Q

Oxidative Phosphorylation - proton motive force

A

The proton-motive force is the electrochemical gradient generated by the ETC across the inner mitochondrial membrane.

65
Q

Oxidative Phosphorylation- ATP synthase

A

ATP Synthase is the enzyme responsible for generating ATP from ADP and an inorganic phosphate (Pi).

66
Q

Oxidative Phosphorylation- F0 portion

A

Is an ion channel. allowing protons to flow down the gradient from the intermembrane space to the matrix.

67
Q

Oxidative Phosphorylation- F1 portion

A

Uses the energy released by the gradient to phosphorylate ADP into ATP

68
Q

Lipid Mobilization in adipocytes involves __ and is regulated by insulin, epinephrine and cortisol

A

Hormone sensitive lipase

69
Q

Lipid Mobilization in lipoprotein involves __.

A

lipoprotein lipase

70
Q

Short chain fatty acids are __ whereas long chain fatty acids are absorbed into micelles and chylomicrons.

A

absorbed into blood

71
Q

Chylomicrons

A

triacylglycerols that transport long chain fatty acids via the lymph system

72
Q

VLDL is a triacylglycerol that transports from liver to __.

A

peripheral tissue

73
Q

IDL is a VDL remnant and transports between triacylglycerol and cholesterol. It picks up __ from HDL.

A

cholesteryl ester

74
Q

LDL

A

A cholesterol for tissue use

75
Q

HDL

A

“good cholesterol” reverse cholesterol transport

76
Q

Apoprotein are important for interactions with lipoproteins forming apolipoproteins. If you had no apolipoproteins then we could expect:

A

1) cannot secrete lipid transport lipoprotein
2) inability to endocytose
3) decreased ability to remove excess cholesterol

77
Q

The key enzyme of cholesterol biosynthesis

A

HMG-CoA reductase

78
Q

Cholesterol metabolism - LCAT

A

Cholesteryl esters for HDL transport

79
Q

Cholesterol metabolism- CETP

A

IDL to LDL transfer esters from HDL

80
Q

An unsaturated fatty acid contains __

A

one or more double bonds

81
Q

A saturated fatty acid contains _

A

no double bonds

82
Q

Fatty Acid Synthesis

A

1) activation 2) bond formation 3) reduction 4) dehydration 5) reduction
(x8)

83
Q

Palmitic Acid

A

16 carbon acid and the only fatty acid that humans can synthesize

84
Q

Fatty Acid Mitochondria Oxidation- Saturated

A

1) Oxidation 2) Hydration 3) Oxidation 4) Cleavage

85
Q

Fatty Acid Mitochondria Oxidation- Unsaturated

A

This requires 1) isomerase 2) additional reductase at cleavage

86
Q

Ketone Bodies are formed due to __ and occurs in the liver.

A

excess acetyl coA during starvation and regenerates acetyl coA

87
Q

Ketolysis generates acetyl coA but

A

does not occur in the liver and only occurs in low energy muscle and brain tissues

88
Q

Protein catabolism occurs during starvation and is fed __

A

into urea cycle for excretion

89
Q

Protein catabolism - Amino Acids pathways

A

1) gluconeogenesis 2) ketone body formation

90
Q

Enzymes lower the activation energy and increase the rate of a reaction. However, what other features should we know about enzymes?

A

1) no change in the equilibrium constant
2) appear in both reactants and products- unchanged
3) no change in deltaG
4) pH and temperature sensitive
5) specific to rxn or rxn class

91
Q

Oxidoreductases catalyze _ reactions.

A

redox

92
Q

Transferases catalyze __.

A

movement of functional groups (i.e. kinases transfer phosphate from ATP to another molecule)

93
Q

Hydrolases catalyze __

A

breaking into two using the addition of water (i.e. phosphatase, lipase, nuclease)

94
Q

Lysases catalyze __ reactions.

A

cleaving 1 molecule into 2 products w/o water (ex. synthases 2 molecules into a single molecule)

95
Q

Isomerases catalyze __

A

the rearrangement of bonds within a molecule ; (aka synthases 2 molecules into a single molecule)

96
Q

Ligases catalyze __

A

addition or synthesis reactions between large molecules and require ATP (i.e. nucleic acid synthesis and repair)

97
Q

Mnemonic for Enzyme Classes

A

LIL Hot (Ligase, Isomerase, Lysase & Hydrolase, Oxidoreductase and Transferase)

98
Q

A holoenzyme is an enzyme with _

A

a cofactor

99
Q

An apoenzyme is an enzyme with _

A

no cofactor

100
Q

Tightly bound groups attached to cofactors or coenzymes

A

prosthetic groups

101
Q

Cofactors are __ or metal ions digested as __.

A

inorganic ; dietary minerals

102
Q

Coenzymes are __ and are vitamins and their derivatives.

A

organic

103
Q

Water soluble vitamins (coenzymes), which are __ and __ ,are easily secreted.

A

Vitamin B and C

104
Q

Fat soluble vitamins (coenzymes) are __ and __

A

A, D, E, K

105
Q

Michaelis- Menten Kinetics state that if substrate concentration increases then the rate will __ until the ___ also known as saturation.

A

increase ; Vmax

106
Q

The rate of a reaction depends upon the concentration of __ and __.

A

enzyme and substrate

107
Q

At 1/2vmax we have km. Km indicates the __ of a substrate.

A

affinity

108
Q

A low km indicates __ substrate efficiency

A

high

109
Q

A high km indicates __ substrate affinity

A

low

110
Q

kcat/Km is a measure of _

A

catalytic efficency

111
Q

a large kcat indicates __ combined with a small Km this would mean high catalytic efficiency

A

high turnover

112
Q

Km cannot be altered by altering

A

the concentration of enzyme or substrate

113
Q

Lineweaver- Burke plots are useful for __. It is a double reciprocal plot of a Michaelis Menten plot.

A

determining type of inhibition

114
Q

Hill Coefficient > 1

A

positive ; after one is bound the affinity for more to bind increases

115
Q

Hill Coefficient < 1

A

negative ; after one ligand is bound the affinity for more decreases

116
Q

Hill Coefficient = 1

A

enzyme is not exhibiting cooperative binding

117
Q

The impact of temperature on enzyme activity

A

increased temperature and increased enzyme activity 2x every 10 celsius until it denatures

118
Q

The impact of pH on enzyme activity

A

there is maximal activity in small pH range (pH= 7.4 ; gastric = 2 ; pancreas = 8.5). Outside of this range because ionization of active site changes it denatures

119
Q

The impact of salinity on enzymes

A

It can disrupt tertiary and quaternary structures

120
Q

Competitive Inhibition (looks like a gas pedal on lineweaver)

A

Km: increased
Vmax: unaffected
Slope: 1/ Vmax

121
Q

Uncompetitive Inhibition

A

Km: decreased
Vmax: reduced
Slope: Km/ Vmax

122
Q

Noncompetitive Inhibition

A

Km: unaffected
Vmax: reduced
Slope: -1/ Km

123
Q

Mixed Inhibition

A

Km: increases or decreases
Vmax: reduced

124
Q

Irreversible inhibition, unlike reversible, alters the enzyme in a way that the active site is unavailable permanently ; new enzymes must be synthesized for the reaction to occur again. An example is __

A

suicide inhibitors and their covalent bonding

125
Q

Regulatory enzymes can experience activation and inhibition. Allosteric sites __

A

can be occupied by activators which increase affinity or enzymatic turnover

126
Q

Regulatory enzymes can experience activation and inhibition. Phosphorylation, covalent modifications with phosphate, or glycosylation, covalent modifications with carbohydrate, can __

A

alter the selectivity of enzymes

127
Q

Regulatory enzymes like __ are secreted in an inactive form and are activated by cleavage

A

zymogens

128
Q

Carbohydrate Metabolism- Glycolysis generates

A

2 NADH and 2 ATP

129
Q

Carbohydrate Metabolism- Pyruvate dehydrogenase generates

A

1 NADH per pyruvate

130
Q

Carbohydrate Metabolism- Citric Acid Cycle generates

A

3 NADH, 1 FADH2, and 1 GTP

131
Q

Carbohydrate Metabolism- Each NADH generates

A

2.5 ATP ; 10 NADH ; 25 ATP

132
Q

Carbohydrate Metabolism- Each FADH2 generates

A

1.5 ATP ; 2 FADH2 ; 3 ATP

133
Q

Carbohydrate Metabolism- Each molecule of glucose generates

A

32 ATP if completely efficient (2 glycolysis, 2 citric acid cycle, 25 NADH, 3 FADH2)

134
Q

Keratin

A

in epithelial cells ; intermediate filament

135
Q

Tubulin

A

makes up microtubules; periphery + and nucleus -

136
Q

Actin

A

microfilament and myofibril ; has + and - sides

137
Q

Myosin

A

motor protein with movement at neck due to sarcomere contraction

138
Q

Kinesins

A

aligning chrom. in metaphase and depolymerizing during anaphase: bring vesicles to +

139
Q

Dyneins

A

aligning chrom. in metaphase and depolymerizing during anaphase: bring vesicles to -

140
Q

Cell Adhesion Molecule: Cadherins

A

Ca+ dependent binding protein

141
Q

Cell Adhesion Molecule: Integrins

A

cell signaling and host defense binding protein

142
Q

Cell Adhesion Molecule: Selectins

A

binding to carbohydrates as a binding protein

143
Q

Immunoglobulins

A

antibodies specific to antigens

1) neutralize
2) opsonization- marking for destruction
3) agglutinate - clumping together and then phagocytosis

144
Q

GPCR

A

Gs stimulates cAMP levels rise
Gi inhibits cAMP levels lower
Gq activates phospholipase C
binding of G switches to active state

145
Q

Electrophoresis separates proteins based by __ . Negative molecules go to the positive anode and positive go to the negative cathode.

A

charge

146
Q

V= Ez / f

A

electric field x net charge / frictional coefficent

147
Q

Electrophoresis uses an electrolytic cell where delta G is __ 0 and E cell is __ 0

A

> ;

148
Q

Native PAGE

A

complexes stay together and we can compare molecular size or charge of proteins

149
Q

SDS Page

A

SDS disrupts all noncovalent interactions which means the functional protein cannot be recaptured. separation is based on molecular mass
the SDS solubilizes the protein uniformly negative charges

150
Q

Isoelectric Focusing

A

protein stops when pH = pI and separation occurs based on PI. the anode has acidic gel and + charge
you use a gel with a pH gradient that encourages a variable change

151
Q

Chromatography: Column

A

polar composition like silica, alumina with a nonpolar solvent

152
Q

Chromatography: Size-Exclusion

A

porous beads larger molecules will elute first as not trapped in small pores

153
Q

Chromatography: Affinity

A

bound receptor or ligand and eluent with receptor for protein of interest

154
Q

Edman Degradation

A

1) breaks disulfide bonds
2) separate polypeptide chains by chromatography
3) use a method to generate peptides (chemical)
4) use another method to generate peptides (enzymatic)
5) separate peptides by chromatography
6) determine sequence by Edman degradation
7) use overlapping peptide sequences to reconstruct the polypeptide sequence

done at N terminus for amino acid sequencing

155
Q

BCA Assay

A

quantitation of total protein in a sample. The principle of this method is that proteins can reduce Cu+2 to Cu+1 in an alkaline solution (the biuret reaction) and result in a purple color formation by bicinchoninic acid

156
Q

Bradford Protein Assay

A

measure the concentration of total protein in a sample. The principle of this assay is that the binding of protein molecules to Coomassie dye under acidic conditions results in a color change from brown to blue.

157
Q

You can use UV to determine concentration for __ amino acids

A

aromatic

MCAT - Kaplan (6 decks)

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