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Quicksheets Biochem Flashcards

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1
Q

binding site competitive

A

active site

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2
Q

binding site noncompetitive

A

allosteric site

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3
Q

binding site mixed

A

allosteric site

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4
Q

binding site uncompetitive

A

allosteric site

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5
Q

impact on Km- competitive

A

increases

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6
Q

impact on Km- noncompetitive

A

no change

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7
Q

impact on Km- mixed

A

increases = prefer enzyme decreases = prefer complex

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8
Q

impact on Km- uncompetitive

A

decreases

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9
Q

impact on vmax- competitive

A

no change

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10
Q

impact on vmax- noncompetitive

A

decreases

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11
Q

impact on vmax- mixed

A

decreases

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12
Q

impact on vmax- uncompetitive

A

decreases

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13
Q

structural proteins functioning includes (6)

A

fibrous; collagen, elastin, keratin, actin, tubulin

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14
Q

motor proteins function and includes (5)

A

force generation, conformational change, myosin, kinesin, dynein

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15
Q

binding proteins function and why

A

binds to a specific substrate, either to sequester it in the body or hold its concentration at steady state

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16
Q

Cell adhesion molecules (CAM) function and include (3)

A

binds cell to other cells or surfaces; includes cadherins, integrins, and selectins

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17
Q

Antibodies (ig)

A

target a specific antigen, which may be a protein on the surface of a pathogen (invading organism) or a toxin

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18
Q

ion channel functions and types (3)

A

ion channels can be used for regulating ion flow into or out of a cell;

includes ungated channels, voltage-gated and ligand-gated channels

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19
Q

enzyme-linked receptors function and what they use to do it

A

cell-signaling through extracellular ligand binding and initiation of second messenger cascades

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20
Q

G protein-coupled receptors

A

have a membrane-bound protein associated with a trimeric G protein.

they also initiate second messenger systems.

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21
Q

Aldoses

A

sugars with aldehydes as their most oxidized group

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22
Q

Ketoses

A

sugars with ketones as their most oxidized groups

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23
Q

triose

A

3 carbon sugar

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24
Q

Sugars with the highest-numbered chiral carbon with the -Oh group on the right

A

D-sugars

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25
Q

D- and L- forms of the same sugar are known as

A

enantiomers

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26
Q

diastereomers thatt differ at exactly one chiral carbon

A

epimers

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27
Q

diastereomer that differs at the anomeric carbon

A

anomer

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28
Q

anomeric carbon

A

the new chiral center formed in ring closure

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29
Q

α-anomers

A

have the -OH on the anomeric carbon trans to the free -CH2OH group

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30
Q

β-anomers

A

have the -OH on the anomeric carbon cis to the free –CH2OH group

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31
Q

what happens during mutarotation

A

one anomeric form shifts to another, with the straight chain form as an intermediate

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32
Q

Glycoside formaiton

A

the basis of building complex carbohydrates and requires the anomeric carbon to link another sugar

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33
Q

sucrose is also known as

A

glucose-α-1,2-fructose

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34
Q

lactose is also known as

A

galactose-β-1,4-glucose

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35
Q

maltose is also known as

A

glucose-α-1,4 glucose

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36
Q

main structural component of plant cell walls; main source of fiber int eh human diet

A

cellulose

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37
Q

main energy storage forms for plants

A

starches (amylose and amylopectin)

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38
Q

major energy storage form for animals

A

glycogen

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39
Q

5-carbon sugars bonded to a nitrogenous base

A

nucleoside

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40
Q

nucleotides

A

nucleosides with 1-3 phosphate groups added

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41
Q

In RNA, ___ pairs with ___ (via __ hydrogen bonds)

A

In RNA, A pairs with U; 2 H bonds

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42
Q

Chargaff’s rules

A

purines and pyrimidines are equal in number in a DNA molecule; A = T and C = G

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43
Q

In eukaryotes, DNA is wound around ____to form ___ which may be stabilized by H1

A

DNA is wound around histone proteins to form nucleosomes which can be stabilized by another H1

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44
Q

Heterochromatin

A

dense, transcriptionally silent DNA

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45
Q

Euchromatin

A

less dense, transcriptionally active dNA

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46
Q

__nm w/ H1; ___ nm w/o H1

A

30 nm w/ H1 10 nm w/o H1

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47
Q

telomeres

A

ends of chromosomes; contain GC-content to prevent DNA unraveling

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48
Q

Centromeres

A

hold sister chromatids together until they are separated during anaphase in mitosis; also high in GC-content

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49
Q

difference in origin of replication between prokaryotic cells and eukaryotic cells

A

prokaryotic = 1 per chromosome while eukaryotic = multiple/chromosome

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50
Q

unwinding of DNA double helix

A

helicase

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51
Q

Stabilization of unwound template strands

A

SS DNA binding protein

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52
Q

Synthesis of RNA primer

A

Primase

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53
Q

difference in synthesis of DNA between prokaryotic cells and eukaryotic cells

A

prokaryotic cells = DNA polymerase III Eukaryotic cells = DNA polymerase α, δ, and ε

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54
Q

difference in removal of RNA primers between prokaryotic cells and eukaryotic cells

A

Prokaryotes = DNA polymerase I (5’-> 3’ exonuclease) Eukaryotes = RNase H (5’-> 3’ exonuclease)

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55
Q

difference in replacement of RNA with DNA between prokaryotic cells and eukaryotic cells

A

Prokaryotes = DNA polymerase I Eukaryotes = DNA polymerase δ

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56
Q

joins Okazaki fragments

A

DNA ligase

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57
Q

Removes positive supercoils ahead of advancing replication forks

A

DNA topoisomerases

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58
Q

synthesis of telomeres

A

doesn’t apply in prokaryotes, applies in telomerase

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59
Q

DNA polymerase

A

synthesizes new DNA strands, reading the template DNA 3’ to 5’ and synthesizing new strand 5’ to 3’

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60
Q

the leading strand require..

A

only one primer and can then be synthesized continuously

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61
Q

DNA cloning

A

introduces a fragment of DNA into a vector plasmid

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62
Q

restriction enzyme/endonuclease

A

cuts both the plasmid and the fragment, leaving them with sticky ends which can bind

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63
Q

recombinant DNA

A

DNA composed of nucleotides from two different sources

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64
Q

cDNA libraries (expression libraries)

A

contain smaller fragments of DNA and only include the eons of genes expressed by the sample tissue; can be used to make recombinant proteins or for gene therapy

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65
Q

Hybridization

A

the joining of complimentary base pair sequences

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66
Q

PCR

A

Automated process by which millions of copies of a DNA sequence can be created from a very small sample by hybridization

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67
Q

DNA molecules can be separated by size using

A

agarose gel electrophoresis

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68
Q

southern blotting

A

detect presence and quantity of various DNA strands in a sample after electrophoresis, the sample is transferred to a membrane that can be probed with ssDNA molecules to look for a sequence of interest

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69
Q

DNA sequencing uses..which does what and why?

A

dideoxyribonucleotides which terminate the DNA chain b/c they lack a 3’-OH group

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70
Q

Central dogma

A

DNA -> RNA -> proteins

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71
Q

___ and ___ allow mutations to occur without affecting the protein

A

redundancy and wobble

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72
Q

silent mutations

A

have no effect on protein synthesis

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73
Q

nonsense 9truncation) mutations

A

produce a premature stop codon

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74
Q

missense mutations

A

produce a codon that codes for a different amino acid

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75
Q

frameshift mutations

A

result from nucleotide addition or deletion and change the reading frame of subsequent codons

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76
Q

RNA is structurally similar to DNA expect: (3)

A
  • substitute ribose sugar for deoxyribose - substitute uracil for thymine - single-strand instead of double-strand
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77
Q

mRNA

A

carries the message from DNA in the nucleus via transcription of the gene; travels into eh cytoplasm to be translate

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78
Q

tRNA

A

brings in amino acids; recognizes the codon on the mRNA using its anticodon

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79
Q

rRNA

A

composes much of the ribosome; enzymatically active

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80
Q

Transcription steps

A

1) helices and topoisomerase unwind DNA double helix 2) RNA polymerase II binds to TATA box within promoter region of gene (25 bp upstream from first transcribed base) 3) hnRNA synthesized from DNA template (antisense) strand

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81
Q

Post transcriptional modifications includ

A

7-methylguanylate triphosphate cap added to 5’ end Poly-A tail added to 3’ end splicing by spliceosomes; introns removed and exons ligated together

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82
Q

where does translation occur

A

at the ribosome

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83
Q

stages of translation

A

initiation, elongation, termination

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84
Q

post translational modifications include (4)

A

* folding by chaperones * quaternary structure formation * protein cleave or signal sequences * covalent addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)

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85
Q

control of gene expression in prokaryotes-operons (2)

A

inducible system (lac operon–typically off but can be turned on) Repressible system (trp operon– typically on but can be turned off)

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86
Q

transcription factors functions

A

search for promoter and enhancer regions int eh DNA

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87
Q

promoters

A

within 25 bp of the transcription start site

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88
Q

enhancers

A

more than 25 bp away from the transcription start site

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89
Q

osmotic pressure

A

(colligative property) the pressure applied to a pure solvent to prevent osmosis and is related to the concentration of the solution II = iMRT

90
Q

passive transport

A

doesn’t require ATP b/c the molecule is moving down its concentration gradient (area of high concentration to an area of low concentration)

91
Q

simple diffusion

A

no transporter required small non polar molecules passively move from an area of high concentration to an area of low concentration until equilibrium is achieved

92
Q

osmosis

A

diffusion of water across a selectively permeable membrane

93
Q

facilitated diffusion

A

uses transport proteins to move impermeable solutes across the cell membrane

94
Q

active transport

A

requires energy in the form of ATP (primary) or on existing favorable ion gradient (secondary)

95
Q

primary active transport

A

requires energy in the form of ATP

96
Q

secondary active transport

A

existing favorable ion gradient

97
Q

Endocytosis

A

engulfing material into cells

98
Q

exocytosis

A

releasing material to the exterior of cells

99
Q

pinocytosis

A

ingestion of liquid into the cell from vesicles formed from the cell membrane

100
Q

phagocytosis

A

ingestion of solid material

101
Q

glycolysis info - occurs in. - yield - oxygen required?

A

* cytoplasm * no oxygen required * yield 2 ATP/glucose

102
Q

glucokinase location and function

A

pancreatic β-islet cells as part of the glucose sensor; responsive to insulin in the liver

103
Q

hexokinase function

A

traps glucose

104
Q

rate limiting step of glycolysis

A

PFK1

105
Q

produces F2,6-BP

A

PFK-2

106
Q

function of F2,6-BP

A

activates PFK-1

107
Q

what produces NADH in glycolysis

A

Glyceraldehyde-3-phosphate dehydrogenase

108
Q

what performs substrate-level phosphorylation in glycolysis

A

3-phosphoglycerate kinase and pyruvate kinase

109
Q

what catalyzes irreversible reactions

A

glucokinase/hexokinase, PFK-1, and pyruvate kinase

110
Q

The NADH produced in glycolysis is oxidized aerobically by ___ and anaerobically by______

A

oxidized aerobically by the mitochondrial electron transport chain and anaerobically by cytoplasmic lactate dehydrogenase

111
Q

function of pyruvate dehydrogenase; stimulated by and inhibited by

A

pyruvate dehydrogenase converts pyruvate to acetyl-CoA simulated by insulin inhibited by acetyl-CoA

112
Q

TCA takes place in… main purpose is to…

A

TCA takes place in mitochondrial matrix main purpose = oxidize acetyl-CoA to CO2 and generate high-energy electron carriers (NADH and FADH2) and GTP

113
Q

TCA pre-steps

A

pyruvate uses PDC to form acetyl CoA

114
Q

Formation of acetyl CoA is stimulated by

A

NAD+

115
Q

Formation by acetyl CoA is inhibited by

A

NADH, Acetyl-CoA

116
Q

TCA step 1

A

citrate formation- Acetyl-CoA + oxaloacetate; citrate synthase; gets citrate

117
Q

inhibits citrate synthase (4)

A

ATP, citrate, NADH, acetyl-COA

118
Q

step 1 TCA - occurs in - type of reaction - reversible/irreversible

A
  • occurs in mitochondrial matrix - condensation reaction - irreversible
119
Q

step 2 TCA - occurs in - type of reaction - creates

A
  • mitochondrial matrix - conformational change (isomerization reaction) - creates a more easily oxidized alcohol
120
Q

Step 2 TCA

A

citrate is isomerize to isocitrate using aconite (intermediate = cis-aconitate)

121
Q

step 3 TCA

A

isocitrate uses IDH-> oxalosuccinate -> α-ketoglutarate

122
Q

step 3 TCA - occurs in - what makes it unique - reversible/irreversible

A
  • occurs in mitochondrial matrix - first step to generate NADH and produce CO2 - irreversible
123
Q

Step 4 TCA - occurs in - reversible/irreversible

A

-occurs in mitochondrial matrix - irreversible

124
Q

step 4 TCA

A

α-ketoglutarate uses the α-ketoglutarate dehydrogenase complex to form succinylcholine-CoA

125
Q

what 2 things make citrate synthase?

A

oxaloacetate and acetyl-CoA

126
Q

step 4 TCA=

A

succinyl-CoA and CO2 formation

127
Q

step 5 TCA=

A

succinate formation

128
Q

Step 5 TCA - occurs in - what makes it unique - energy derived from

A
  • occurs in mitochondrial matrix - substrate levle phosphorylation; GTP is generated directly - energy derived from thirster bond in succinyl-CoA
129
Q

step 6 TCA - occurs in - what makes it unique

A

fumarate formation occurs in mitochondrial membrane - SDH is also a member protein of the ETC - FAD is covalently bonded to SDH - only step that produces FADH2

130
Q

step 6 TCA =

A

succinate + Succinate dehydrogenase = Fumarate

131
Q

Step 7 TCA =

A

fumarate + fumarate = malate

132
Q

step 7 TCA - occurs in - what makes it unique

A

occurs in mitochondrial matrix H2O added across double bond

133
Q

step 8 TCA occurs in what happens

A

oxaloacetate reformed - occurs in mitochondrial matrix -oxaloacetate regenerated

134
Q

step 8 TCA =

A

malate + malate dehydrogenase (MDH) = oxaloacetate

135
Q

in the TCA, ATP and NADH inhibit

A

PDC, CS, IDH, αΚDC

136
Q

in the TCA, ADP and NAD+ activate

A

PDC, CS, IDH, αKDC

137
Q

in the TCA, Ca2+ activate

A

PDC, IDH, αKDC

138
Q

in the TCA, succinylcholine CoA is inhibited by

A

CS and αKDC

139
Q

Net results of the TCA

A

2 Acetyl-CoA used 6 NADH made 2 FADH₂ made 2 GTP made

140
Q

ETC takes place in the…

A

inner mitochondrial membrane

141
Q

shuttle mechanisms in the ETC

A

glycerol 3-phosphate shuttle Malate-aspartate shuttle

142
Q

Glycolysis net results

A

2 NADH 2 ATP 2 pyruvate

143
Q

step 1 glycolysis overview

A

glucose + hexokinase = glucose 6-P

144
Q

what happens in step 1 glycolysis (2) - reversible/irreversible

A

ATP is hydrolyzed Irreversible traps glucose in cell

145
Q

in glycolysis, hexokinase is inhibited by

A

buildup of glucose 6-P

146
Q

PFK-2 occurs in the

A

liver

147
Q

Step 3 glycolysis - what happens - reversible/irreversible

A

atp is hydrolyzed irreversible rate-limiting step PFK1

148
Q

Step 6 glycolysis - what is generated - intermediate produced - reversible/irreversible

A

G3P + G3PD = 1,3-BPG NADH is generated produces high-energy intermediate reversible

149
Q

step 7 glycolysis - reversible/irreversible - what is generated - unique?

A

1,3 bpg + PGK = 3 phosphoglycerate atp is generated substrate-level phosphorylation reversible

150
Q

step 10 glycolysis - reversible/irreversible - what is generated - unique?

A

PEP + pyruvate kinase = pyruvate ATP is generated substrate-level phosphorylation irreversible

151
Q

proton-motive force

A

the electrochemical gradient generated by the ETC across the inner mitochondrial membrane

152
Q

the inter membrane space has a higher concentration of protons than the matrix; this gradient stores energy, which can be used to form ATP via…

A

chemiosmotic coupling

153
Q

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

A

ATP Synthase

154
Q

Complex I

A

NADH-CoQ oxidoreductase

155
Q

Complex II

A

Succinate-CoQ oxidoreductase

156
Q

Complex III

A

CoQH₂-cytochrome c oxidoreductase

157
Q

Q cycle

A

complex III two electrons are shuttled from a molecule of ubiquinol (CoQH₂) near the intermembrane space to a molecule of ubiquinone (CoQ) near the mitochondrial matrix

158
Q

complex IV

A

cytochrome c oxidase

159
Q

Glycolysis summary in terms of energy yield

A

2 NADH 2 ATP

160
Q

Pyruvate dehydrogenase summary in terms of energy yield

A

1 NADH (2NADH per molecule of glucose b/c each glucose forms 2 molecules of pyruvate)

161
Q

Citric acid cycle summary in terms of energy yield

A

3 NADH 1 FADH2 1 GTP double per molecule of glucose

162
Q

Each NADH summary in terms of energy yield

A

2.5 ATP

163
Q

Each FADH2 summary in terms of energy yield

A

1.5 ATP

164
Q

Total energy yield per molecule of glucose

A

30-32 ATP

165
Q

glycogenesis

A

building glycogen using glycogen synthase and branching enzyme

166
Q

glycogen synthase and what it’s activated by

A

creates α-1,4 glycosidic links between glucose molecules; activated by insulin in the liver and muscles

167
Q

branching enzyme– what it does and what it uses

A

it moves a block of oligoglucose from one chain and connects it as a branch using an α-1,6 glycosidic link

168
Q

glycogenolysis

A

breakdown of glycogen using glycogen phosphorylase and debranching enzyme

169
Q

glycogen phosphorylase

A

remove single glucose 1-phosphate molecules by breaking α-1,4 glycosidic links

170
Q

in the liver, glycogen phosphorylase is activated by

A

glucagon to prevent low blood sugar

171
Q

in exercising skeletal muscle, glycogen phosphorylase is activated by

A

epinephrine and AMP to provide glucose for the muscle

172
Q

Debranching enzyme function

A

moves a block of oligoglucose from one branch and connects it to the chain using an α,1-4 glycosidic link

173
Q

Gluconeogenesis occurs in the… and predominantly in the

A

occurs in the cytoplasm and mitochondria, but predominantly in the liver

174
Q

three irreversible steps of glycolysis and what enzymes bypass

A
  • pyruvate carboxylase and PEP carboxykinase bypass pyruvate kinase - fructose-1,6-bisphosphate bypasses phosphofructokinase-1 - Glucose-6-phosphatase bypasses hexokinase/glucokinase
175
Q

pentose phosphate pathway occurs in the…. generates.. rate limiting step… activated by… inhibited by…

A

Pentose phosphate pathway: - occurs in the cytoplasm - generates NADPH and sugars - Rate limiting enzyme is G6PD - activated by NADP+ and insulin - Inhibited by NADPH

176
Q

The key enzyme in cholesterol biosynthesis is

A

HMG-CoA reductase

177
Q

the only fatty acid that humans can synthesize =

A

palmitic acid

178
Q

palmitic acid is produced in the—

A

palmitic acid is produced in the cytoplasm from acetyl-CoA transported out of the mitochondria

179
Q

Fatty acid oxidation occurs in the-=…

A

fatty acid oxidation occurs in the mitochondria; following transport by the carnet shuttle, via β-oxidation

180
Q

what happens under prolonged starvation?

A

ketone bodies form due to excess acetyl-CoA in the liver

181
Q

Ketolysis

A

regenerates acetyl-CoA for use as an energy source in peripheral tissues

182
Q

protein digestion occurs primarily in the…

A

small intestine

183
Q

Describe what happens in the postpradial state

A

the postprandial state is the well-fed (absorptive) state where insulin secretion is high and anabolic metabolism prevails

184
Q

describe what happens in the post absorptive state

A

this is the fasting state and insulin secretion decreases while glucagon and catecholamine secretion increases

185
Q

describes what happens in prolonged fasting state

A

glucagon and catecholamine secretion increase and most tissues rely on fatty acids

186
Q

tissue-specific metabolism: liver

A

blood glucose maintained through glycogenolysis and gluconeogenesis Processes lipids, cholesterol, bile, urea, and toxins

187
Q

tissue-specific metabolism: adipose

A

stores and releases lipids

188
Q

tissue-specific metabolism: resting muscle

A

conserves carbohydrates as glycogen and uses free fatty acids for fuel

189
Q

tissue-specific metabolism: active muscle

A

may use anaerobic metabolism, oxidative phosphorylation, direct phosphorylation (creatine phosphate), or fatty acid oxidation

190
Q

tissue-specific metabolism: cardiac muscle uses

A

fatty acid oxidation

191
Q

tissue-specific metabolism: brain uses

A

glucose except in prolonged starvation where it can use ketolysis

192
Q

All amino acids are chiral (L) except for

A

glycine

193
Q

All aminoa cids have S configuration except for

A

cysteine

194
Q

Nonpolar, nonaromatic amino acids include

A

G, L, A, M, V, I, P

195
Q

Positively charged amino acids include

A

R, K, H

196
Q

Negatively chaged amino acids

A

D, E

197
Q

polar amino acids

A

S, T, C, N, Q

198
Q

Aromatic side chain amino aicds

A

W, F, Y

199
Q

Amino acids in low ph =

A

fully protonated

200
Q

amino acids at high (basic) pH =

A

fully deprotontated

201
Q

pI is determined by

A

average the pKa values that refer to protonation and deprotonation of the zwitterion

202
Q

Peptide bond formation:

  • type of reaction
  • how it happens
  • what the bonds are broken by
A

Peptide bond formation is a condensation/dehydration reaction.

formed with a nucleophilic amino group attacking an electrophilic carbonyl

peptide bonds are broken by hydrolysis

203
Q

Primary structure

A

linear structure of amino acids

204
Q

secondary structure

A

local structure; stabilized by H bonding; includes α helices and β-pleated sheets

205
Q

Tertiary structure

A

3D structure stabilized by hydrophobic interactions, acid-base interactions (salt bridges), H bonding, and disulfide bonds

2 cysteine moleucles = cystine +2H+ + 2e-

206
Q

Quaternary structure

A

interactionsbetween subunits; heat and solutes can cause denaturation

207
Q

effect of enzymes on activation energy, ∆G, ∆H, and kinetics

A

enzymes:

  • Lower activation energy
  • don’t alter ∆G or ∆H
  • change the rate (kinetics) at which equilibrium is reached
208
Q

Cooperative enzymes show a ____ curve

A

sigmoidal

209
Q

Ligases

A

joins two large biomolecules, often of the same type

210
Q

isomerases

A

catalyze the interconversion of isomers, including both constitutional and stereoisomers

211
Q

Lyases

A

catalyze cleavage w/o the addition of water and w/o the transfer of electrons

212
Q

reverse reaction of lyase is

A

synthesis

213
Q

hydrolase

A

catalyze cleavage with the addition of water

214
Q

oxidoreductases

A

catalyze oxidaiton-reduction reactions that involve the transfer of electorns

215
Q

transferases

A

move a functional group form one molecule to another

216
Q

relationship between substrate concentration and reaction rate

A

as substrate concentration increases, reaction rate also inreases until a max value is reached

217
Q

enzyme kinetics v equation

A

v = vmax[s]/Km+[s]

218
Q

at 1/2 vmax, [S] =?

A

At 1/2 vmax, [S] = Km

219
Q
A

D-fructose

220
Q
A

D-glucose

221
Q
A

D-galactose

222
Q
A

D-mannose

Kaplan mcat flashcards (8 decks)

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