Quicksheets Biochem Flashcards
1
Q
binding site competitive
A
active site
2
Q
binding site noncompetitive
A
allosteric site
3
Q
binding site mixed
A
allosteric site
4
Q
binding site uncompetitive
A
allosteric site
5
Q
impact on Km- competitive
A
increases
6
Q
impact on Km- noncompetitive
A
no change
7
Q
impact on Km- mixed
A
increases = prefer enzyme decreases = prefer complex
8
Q
impact on Km- uncompetitive
A
decreases
9
Q
impact on vmax- competitive
A
no change
10
Q
impact on vmax- noncompetitive
A
decreases
11
Q
impact on vmax- mixed
A
decreases
12
Q
impact on vmax- uncompetitive
A
decreases
13
Q
structural proteins functioning includes (6)
A
fibrous; collagen, elastin, keratin, actin, tubulin
14
Q
motor proteins function and includes (5)
A
force generation, conformational change, myosin, kinesin, dynein
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
16
Q
Cell adhesion molecules (CAM) function and include (3)
A
binds cell to other cells or surfaces; includes cadherins, integrins, and selectins
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
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
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
20
Q
G protein-coupled receptors
A
have a membrane-bound protein associated with a trimeric G protein.
they also initiate second messenger systems.
21
Q
Aldoses
A
sugars with aldehydes as their most oxidized group
22
Q
Ketoses
A
sugars with ketones as their most oxidized groups
23
Q
triose
A
3 carbon sugar
24
Q
Sugars with the highest-numbered chiral carbon with the -Oh group on the right
A
D-sugars
25
D- and L- forms of the same sugar are known as
enantiomers
26
diastereomers thatt differ at exactly one chiral carbon
epimers
27
diastereomer that differs at the anomeric carbon
anomer
28
anomeric carbon
the new chiral center formed in ring closure
29
α-anomers
have the -OH on the anomeric carbon trans to the free -CH2OH group
30
β-anomers
have the -OH on the anomeric carbon cis to the free --CH2OH group
31
what happens during mutarotation
one anomeric form shifts to another, with the straight chain form as an intermediate
32
Glycoside formaiton
the basis of building complex carbohydrates and requires the anomeric carbon to link another sugar
33
sucrose is also known as
glucose-α-1,2-fructose
34
lactose is also known as
galactose-β-1,4-glucose
35
maltose is also known as
glucose-α-1,4 glucose
36
main structural component of plant cell walls; main source of fiber int eh human diet
cellulose
37
main energy storage forms for plants
starches (amylose and amylopectin)
38
major energy storage form for animals
glycogen
39
5-carbon sugars bonded to a nitrogenous base
nucleoside
40
nucleotides
nucleosides with 1-3 phosphate groups added
41
In RNA, ___ pairs with ___ (via __ hydrogen bonds)
In RNA, A pairs with U; 2 H bonds
42
Chargaff's rules
purines and pyrimidines are equal in number in a DNA molecule; A = T and C = G
43
In eukaryotes, DNA is wound around \_\_\_\_to form ___ which may be stabilized by H1
DNA is wound around histone proteins to form nucleosomes which can be stabilized by another H1
44
Heterochromatin
dense, transcriptionally silent DNA
45
Euchromatin
less dense, transcriptionally active dNA
46
\_\_nm w/ H1; ___ nm w/o H1
30 nm w/ H1 10 nm w/o H1
47
telomeres
ends of chromosomes; contain GC-content to prevent DNA unraveling
48
Centromeres
hold sister chromatids together until they are separated during anaphase in mitosis; also high in GC-content
49
difference in origin of replication between prokaryotic cells and eukaryotic cells
prokaryotic = 1 per chromosome while eukaryotic = multiple/chromosome
50
unwinding of DNA double helix
helicase
51
Stabilization of unwound template strands
SS DNA binding protein
52
Synthesis of RNA primer
Primase
53
difference in synthesis of DNA between prokaryotic cells and eukaryotic cells
prokaryotic cells = DNA polymerase III Eukaryotic cells = DNA polymerase α, δ, and ε
54
difference in removal of RNA primers between prokaryotic cells and eukaryotic cells
Prokaryotes = DNA polymerase I (5'-\> 3' exonuclease) Eukaryotes = RNase H (5'-\> 3' exonuclease)
55
difference in replacement of RNA with DNA between prokaryotic cells and eukaryotic cells
Prokaryotes = DNA polymerase I Eukaryotes = DNA polymerase δ
56
joins Okazaki fragments
DNA ligase
57
Removes positive supercoils ahead of advancing replication forks
DNA topoisomerases
58
synthesis of telomeres
doesn't apply in prokaryotes, applies in telomerase
59
DNA polymerase
synthesizes new DNA strands, reading the template DNA 3' to 5' and synthesizing new strand 5' to 3'
60
the leading strand require..
only one primer and can then be synthesized continuously
61
DNA cloning
introduces a fragment of DNA into a vector plasmid
62
restriction enzyme/endonuclease
cuts both the plasmid and the fragment, leaving them with sticky ends which can bind
63
recombinant DNA
DNA composed of nucleotides from two different sources
64
cDNA libraries (expression libraries)
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
65
Hybridization
the joining of complimentary base pair sequences
66
PCR
Automated process by which millions of copies of a DNA sequence can be created from a very small sample by hybridization
67
DNA molecules can be separated by size using
agarose gel electrophoresis
68
southern blotting
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
69
DNA sequencing uses..which does what and why?
dideoxyribonucleotides which terminate the DNA chain b/c they lack a 3'-OH group
70
Central dogma
DNA -\> RNA -\> proteins
71
\_\_\_ and ___ allow mutations to occur without affecting the protein
redundancy and wobble
72
silent mutations
have no effect on protein synthesis
73
nonsense 9truncation) mutations
produce a premature stop codon
74
missense mutations
produce a codon that codes for a different amino acid
75
frameshift mutations
result from nucleotide addition or deletion and change the reading frame of subsequent codons
76
RNA is structurally similar to DNA expect: (3)
- substitute ribose sugar for deoxyribose - substitute uracil for thymine - single-strand instead of double-strand
77
mRNA
carries the message from DNA in the nucleus via transcription of the gene; travels into eh cytoplasm to be translate
78
tRNA
brings in amino acids; recognizes the codon on the mRNA using its anticodon
79
rRNA
composes much of the ribosome; enzymatically active
80
Transcription steps
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
81
Post transcriptional modifications includ
7-methylguanylate triphosphate cap added to 5' end Poly-A tail added to 3' end splicing by spliceosomes; introns removed and exons ligated together
82
where does translation occur
at the ribosome
83
stages of translation
initiation, elongation, termination
84
post translational modifications include (4)
\* folding by chaperones \* quaternary structure formation \* protein cleave or signal sequences \* covalent addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)
85
control of gene expression in prokaryotes-operons (2)
inducible system (lac operon--typically off but can be turned on) Repressible system (trp operon-- typically on but can be turned off)
86
transcription factors functions
search for promoter and enhancer regions int eh DNA
87
promoters
within 25 bp of the transcription start site
88
enhancers
more than 25 bp away from the transcription start site
89
osmotic pressure
(colligative property) the pressure applied to a pure solvent to prevent osmosis and is related to the concentration of the solution II = iMRT
90
passive transport
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
simple diffusion
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
osmosis
diffusion of water across a selectively permeable membrane
93
facilitated diffusion
uses transport proteins to move impermeable solutes across the cell membrane
94
active transport
requires energy in the form of ATP (primary) or on existing favorable ion gradient (secondary)
95
primary active transport
requires energy in the form of ATP
96
secondary active transport
existing favorable ion gradient
97
Endocytosis
engulfing material into cells
98
exocytosis
releasing material to the exterior of cells
99
pinocytosis
ingestion of liquid into the cell from vesicles formed from the cell membrane
100
phagocytosis
ingestion of solid material
101
glycolysis info - occurs in. - yield - oxygen required?
\* cytoplasm \* no oxygen required \* yield 2 ATP/glucose
102
glucokinase location and function
pancreatic β-islet cells as part of the glucose sensor; responsive to insulin in the liver
103
hexokinase function
traps glucose
104
rate limiting step of glycolysis
PFK1
105
produces F2,6-BP
PFK-2
106
function of F2,6-BP
activates PFK-1
107
what produces NADH in glycolysis
Glyceraldehyde-3-phosphate dehydrogenase
108
what performs substrate-level phosphorylation in glycolysis
3-phosphoglycerate kinase and pyruvate kinase
109
what catalyzes irreversible reactions
glucokinase/hexokinase, PFK-1, and pyruvate kinase
110
The NADH produced in glycolysis is oxidized aerobically by ___ and anaerobically by\_\_\_\_\_\_
oxidized aerobically by the mitochondrial electron transport chain and anaerobically by cytoplasmic lactate dehydrogenase
111
function of pyruvate dehydrogenase; stimulated by and inhibited by
pyruvate dehydrogenase converts pyruvate to acetyl-CoA simulated by insulin inhibited by acetyl-CoA
112
TCA takes place in... main purpose is to...
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
TCA pre-steps
pyruvate uses PDC to form acetyl CoA
114
Formation of acetyl CoA is stimulated by
NAD+
115
Formation by acetyl CoA is inhibited by
NADH, Acetyl-CoA
116
TCA step 1
citrate formation- Acetyl-CoA + oxaloacetate; citrate synthase; gets citrate
117
inhibits citrate synthase (4)
ATP, citrate, NADH, acetyl-COA
118
step 1 TCA - occurs in - type of reaction - reversible/irreversible
- occurs in mitochondrial matrix - condensation reaction - irreversible
119
step 2 TCA - occurs in - type of reaction - creates
- mitochondrial matrix - conformational change (isomerization reaction) - creates a more easily oxidized alcohol
120
Step 2 TCA
citrate is isomerize to isocitrate using aconite (intermediate = cis-aconitate)
121
step 3 TCA
isocitrate uses IDH-\> oxalosuccinate -\> α-ketoglutarate
122
step 3 TCA - occurs in - what makes it unique - reversible/irreversible
- occurs in mitochondrial matrix - first step to generate NADH and produce CO2 - irreversible
123
Step 4 TCA - occurs in - reversible/irreversible
-occurs in mitochondrial matrix - irreversible
124
step 4 TCA
α-ketoglutarate uses the α-ketoglutarate dehydrogenase complex to form succinylcholine-CoA
125
what 2 things make citrate synthase?
oxaloacetate and acetyl-CoA
126
step 4 TCA=
succinyl-CoA and CO2 formation
127
step 5 TCA=
succinate formation
128
Step 5 TCA - occurs in - what makes it unique - energy derived from
- occurs in mitochondrial matrix - substrate levle phosphorylation; GTP is generated directly - energy derived from thirster bond in succinyl-CoA
129
step 6 TCA - occurs in - what makes it unique
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
step 6 TCA =
succinate + Succinate dehydrogenase = Fumarate
131
Step 7 TCA =
fumarate + fumarate = malate
132
step 7 TCA - occurs in - what makes it unique
occurs in mitochondrial matrix H2O added across double bond
133
step 8 TCA occurs in what happens
oxaloacetate reformed - occurs in mitochondrial matrix -oxaloacetate regenerated
134
step 8 TCA =
malate + malate dehydrogenase (MDH) = oxaloacetate
135
in the TCA, ATP and NADH inhibit
PDC, CS, IDH, αΚDC
136
in the TCA, ADP and NAD+ activate
PDC, CS, IDH, αKDC
137
in the TCA, Ca2+ activate
PDC, IDH, αKDC
138
in the TCA, succinylcholine CoA is inhibited by
CS and αKDC
139
Net results of the TCA
2 Acetyl-CoA used 6 NADH made 2 FADH₂ made 2 GTP made
140
ETC takes place in the...
inner mitochondrial membrane
141
shuttle mechanisms in the ETC
glycerol 3-phosphate shuttle Malate-aspartate shuttle
142
Glycolysis net results
2 NADH 2 ATP 2 pyruvate
143
step 1 glycolysis overview
glucose + hexokinase = glucose 6-P
144
what happens in step 1 glycolysis (2) - reversible/irreversible
ATP is hydrolyzed Irreversible traps glucose in cell
145
in glycolysis, hexokinase is inhibited by
buildup of glucose 6-P
146
PFK-2 occurs in the
liver
147
Step 3 glycolysis - what happens - reversible/irreversible
atp is hydrolyzed irreversible rate-limiting step PFK1
148
Step 6 glycolysis - what is generated - intermediate produced - reversible/irreversible
G3P + G3PD = 1,3-BPG NADH is generated produces high-energy intermediate reversible
149
step 7 glycolysis - reversible/irreversible - what is generated - unique?
1,3 bpg + PGK = 3 phosphoglycerate atp is generated substrate-level phosphorylation reversible
150
step 10 glycolysis - reversible/irreversible - what is generated - unique?
PEP + pyruvate kinase = pyruvate ATP is generated substrate-level phosphorylation irreversible
151
proton-motive force
the electrochemical gradient generated by the ETC across the inner mitochondrial membrane
152
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...
chemiosmotic coupling
153
the enzyme responsible for generating ATP from ADP and an inorganic phosphate (Pi)
ATP Synthase
154
Complex I
NADH-CoQ oxidoreductase
155
Complex II
Succinate-CoQ oxidoreductase
156
Complex III
CoQH₂-cytochrome c oxidoreductase
157
Q cycle
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
complex IV
cytochrome c oxidase
159
Glycolysis summary in terms of energy yield
2 NADH 2 ATP
160
Pyruvate dehydrogenase summary in terms of energy yield
1 NADH (2NADH per molecule of glucose b/c each glucose forms 2 molecules of pyruvate)
161
Citric acid cycle summary in terms of energy yield
3 NADH 1 FADH2 1 GTP double per molecule of glucose
162
Each NADH summary in terms of energy yield
2.5 ATP
163
Each FADH2 summary in terms of energy yield
1.5 ATP
164
Total energy yield per molecule of glucose
30-32 ATP
165
glycogenesis
building glycogen using glycogen synthase and branching enzyme
166
glycogen synthase and what it's activated by
creates α-1,4 glycosidic links between glucose molecules; activated by insulin in the liver and muscles
167
branching enzyme-- what it does and what it uses
it moves a block of oligoglucose from one chain and connects it as a branch using an α-1,6 glycosidic link
168
glycogenolysis
breakdown of glycogen using glycogen phosphorylase and debranching enzyme
169
glycogen phosphorylase
remove single glucose 1-phosphate molecules by breaking α-1,4 glycosidic links
170
in the liver, glycogen phosphorylase is activated by
glucagon to prevent low blood sugar
171
in exercising skeletal muscle, glycogen phosphorylase is activated by
epinephrine and AMP to provide glucose for the muscle
172
Debranching enzyme function
moves a block of oligoglucose from one branch and connects it to the chain using an α,1-4 glycosidic link
173
Gluconeogenesis occurs in the... and predominantly in the
occurs in the cytoplasm and mitochondria, but predominantly in the liver
174
three irreversible steps of glycolysis and what enzymes bypass
- pyruvate carboxylase and PEP carboxykinase bypass pyruvate kinase - fructose-1,6-bisphosphate bypasses phosphofructokinase-1 - Glucose-6-phosphatase bypasses hexokinase/glucokinase
175
pentose phosphate pathway occurs in the.... generates.. rate limiting step... activated by... inhibited by...
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
The key enzyme in cholesterol biosynthesis is
HMG-CoA reductase
177
the only fatty acid that humans can synthesize =
palmitic acid
178
palmitic acid is produced in the---
palmitic acid is produced in the cytoplasm from acetyl-CoA transported out of the mitochondria
179
Fatty acid oxidation occurs in the-=...
fatty acid oxidation occurs in the mitochondria; following transport by the carnet shuttle, via β-oxidation
180
what happens under prolonged starvation?
ketone bodies form due to excess acetyl-CoA in the liver
181
Ketolysis
regenerates acetyl-CoA for use as an energy source in peripheral tissues
182
protein digestion occurs primarily in the...
small intestine
183
Describe what happens in the postpradial state
the postprandial state is the well-fed (absorptive) state where insulin secretion is high and anabolic metabolism prevails
184
describe what happens in the post absorptive state
this is the fasting state and insulin secretion decreases while glucagon and catecholamine secretion increases
185
describes what happens in prolonged fasting state
glucagon and catecholamine secretion increase and most tissues rely on fatty acids
186
tissue-specific metabolism: liver
blood glucose maintained through glycogenolysis and gluconeogenesis Processes lipids, cholesterol, bile, urea, and toxins
187
tissue-specific metabolism: adipose
stores and releases lipids
188
tissue-specific metabolism: resting muscle
conserves carbohydrates as glycogen and uses free fatty acids for fuel
189
tissue-specific metabolism: active muscle
may use anaerobic metabolism, oxidative phosphorylation, direct phosphorylation (creatine phosphate), or fatty acid oxidation
190
tissue-specific metabolism: cardiac muscle uses
fatty acid oxidation
191
tissue-specific metabolism: brain uses
glucose except in prolonged starvation where it can use ketolysis
192
All amino acids are chiral (L) except for
glycine
193
All aminoa cids have S configuration except for
cysteine
194
Nonpolar, nonaromatic amino acids include
G, L, A, M, V, I, P
195
Positively charged amino acids include
R, K, H
196
Negatively chaged amino acids
D, E
197
polar amino acids
S, T, C, N, Q
198
Aromatic side chain amino aicds
W, F, Y
199
Amino acids in low ph =
fully protonated
200
amino acids at high (basic) pH =
fully deprotontated
201
pI is determined by
average the pKa values that refer to protonation and deprotonation of the zwitterion
202
Peptide bond formation:
- type of reaction
- how it happens
- what the bonds are broken by
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
Primary structure
linear structure of amino acids
204
secondary structure
local structure; stabilized by H bonding; includes α helices and β-pleated sheets
205
Tertiary structure
3D structure stabilized by hydrophobic interactions, acid-base interactions (salt bridges), H bonding, and disulfide bonds
2 cysteine moleucles = cystine +2H+ + 2e-
206
Quaternary structure
interactionsbetween subunits; heat and solutes can cause denaturation
207
effect of enzymes on activation energy, ∆G, ∆H, and kinetics
enzymes:
- Lower activation energy
- don't alter ∆G or ∆H
- change the rate (kinetics) at which equilibrium is reached
208
Cooperative enzymes show a ____ curve
sigmoidal
209
Ligases
joins two large biomolecules, often of the same type
210
isomerases
catalyze the interconversion of isomers, including both constitutional and stereoisomers
211
Lyases
catalyze cleavage w/o the addition of water and w/o the transfer of electrons
212
reverse reaction of lyase is
synthesis
213
hydrolase
catalyze cleavage with the addition of water
214
oxidoreductases
catalyze oxidaiton-reduction reactions that involve the transfer of electorns
215
transferases
move a functional group form one molecule to another
216
relationship between substrate concentration and reaction rate
as substrate concentration increases, reaction rate also inreases until a max value is reached
217
enzyme kinetics v equation
v = vmax[s]/Km+[s]
218
at 1/2 vmax, [S] =?
At 1/2 vmax, [S] = Km
219
D-fructose
220
D-glucose
221
D-galactose
222
D-mannose
