Biochemistry Flashcards
(124 cards)
1
Q
Amino Acids: w/ non-polar, non-aromatic side chains (7)
A
Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline
2
Q
Amino Acids: w/ Aromatic side chain, uncharged (3)
A
Tryptophan, Phenylalaline, Tyrosine
3
Q
Amino Acids: w/ polar side chains (5)
A
Serine, Threonine, Asparagine, Glutamine, Cysteine
4
Q
Amino Acids: w/ negatively charged, acidic side chains (2)
A
Aspartic Acid (aspartate), Glutamic Acid (glutamate)
5
Q
Amino Acids: w/ positively charged, basic side chains (3)
A
Lysine, Arginine, and Histidine
6
Q
Ionizable groups _____ protons under acidic conditions
A
gain protons
low pH tends to protonate groups
7
Q
Ionizable groups _____ protons under basic conditions
A
lose protons
high pH tend to de-protonate groups
8
Q
pka of carboxyl groups
A
2
9
Q
pka of amino group
A
9-10
10
Q
plane geometry of sp2 and sp3 hybridizations
A
sp2 bonds fall within the same plane
sp3 bonds do not fall within the same plane
11
Q
Primary protein structure
A
linear (N term to C term)
stabilized by covalent bonds between adjacent amino aicds
12
Q
Secondary protein structure
A
local structure, due to H bonding between near amino acids
alpha-helices and beta-pleated sheets
13
Q
Tertiary protein structure
A
protein folding
determined by hydrophilic and hydrophobic interactions between R groups
and disulfide bonds
14
Q
Quaternary Structure
A
not all proteins have this
aggregate multiple subunits, Hb
Purpose: reduce surface area, bring catalytic sites together
15
Q
Enzyme Classifications (6)
A
LI'L HOT Oxidoreductases Transferases Hydrolases Lysases Isomerases Ligases
16
Q
Oxidoreductases
A
catalyze redox reactions
reductant (e- donor) and oxidant (e- acceptor)
common names: “dehydrogenase” “reductase” “oxidase”
17
Q
Transferases
A
catalyze movement functional group from one to another
“kinases” catalyze movement of phosphate group
18
Q
Hydrolases
A
catalyze breaking compound into two using H2O
“phosphatase, nucleases, lipase”
[substrate]hydrolase, [substrate]ase
19
Q
Lyases
A
catalyze cleavage of a single molecule into two products (without water)
can catalyze the reverse
“synthase”
20
Q
Isomerases
A
catalyze rearrangement of bonds within a molecule (stereoisomers and constitutional isomers)
-Can be considered oxidoreductase, transferase, lyase, but NOT ligase
21
Q
Ligase
A
catalyze addition or synthesis reactions
require ATP (all ligases require it)
[substrate] synthase, [substrate] synthetase
22
Q
5 ways to reduce activation energy
A
- Transition state stabilization
- Microenvironment Adjustments
- Adjusting substrate proximity
- Transient Covalent bonding
- Reactant destabilization
23
Q
Apoenzymes
A
enzymes without their cofactor
24
Q
Holoenzymes
A
enzymes with their cofactor
25
Prosthetic groups
tightly bound cofactors/coenzymes necessary for enzyme function
26
Cofactors
inorganic molecules, metal ions, ingested dietary minerals
27
Coenzymes
small organic groups, vitamins, their derivatives
28
Water soluble vitamins
```
ascorbic acid (vitamin C)
B complex vitamins
```
29
B complex vitamins (1,2,3,5,6,7,9,12)
```
1- thiamine
2- riboflavin
3- niacin
5- pantothenic acid
6- pyridoxal phosphate
7- biotin
9- folic acid
12- cyanocobalamin
```
30
Fat soluble vitamins
Vitamin A, D, E, K
31
Michaelis Menten constant
```
Km = velocity at 1/2 Vmax
measure of E-S affinity
faster enzyme (greater affinity) low Km
```
32
Types of Reversible Inhibitions
Competitive, noncompetitive, mixed, uncompetitive
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Competitive Inhibition
occupies active site, inhibitor can completely block
-will be overcome by an increase in [S]
no effect on Vmax, increases Km
34
Noncompetitive Inhibition
bind to allosteric sites instead of active site (changes enzyme conformation)
do not compete for the same site, cannot be overcome by increase in [S]
decreases Vmax, no effect on Km
35
Mixed Inhibition
can bind to enzyme or E-S complex (different affinities)
binds at allosteric sites
changes Km depending on binding affinity
-if it prefers enzyme = increases Km
-if it prefers E-S complex = decreases Km
36
Uncompetitive Inhibition
bind only to ES complex, locks S in place and prevents release
decreases BOTH Vmax and Km
37
Irreversible Inhibition
- active site unavailable for prolonged period
- enzyme is permanently altered
- prime drug mechanism
- cannot reverse w/ removal of irreversible enzymes
38
Regulated Enzymes (3)
1. Allosteric Enzymes
2. Covalently Modified Enzymes
3. Zymogens
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Allosteric Enzymes
multiple binding sites
| molecules binding to the allosteric site are either activators or inhibitors -- causes a conformational change
40
Covalently Modified Enzymes
activated or deactivated by phosphorylations or dephosphorylation
41
Zymogens
```
some enzymes are quite dangerous, and are released in their inactive forms
contain catalytic (active) domain and regulatory domain
```
42
5 Primary Structure proteins
1. Collagen
2. Elastin
3. Keratin
4. Actin
5. Tubulin
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Collagen
extracellular matrix of connective tissue, strength and flexibility
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Elastin
Important component of extracellular matrix of connective tissue
fx. straighten/recoil like a spring
45
Keratin
intermediate filament proteins in epithelial cells
fx. mechanical integrity of cells (hair and nails)
regulatory protein
46
Actin
component of microfilaments and thin filaments in myofibrils
most abundant in eukaryotic cells
polarity = allows motor proteins to travel unidirectionally
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Tubulin
component of microtubules -- structure, chromosome separation, intracellular support
polarity
48
3 Motor Proteins
1. Myosin
2. Kinesins
3. Dyneins
49
Myosin
primary motor protein
interacts with actin
thick filament in myofibril and cellular transport
50
Kinesins
motor protein associated with microtubules
| 2 heads remain attached to tubulin always = aligns chromosomes
51
Dyneins
associated with microtubules and 2 heads (one always attached to tubulin)
52
Cell Adhesion Molecules (CAMs) (3)
Cadherins
Integrins
Selectins
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Cadherins
glycoproteins mediate calcium dependent cell adhesion
54
Integrins
extracellular matrix binding, signaling, promoting cell adhesion
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Selectins
bind carbohydrate molecules, weakest type, expressed in cells that line blood vessels, vital role in inflammation and defense
56
Biosignaling: Ion channels
via Facilitated Diffusion
1. Ungated channels: no gates (potassium channels)
2. Voltage-gated channels: regulated by membrane potential change
3. Ligand-gated channels: binding to channel causes it to open and close
57
Three primary protein domains (enzyme linked receptors)
Membrane-spanning Domain
Ligand-binding Domain
Catalytic Domain
58
Electrophoresis
using an electric field
proteins move according to NET charge and SIZE
(-) charge moves towards (+) anode
(+) charge moves towards (-) cathode
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SDS-Page
disrupts all non covalent interactions = denature proteins
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Mutarotation
if hemiacetal is in water = spont. cycle in open and closed form
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IUPAC: Sucrose
glucose-alpha-1,2-fructose
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IUPAC: lactose
galactose-beta-1,4-glucose
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IUPAC: maltose
glucose-alpha-1,4-glucose
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Sphingolipids (and 5 types)
```
structural lipids
-backbone: sphingosine or sphingoid
sphingophospholipids
sphingomyelins
glycosphingolipids
gangliosides
waxes
```
65
Sphingophospholipids
may also be phospholipid w/ phosphodiester bond
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Sphingomyelins
contain phosphatidylcholine or phosphatidylethanolamine head group
-major component of myeline sheath
67
Glycosphinogolipids
attached to sugar not phosphate
| cerebrosides = one sugar attached, globosides = two or more sugars attached
68
Gangliosides
oligosaccharides w/ 1 or more terminal N-acetylneuraminic acid
69
Waxes
long chain fatty acids "esterified" to long chain alcohols
70
two types of Signaling Lipids
Terpenes
| Steroids
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Terpenes
odiferous steroid precursors from isoprene
| terpenoids: from terpenes via oxygenation or backbone rearrangement
72
Steroids
3 cyclohexane rings + 1 cyclopentane ring
steroid hormones: high affinity receptors (work event at low concentrations), gene expression and metabolism
Cholesterol
Prostaglandins
Fat Soluble Vitamins
73
Steroids: Cholesterol
steroid in membrane fluidity and stability
74
Steroids: Prostaglandins
autocrine and paracrine signaling, regulatory cAMP levels, effect smooth muscle contraction, body Temp, sleep/wake, pain, fever
75
Steroids: Fat Soluble Vitamins
A: Carotene = retinol for vision, retinoic acid = epithelial development
D: Cholecalciferol = calcitriol in kidneys, regulates Ca and P, promotes bone formation
E: tocopherols = antioxidants, aromatic rings that destroy free radicals
K: Phylloquinone + menciquinones = promote clotting factor
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Purines
2 rings, Adenine and Guanine
77
Pyrimidine
1 ring, cytosine, thymine, uracil
78
Purine - Pyrimidine pairs
A -- T
| G -- C
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Helicase
enzyme, unwinds DNA generating 2 ssDNA templates ahead of polymerase
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DNA topoisomerase
```
function in response to supercoiling
introduce (-) supercoils
```
81
Start codon
AUG
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Stop codons
UAA, UAG, UGA
83
DNA to DNA
replication (new DNA synthesized in 5' to 3' direction
| template read 3' to 5'
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DNA to RNA
Transcription (new RNA synthesized 5' to 3' direction (template read 3' to 5')
85
RNA to Protein
Translation (mRNA read 5' to 3' direction)
86
"Wobble"
silent mutation tat affects the third base pair
| protects against mutations
87
Three types of RNA in transcription
mRNA: carries DNA nucleus to cytoplasm to be translated
tRNA: brings aa in, recognizes codons on mRNA using anticodon
rRNA: ribosome, enzymatically active, synthesized in nucleus
88
Three metabolic states
1. Postprandial state/Well-fed state
2. Postabsorptive/Fasting state
3. Prolonged fasting state (starvation)
89
Postprandial state/Well-fed state
blood glucose rises, stimulating insulin release
90
Postabsorptive/Fasting state
5 hours after food
counter regulating hormones: opposite effect of insulin on muscle, adipose tissue, liver
(Glucagon, Cortisol, Epinephrine, Norepinephrine, GH)
Glucogenolysis beings immediately, gluconeogenesis begins 12 hours later
91
Prolonged fasting state (starvation)
higher glucagon levels, lower glycogen levels
| increase [glucose] via gluconeogenesis
92
levels of protein organization
```
1 = string
2 = alpha helices and beta pleats
3 = interactions, disulfide bridges, H bonding, hydrophobicity
4 = multiple sub units
```
93
Insulin in muscles does
entry of glucose
glycogen synthesis
protein synthesis
94
Insulin in adipose tissue
entry of glucose
| triacylglycerol synthesis
95
Insulin in liver
glycogen synthesis
96
Insulin in nervous tissue
obtains energy via oxidation of glucose to CO2 and water during well fed/normal states
- grey matter: high glucose consumption
- white matter: low glucose consumption
97
Preferred fuel sources during well-fed and fasting state: liver
well fed: glucose, amino acids
| fasting: fatty acids
98
Preferred fuel sources during well-fed and fasting state: Resting skeletal muscle
well fed: glucose
fasting: fatty acids
prolonged fasting: ketones
99
Preferred fuel sources during well-fed and fasting state: Cardiac muscle
well fed: fatty acids
| fasting: fatty acids/ketones
100
Preferred fuel sources during well-fed and fasting state: adipose tissue
well fed: glucose
| fasting: fatty acids
101
Preferred fuel sources during well-fed and fasting state: brain
well fed: glucose
fasting: glucose
prolonged fasting: ketones
102
Preferred fuel sources during well-fed and fasting state: RBCs
well fed: glucose
| fasting: glucose
103
three types of cell-cell junctions
gap junctions
tight junctions
desmosomes
104
gap junctions
rapid exchange of ions and other small molecules
105
tight junctions
prevent paracellular transport
| dont provide intercellular transport
106
desmosomes
and hemidesmosomes
| -anchor layers of epithelial tissue together
107
three types of passive transport
1. simple diffusion
2. Osmosis
3. Facilitated diffusion
108
two more important types of glucose transporters
GLUT 2 = low affinity transporter=high Km
-found in the liver for glucose storage
-and in pancreatic beta-islet cells as a glucose sensor
GLUT 4 = high affinity = low Km
-found in adipose tissue and muscle = stimulated by insulin
109
Glucokinase
- converts glucose to glucose 6-phosphate
- present in pancreatic Beta-islet cells (glucose sensor)
- responsive to insulin in the liver
110
Hexokinase
converts glucose to glucose 6-phosphate in peripheral tissues
111
Phosphofructokinas-1 (PFK-1)
- phosphorylates fructose 6-phosphate to fructose 1,6-biphosphate
- RATE LIMITING STEP
- stimulated by/activated by AMP and F 2,6-BP
- inhibited by ATP and citrate
112
Phosphofructokinase-2 (PFK-2)
- produces F 2,6-BP
- activates PFK-1
- activated by insulin
- Inhibited by glucagon
113
Glyceraldehyde-3-phosphate dehydrogenase
produces NADH
| feeds into ETC
114
3-Phosphoglycerate Kinase (and pyruvate kinase)
- each perform substrate level phosphorylation
| - places inorganic phosphate (Pi) onto ADP
115
NADH
produced in glycolysis
oxidized by mitochondria in ETC when O2 is present
If O2 and mitochondria are absent = NADH is oxidized by lactate dehydrogenase
116
two types of monosaccharides and their functions
Galactose = lactose in milk, trapped in cell by galactokinase, converted to glucose 1-phosphate via galactose-1-phosphate
Fructose = honey, fruit, sucrose, commonly trapped in cell by fructokinase, cleaved by aldolase B = glyceraldehyde + DHAP
117
Pyruvate Dehydrogenase
complex enzyme tat convert pyruvate to acetyl CoA
stimulated by insulin
inhibited by acetyl-CoA
118
Glycogenesis
glycogen synthesis using 2 main enzymes
- glycogen synthase: creates a-1,4-glycosidic links
- branching enzyme: creates a-1,6-glycosidic links
119
Glycogenolysis
breakdown of glycogen w/ 2 main enzymes
- glycogen phosphorylase: breaks a-1,4 link
- debranching enzyme: connects a-1,4 and breaks/releases the a-1,6 link
120
Gluconeogenesis
located predominantly in liver (but also cytoplasm and mitochondria)
- reverse of glycolysis
- three main enzymes that bypass irreversible steps
1. Pyruvate carboxylase
2. Fructose-1,6 Biphosphate
3. Glucose-6-Phosphate
121
Pentose Phosphate Pathway
"hexose monophosphate (HMP) shunt"
- located in cytoplasm
- generates NADPH and sugars
- rate limiting enzyme = glucose-6-phosphate dehydrogenase (activated by NADP+ and insulin, inhibited by NADPH)
122
5 enzyme complex that produces Acetyl-CoA
1. Pyruvate Dehydrogenase
2. Dihydrolipoyl Transacetylase
3. Dihydrolipoyl Dehydrogenase
4. Pyruvate dehydrogenase kinase
5. Pyruvate dehydrogenase phosphatase
123
where does the citric acid cycle take place
in mitochondrial matrix
124
8 important enzymes of citric acid cycle
1. Citrate Synthase
2. Aconitase
3. Isocitrate dehydrogenase
4. a-ketoglutarate dehydrogenase complex
5. succinylcholine-CoA synthase
6. Succinate dehydrogenase
7. fumarase
8. malate dehydrogenase
