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Biochemistry > FINALS LISTS > Flashcards

FINALS LISTS Flashcards

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1
Q

Macromolecules

A

Amino Acid/Proteins
Carbohydrates
Lipids
Nucleic Acids

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2
Q

Types of Metabolism

A 
Anabolism (consume)
Catabolism (produces)
Amphibolic (both)
Phototrophs (use photons)
Chemotrophs (use chemicals)
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3
Q

Hydrogen Bonding Properties

A 
Polar Bond Donor
Unequal sharing of protons btw acceptor & donor
Lone pair of electrons on acceptor
Linear bond angle from donor to acceptor
Particular electronegative atoms NOSF
Closer than Van Der Waals Radii
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4
Q

Electrostatic Interaction
(Noncovalent Interaction)
Strongest —> Weakest

A

Monopole-Monopole/ Charge Charge/ Ionic Bond
Monopole-Dipole
Dipole-Dipole
Dipole- Induced Dipole
Induced Dipole- Induced Dipole/ London Dispersion/Van der Waals

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5
Q

Types of Bonds

A

Covalent- chemical bond sharing of e-
Ionic- chemical bond involving charges
Hydrogen- polar molecules

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6
Q

Henderson Hasselbach Equation

A

pH=pKa + log ( [conjugate base]/ [weak acid])

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7
Q

Types of Chromatography

A

Ion Exchange - charge
Gel Permeation- size
Affinity - specificity of binding interaction
Absorption- solubility
HPLC- high performance liquid chromatography

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8
Q

Types of Electrophoresis

factors: size, shape, charge

A 
native-PAGE- charge & size
SDS-PAGE-size 
Isoelectric focusing- pI
capillary electrophoresis
band detection
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9
Q

Types of Assays

A

Bicinchoninic Acid (BCA)- add Copper at high pH
Lowry- Biruet then phenol reagent
Absorbance- 280 aromatics, 210 peptides
Bradford/Coomassie Blue- dye binding, fast

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10
Q

How to find Amino Acid Composition

A

Acid hydrolysis
Column Chromatography
Amino Acid Sequencing

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11
Q

N terminus attackers

A 
2,4-dinitroflurobenzene ( Sanger's Reagent)
Dansyl Reaction ( sulfonyl chloride)
phenylisothiocyanate (Edman degradation)
Leucine Amino Peptidase ( not Pro)
Aminopeptidase M (all free)
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12
Q

C terminus attackers

A 
Carboxypeptidase A (not Arg, Lys, Pro)
Carboxypeptidase B ( only Arg, Lys)
Carboxypeptidase C (all)
Carboxypeptidase Y (all, Gly slow)
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13
Q

Cleavage at carboxyl side

A 
Trypsin (lys, arg)
Chymotrypsin (phe, tyr, trp)
Cyanogen Bromide (met)
S. aureus (glu, asp)
Clostripain (arg)
Thermolysin (Ile, Leu, Val)
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14
Q

Disulfide Bond Reducers

A

Performic Acid Oxidation
2 Mercaptoethanol
Iodoacetate/ Iodoacetamide

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15
Q

Basic Rules of Protein Structure

Think ANDCTT

A 
alpha helix & beta sheet composition varies
no knots in chain
domains exist
centers tend to be hydrophobic
trans peptide bond
tightly folded
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16
Q

Levels of Protein Organization

A

Primary Sequence
Secondary Structure
Tertiary Folding
Quaternary Association

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17
Q

Factors which stabilize Tertiary Folding of Proteins

A 
hydrophobic effect
hydrogen bonds
van der waals/ london dispersion/hydrophobic
ion pairs/ monopole-monopole
disulfide bonds
dipole-dipole (rare)
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18
Q

Destabilizing Forces/ Molecules

A

detergents
chaotropic agents
pH
heat

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19
Q

Anfinsen Experiment Conclusions

A

not a random search process
primary sequence determines tertiary structure
disulfide bonds do not direct folding

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20
Q

Allosteric Effectors of Hemoglobin

A 
Oxygen (oxy form)
Carbon Monoxide (oxy form)
Carbon Dioxide- direct & indirect (deoxy form)
Protons- Bohr Effect (deoxy form)
2, 3- bisphsophoglycerate (deoxy form)
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21
Q

Enzyme Classification

A
  1. Oxidoreductase
  2. Transferase
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases
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22
Q

Initial Velocity Eqn

A

Vo= d[P]/dt = -d[S]/dt when t=0

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23
Q

Michaelis Menten Equation

A

Vo= Vmax[S]/ Km + [S]

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24
Q

Vmax Equation

A

Vmax = kcat [Et]

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25
Km Eqn ( affinity of enzyme for substrate)
Km = (k-1 + k2) / k1
26
Reverse Inhibitors
``` Competitive ( I binds to E only) [Classical vs. Nonclassical] Non competitive ( I binds to E & ES) Uncompetitive ( I binds to ES) ```
27
Zymogens
``` Proinsulin Pepsinogen Trypsinsogen Chymotrypsinogen A Proelastin ```
28
How do enzymes speed up reactions? | dec. activation energy
``` Acid Base Catalysis Covalent Catalysis Intermediate Formation Proximity Effect Transition State Stabilization ```
29
Catalytic Triad of Chymotrypsin
``` ABC - 3,4 & 5,6 CC - 2-4 & 5-7 IF- 2,4 & 5, 7 PE- 2-7, 3&6 full TSS - 3&6 ```
30
ATP- adenosine 5' triphosphate
transfer of phosphory or nucleotidyl groups cosub vita source n/a
31
NAD+- nicotinamide adenine dinucleotide
oxidation reduction reaction involving 2 electron transfers cosub vita source Niacin
32
FAD- flavin adenine dinucleotide
oxidation reduction involving 1 & 2 electron transfers prosthetic vita source riboflavin
33
PLP- pryridoxal 5'-phosphate
transfer of groups to and from amino acids prosthetic vita source pyridoxine
34
Coenzyme A
transfer of acyl groups cosub vita source Panthothenate
35
THF- tetrahydrofolate
transfer of 1 carbon substituents esp formly & hydroxyl methyl groups; provides the methyl group for thymine in DNA cosub vita source Folate
36
Q-Ubiquinone
lipid soluble electron carrier cosub vita source none
37
TPP- Thiamine Pyrophosphate
transfer of multi carbon fragments containing a carbonyl group prosthetic vita source thiamine
38
Lipoamide
oxidation of hydroxyl alkyl group from TPP and subsequent transfer as an acyl group prosthetic vita source none
39
Biotin
ATP dependent carboxylation of substrates or carboxyl group transfer between substrates prosthetic vita source Biotin
40
Amylose (plants)
Glucose alpha (1 ->4) linear
41
amylopectin (plants)
glucose | alpha (1 -->4), alpha (1 -->6) branches
42
glycogen (Animals)
glucose | alpha (1-->4), alpha (1 -->6) branches
43
cellulose (plant cell walls)
glucose | beta (1-->4)
44
chitin (exoskeleton)
glucose | beta ( 1-->4)
45
Pectin (plant cells walls)
alpha (1-->4)
46
Storage as polysaccharide vs. monosaccharide
high density low diffusion low osmotic pressure high energy bonds
47
Carbohydrates linked to proteins by
N-linked O-linked P- linked
48
sucrose
alpha-D- glucopyranosyl-(1-->2)-beta-D-fructofuranoside | go father son
49
lactose
beta-D-galactopyranosyl-(1-->4)-alpha-D-glucopyranose | go good luck
50
Sphingolipids
``` 1- phosphate 1/3- OH 2- amino 2- fatty acide (amide bond) 3- long alkyl chain 4/5- trans double bond ```
51
Steroids
``` fused planr rings 4 rings- three 6 member, one 5 member OH on ring A Isoprene on ring D Hydrophobic few if any double bonds ```
52
Lipid Structure
``` monomers monolayers micelles bilayer liposomes ```
53
Transports
simple diffusion channels & pores passive transport active transport - primary & secondary
54
3 different paths of movement across membranes
uniport antiport symport
55
Adenyly Cyclase
``` ext. signal+transmembrane receptor g-protein adenyly cyclase cAMP PKA ``` Holes 1. no ext signal 2. Gprotein- GTPase activity 3. cyclic phosphodiesterase 4. protein phosphatases
56
Inositol Phospholipid
``` ext. signal + transmembrane receptor G protein Phospholipase C IP3+DAG, Ca PKC ``` Holes 1. no ext signal 2. G protein GTPase 3. IP3 hydrolyzed 4. [Ca] dec. 5. Protein phosphatase 6. DAG recycled
57
Receptor Tyrosine Kinase
growth Hormone + RTK dimerizes & autophosphorylates then recruits docking proteins RAS RAF (MAPKKK) MEK (MAPKK)--> MAPK (diffuses via nuclear pore) phosphorylates transcription factor Holes 1. no ext signal 2. RTK dephosphorylation by phosphatase 3. GAP hydrolyzes GTP on Ras 4. Protein Phosphatases dephosphorylates cascade 5. transcription factors dephosphorylated
58
of bases
``` mRNA - 100-300 or < 300 rRNA - 28S - 4700 18S - 1900 5.8S- 160 5S- 120 ```
59
A-DNA
shorter and fatter open center anti right handedness
60
B-DNA
medium length and width filled center anti right handedness
61
Z-DNA
longer and skinner filled cylinder syn@G, anti@C left handedness
62
Forces that hold secondary structure of DNA together
1. hydrophobic effect 2. stacking interaction 3. hydrogen bonds 4. electrostatic interactions
63
Thermal Annealing
1. uniqueness of sequence 2. length of sequence 3. concentration of sequence
64
Probes
Southern- RNA Northern - DNA Western - Protein Microarray
65
Metabolic Pathways
Linear- different product Cyclic- same product Spiral- shorter/longer product
66
What cells do?
segregation and concentration of metabolites generate energy --> ATP genes --> enzymes --> metabolism activity limited by resources/environment operate in steady state mode
67
Hydrolysis of ATP
ATP --> ADP + Pi | -30.5 kJ/moles
68
Higher Energy than ATP hydrolysis | CAMMP
``` Cyclic phosphodiester Acid anhydride Methyl Phosphoguanidium Mixed Phosphoanhydride Phosphoenolester ```
69
Same Energy than ATP hydrolysis | GTPP
Glycosidic Thioester Phosphoanydride Phosphoguanidium
70
Less Energy than ATP hydrolysis | PEP
Phosphoester Ester Phosphoacetal
71
Why is ATP so energetic?
increase salvation increase resonance decrease charge repulsion
72
Two Important Enzymes
``` 1. adenylate kinase intermembrane space AMP + ATP 2 ADP 2. nucleoside diphosphate kinase found in outer membrane & intermembrane space NDP + ATP NTP + ADP ```
73
Glycolysis Enzymes
``` Hexokinase (2) Glucose 6-phosphate isomerase (5) Phosphofructokinase 1 (2) Aldolase (4) Triose phosphate isomerase (5) Glyceraldehyde 3-phosphate dehydrogenase (1) Phosphoglycerate kinase (2) phosphoglycerate mutase (5) Enolase (4) Pyruvate Kinase (2) ```
74
Pyruvate --> Ethanol
pyruvate decarboxylase | alcohol dehydrogenase
75
Pyruvate --> Lactate
lactate dehydrogenase
76
Pyruvate --> Acetyl CoA
pyruvate dehydrogenase
77
Pyruvate --> Oxaloacetate
pyruvate carboxylase
78
Fructose enters Glycolysis by Enzymes
1-step = hexokinase (Step 3G) ``` 2 step = fructokinase fructose 1 phosphate aldolase triose kinase (Step5, 6) ```
79
Galactose enters Glycolysis by Enzymes
galactokinase galactose 1 phosphate uridyltransferase UDP glucose 4 epimerase phosphoglucomutase (step 2G)
80
Mannose enters Glycolysis by Enzymes
hexokinase phosphomannose isomerase (step 3G)
81
Glycerol enters Glycolysis by Enzymes
Glycerol Kinase glycerol 3 phosphate dehydrogenase (step 5)
82
Glycogen enters Glycolysis by Enzymes
``` Degradation phosphorylase phosphoglucomutase Synthesis phosphoglucomutase UDP-glucose pyrophosphorylase glycogen synthase ```
83
Bisphoshoglycerate shunt
bisphosphoglycerate mutase | 2,3 bisphosphoglycerate phosphatase
84
Pentose phosphate shunt
reducing power immediately source of pentose interconverts carbohydrates
85
Gluconeogenesis
pyruvate carboxylase phophoenolpyruvate carboxykinase fructose 1,6-bisphosphatase glucose 6-phosphatase
86
TCA Enzymes
``` citrate synthase (2) aconitase (4) isocitrate dehydrogenase (1) alpha ketoglutarate dehydrogenase (1) succinyl CoA synthetase (6) succinate dehydrogenase (1) fumarase (4) malate dehydrogenase (1) ```
87
Glyoxylate Shunt
``` citrate synthase aconitase isocitrate lyase malate synthase malate dehydrogenase ```
88
Outer membrane
porin nucleoside diphosphokinase phospholipase A1 & A2
89
Intermembrane Space
adenylate kinase nucleoside diphosphokinase sulfite oxidase cytochrome c
90
Inner Membrane
``` cytochromes b, c, a, a3 NADH dehydrogenase Succinate dehydrogenase Ubiquionone ATP synthetase translocases ```
91
Matrix
``` TCA enzymes pyruvate dehydrogenase pyruvate carboxylase glutamate dehydgrogenase aspartate glutamate aminotransferase ```
92
Complex I
NADH Ubiquinone Oxidoreductase NADH + Q --> NAD+ + QH2 6/4 FMN & FeS
93
Complex II
Succinate Ubiquinone Oxidoreductase Succinate + Q --> Fumarate + QH2 2/0 FAD , FeS, cytochrome b
94
Complex III
Ubiquinol Cytochrome c Oxidoreductase cytochrome c + QH2 ---> cytochrome c + Q 2/4 FeS, cytochrome bH, cytochrome bL, cytochrome c1
95
Complex IV
cytochrome c oxidase cytochrome c + O2 --> cytochrome c + H20 2/2 CuA, CuB, cytochrome a, cytochrome a3
96
Complex V
ATP synthase ADP + Pi --> ATP + H2O 3/3
97
Beta Oxidation Enzymes
Acyl CoA dehydrogenase 2-enoly CoA hydratase L-3-hydroxyacyl CoA dehydrogenase 3-ketoacyl-CoA thiolase

Biochemistry (11 decks)

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