Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry > FINALS LISTS > Flashcards

FINALS LISTS Flashcards

1
Q

Macromolecules

A

Amino Acid/Proteins
Carbohydrates
Lipids
Nucleic Acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Types of Metabolism

A 
Anabolism (consume)
Catabolism (produces)
Amphibolic (both)
Phototrophs (use photons)
Chemotrophs (use chemicals)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Types of Bonds

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Henderson Hasselbach Equation

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Types of Chromatography

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Types of Electrophoresis

factors: size, shape, charge

A 
native-PAGE- charge & size
SDS-PAGE-size 
Isoelectric focusing- pI
capillary electrophoresis
band detection
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

How to find Amino Acid Composition

A

Acid hydrolysis
Column Chromatography
Amino Acid Sequencing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Disulfide Bond Reducers

A

Performic Acid Oxidation
2 Mercaptoethanol
Iodoacetate/ Iodoacetamide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Levels of Protein Organization

A

Primary Sequence
Secondary Structure
Tertiary Folding
Quaternary Association

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Destabilizing Forces/ Molecules

A

detergents
chaotropic agents
pH
heat

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Anfinsen Experiment Conclusions

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Enzyme Classification

A
  1. Oxidoreductase
  2. Transferase
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Initial Velocity Eqn

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Michaelis Menten Equation

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Vmax Equation

A

Vmax = kcat [Et]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Km Eqn ( affinity of enzyme for substrate)

A

Km = (k-1 + k2) / k1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Reverse Inhibitors

A 
Competitive ( I binds to E only) [Classical vs. Nonclassical]
Non competitive ( I binds to E & ES)
Uncompetitive ( I binds to ES)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Zymogens

A 
Proinsulin
Pepsinogen
Trypsinsogen
Chymotrypsinogen A
Proelastin
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

How do enzymes speed up reactions?

dec. activation energy

A 
Acid Base Catalysis
Covalent Catalysis
Intermediate Formation
Proximity Effect 
Transition State Stabilization
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Catalytic Triad of Chymotrypsin

A 
ABC - 3,4 & 5,6
CC - 2-4 & 5-7
IF- 2,4 & 5, 7
PE- 2-7, 3&6 full
TSS - 3&6
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

ATP- adenosine 5’ triphosphate

A

transfer of phosphory or nucleotidyl groups
cosub
vita source n/a

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

NAD+- nicotinamide adenine dinucleotide

A

oxidation reduction reaction involving 2 electron transfers
cosub
vita source Niacin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

FAD- flavin adenine dinucleotide

A

oxidation reduction involving 1 & 2 electron transfers
prosthetic
vita source riboflavin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

PLP- pryridoxal 5’-phosphate

A

transfer of groups to and from amino acids
prosthetic
vita source pyridoxine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Coenzyme A

A

transfer of acyl groups
cosub
vita source Panthothenate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

THF- tetrahydrofolate

A

transfer of 1 carbon substituents esp formly & hydroxyl methyl groups; provides the methyl group for thymine in DNA
cosub
vita source Folate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

Q-Ubiquinone

A

lipid soluble electron carrier
cosub
vita source none

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

TPP- Thiamine Pyrophosphate

A

transfer of multi carbon fragments containing a carbonyl group
prosthetic
vita source thiamine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Lipoamide

A

oxidation of hydroxyl alkyl group from TPP and subsequent transfer as an acyl group
prosthetic
vita source none

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Biotin

A

ATP dependent carboxylation of substrates or carboxyl group transfer between substrates
prosthetic
vita source Biotin

40
Q

Amylose (plants)

A

Glucose
alpha (1 ->4)
linear

41
Q

amylopectin (plants)

A

glucose

alpha (1 –>4), alpha (1 –>6) branches

42
Q

glycogen (Animals)

A

glucose

alpha (1–>4), alpha (1 –>6) branches

43
Q

cellulose (plant cell walls)

A

glucose

beta (1–>4)

44
Q

chitin (exoskeleton)

A

glucose

beta ( 1–>4)

45
Q

Pectin (plant cells walls)

A

alpha (1–>4)

46
Q

Storage as polysaccharide vs. monosaccharide

A

high density
low diffusion
low osmotic pressure
high energy bonds

47
Q

Carbohydrates linked to proteins by

A

N-linked
O-linked
P- linked

48
Q

sucrose

A

alpha-D- glucopyranosyl-(1–>2)-beta-D-fructofuranoside

go father son

49
Q

lactose

A

beta-D-galactopyranosyl-(1–>4)-alpha-D-glucopyranose

go good luck

50
Q

Sphingolipids

A 
1- phosphate 
1/3- OH
2- amino
2- fatty acide (amide bond)
3- long alkyl chain
4/5- trans double bond
51
Q

Steroids

A 
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
Q

Lipid Structure

A 
monomers
monolayers
micelles
bilayer
liposomes
53
Q

Transports

A

simple diffusion
channels & pores
passive transport
active transport - primary & secondary

54
Q

3 different paths of movement across membranes

A

uniport
antiport
symport

55
Q

Adenyly Cyclase

A 
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
Q

Inositol Phospholipid

A 
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
Q

Receptor Tyrosine Kinase

A

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
Q

of bases

A 
mRNA - 100-300 or < 300
rRNA - 28S - 4700
             18S - 1900
             5.8S- 160
               5S- 120
59
Q

A-DNA

A

shorter and fatter
open center
anti
right handedness

60
Q

B-DNA

A

medium length and width
filled center
anti
right handedness

61
Q

Z-DNA

A

longer and skinner
filled cylinder
syn@G, anti@C
left handedness

62
Q

Forces that hold secondary structure of DNA together

A
  1. hydrophobic effect
  2. stacking interaction
  3. hydrogen bonds
  4. electrostatic interactions
63
Q

Thermal Annealing

A
  1. uniqueness of sequence
  2. length of sequence
  3. concentration of sequence
64
Q

Probes

A

Southern- RNA
Northern - DNA
Western - Protein
Microarray

65
Q

Metabolic Pathways

A

Linear- different product
Cyclic- same product
Spiral- shorter/longer product

66
Q

What cells do?

A

segregation and concentration of metabolites
generate energy –> ATP
genes –> enzymes –> metabolism
activity limited by resources/environment
operate in steady state mode

67
Q

Hydrolysis of ATP

A

ATP –> ADP + Pi

-30.5 kJ/moles

68
Q

Higher Energy than ATP hydrolysis

CAMMP

A 
Cyclic phosphodiester
Acid anhydride
Methyl Phosphoguanidium
Mixed Phosphoanhydride
Phosphoenolester
69
Q

Same Energy than ATP hydrolysis

GTPP

A

Glycosidic
Thioester
Phosphoanydride
Phosphoguanidium

70
Q

Less Energy than ATP hydrolysis

PEP

A

Phosphoester
Ester
Phosphoacetal

71
Q

Why is ATP so energetic?

A

increase salvation
increase resonance
decrease charge repulsion

72
Q

Two Important Enzymes

A 
1. adenylate kinase
    intermembrane space
    AMP + ATP  2 ADP
2. nucleoside diphosphate kinase
    found in outer membrane & intermembrane space
   NDP + ATP  NTP + ADP
73
Q

Glycolysis Enzymes

A 
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
Q

Pyruvate –> Ethanol

A

pyruvate decarboxylase

alcohol dehydrogenase

75
Q

Pyruvate –> Lactate

A

lactate dehydrogenase

76
Q

Pyruvate –> Acetyl CoA

A

pyruvate dehydrogenase

77
Q

Pyruvate –> Oxaloacetate

A

pyruvate carboxylase

78
Q

Fructose enters Glycolysis by Enzymes

A

1-step = hexokinase (Step 3G)

2 step = fructokinase
               fructose 1 phosphate aldolase
               triose kinase (Step5, 6)
79
Q

Galactose enters Glycolysis by Enzymes

A

galactokinase
galactose 1 phosphate uridyltransferase
UDP glucose 4 epimerase
phosphoglucomutase (step 2G)

80
Q

Mannose enters Glycolysis by Enzymes

A

hexokinase
phosphomannose isomerase
(step 3G)

81
Q

Glycerol enters Glycolysis by Enzymes

A

Glycerol Kinase
glycerol 3 phosphate dehydrogenase
(step 5)

82
Q

Glycogen enters Glycolysis by Enzymes

A 
Degradation
   phosphorylase
   phosphoglucomutase 
Synthesis
   phosphoglucomutase
   UDP-glucose pyrophosphorylase
  glycogen synthase
83
Q

Bisphoshoglycerate shunt

A

bisphosphoglycerate mutase

2,3 bisphosphoglycerate phosphatase

84
Q

Pentose phosphate shunt

A

reducing power immediately
source of pentose
interconverts carbohydrates

85
Q

Gluconeogenesis

A

pyruvate carboxylase
phophoenolpyruvate carboxykinase
fructose 1,6-bisphosphatase
glucose 6-phosphatase

86
Q

TCA Enzymes

A 
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
Q

Glyoxylate Shunt

A 
citrate synthase
aconitase
isocitrate lyase
malate synthase
malate dehydrogenase
88
Q

Outer membrane

A

porin
nucleoside diphosphokinase
phospholipase A1 & A2

89
Q

Intermembrane Space

A

adenylate kinase
nucleoside diphosphokinase
sulfite oxidase
cytochrome c

90
Q

Inner Membrane

A 
cytochromes b, c, a, a3
NADH dehydrogenase
Succinate dehydrogenase
Ubiquionone
ATP synthetase
translocases
91
Q

Matrix

A 
TCA enzymes
pyruvate dehydrogenase
pyruvate carboxylase
glutamate dehydgrogenase
aspartate glutamate aminotransferase
92
Q

Complex I

A

NADH Ubiquinone Oxidoreductase
NADH + Q –> NAD+ + QH2
6/4
FMN & FeS

93
Q

Complex II

A

Succinate Ubiquinone Oxidoreductase
Succinate + Q –> Fumarate + QH2
2/0
FAD , FeS, cytochrome b

94
Q

Complex III

A

Ubiquinol Cytochrome c Oxidoreductase
cytochrome c + QH2 —> cytochrome c + Q
2/4
FeS, cytochrome bH, cytochrome bL, cytochrome c1

95
Q

Complex IV

A

cytochrome c oxidase
cytochrome c + O2 –> cytochrome c + H20
2/2
CuA, CuB, cytochrome a, cytochrome a3

96
Q

Complex V

A

ATP synthase
ADP + Pi –> ATP + H2O
3/3

97
Q

Beta Oxidation Enzymes

A

Acyl CoA dehydrogenase
2-enoly CoA hydratase
L-3-hydroxyacyl CoA dehydrogenase
3-ketoacyl-CoA thiolase

Biochemistry (11 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions