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Courses > BIOC12: BIOCHEM (Midterm) > Flashcards

BIOC12: BIOCHEM (Midterm) Flashcards

1
Q

what are the 4 groups of macromolecules?

A
  • nucleic acids
  • proteins
  • carbohydrates
  • lipids
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2
Q

a group of molecules that are largely hydrophobic and only sparingly soluble in water

A

lipids

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3
Q

what does in vitro mean?

A

outside a living cell

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4
Q

protein or RNA biomolecules that function as reaction catalysts to increase the rates of biochemical rxns

A

enzyme

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5
Q

sequences of biochemical reactions coordinated and controlled by a cell in response to available energy

A

metabolic pathway(s)

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6
Q

mechanisms that facilitate communication b/w cells, often initiated through the binding of small molecules to proteins called receptors

A

signal transduction

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7
Q

nitrogen-containing molecules that function primarily as the building blocks for proteins

A

amino acids

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8
Q

what are nucleotides made of?

A
  • a nitrogenous base
  • a 5-membered sugar (ribose / deoxyribose)
  • 1-3 phosphate groups
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9
Q

what are the 5 nucleotide bases?

A

adenine
guanine
cytosine
thymine
uracil

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10
Q

compounds formed only of carbon, oxygen, and hydrogen (with a 2:1 ratio of hydrogen to oxygen atoms)

A

simple sugars (aka carbohydrates)

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11
Q

when polar and non-polar chemical properties are contained within the same molecule

A

amphipathic

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12
Q

a molecule consisting of a polar carboxyl group (COOH) covalently linked to a non-polar extended hydrocarbon chain

A

fatty acid

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13
Q

a covalent bond b/w the alpha amino group of one a.a. and the alpha carboxyl group of another a.a.

A

peptide bond

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14
Q

any of a group of small biomolecules that serve as reactants and products in biochemical reactions within cells

A

metabolite

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15
Q

the rate at which reactants and products are interconverted in a metabolic pathway

A

metabolic flux

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16
Q

metabolite/hormone/peptide that binds to target proteins and alters their structure and function to control biochemical processes

A

ligand

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17
Q

a set of metabolic processes and reactions that uses oxygen to generate ATP

A

aerobic respiration

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18
Q

the process of oxidizing water to capture chemical energy and generate oxygen

A

photosynthesis

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19
Q

the conversion of carbon dioxide to organic compounds (particularly glucose)

A

carbon fixation

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20
Q

a reaction in which electrons are transferred from a compound of lower reduction potential (more negative) to one of higher reduction potential (more positive)

A

redox reaction

(oxidation-reduction)

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21
Q

_____ refers to a collection of matter in a defined space while _____ refers to everything else

A

system refers to a collection of matter in a defined space while surroundings refers to everything else

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22
Q

a system in which matter and energy are freely exchanged with the surroundings

A

open system

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23
Q

a system in which energy is exchanged with the surroundings but matter is not

A

closed system

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24
Q

a system in which neither matter nor energy are exchanged with the surroundings

A

isolated system

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25
Q

what is the 1st law of thermodynamics?

A

1st law: energy cannot be created or destroyed, only converted from one form to another

ΔE = Efinal − Einitial = q − w

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26
Q

a rxn that gives off heat is called _____ and has a (-/+) ΔH value, while a rxn that absorbs heat is called _____ and has a (-/+) ΔH value

A

a rxn that gives off heat is called exothermic and has a (-) ΔH value, while a rxn that absorbs heat is called endothermic and has a (+) ΔH value

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27
Q

what is the 2nd law of thermodynamics?

A

2nd law: in the absence of an energy input, all spontaneous processes in the universe tend toward dispersal of energy (disorder = entropy)

ΔSuniverse = ΔSsystem + ΔSsurroundings > 0

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28
Q

a measure of the spontaneity of a rxn

A

Gibbs free energy (G)

ΔG = ΔH − TΔS

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29
Q

a weak non-covalent bond in which hydrogen is shared b/w 2 electronegative atoms

A

hydrogen bond

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30
Q

what is the bond strength of a single H-bond?

A

20 kJ/mol

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31
Q

weak interactions b/w oppositely charged atoms or groups

A

ionic interactions

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32
Q

weak interactions b/w the dipoles of nearby electrically neutral molecules

A

van der Waals interactions

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33
Q

a type of weak interaction due to the tendency of hydrophobic molecules to pack close together away from water

A

hydrophobic effects

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34
Q

a difference in pressure across a semipermeable membrane caused by osmosis across the membrane

A

osmotic pressure

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35
Q

the diffusion of solvent molecules from a region of lower solute [] to one of higher solute []

A

osmosis

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36
Q

molecules are attracted to both polar and nonpolar environments

A

amphiphilic molecules

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37
Q

an aqueous solution that resists changes in pH because of the protonation or deprotonation of an acid-base conjugate pair

A

buffers

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38
Q

a weak acid with more than one dissociable H+

A

polyprotic acid

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39
Q

a.a. within a polypeptide chain

A

residues

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40
Q

short polypeptides that contain less than 40 a.a.

A

oligopeptides/peptides

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41
Q

each polypeptide chain is called a protein _____

A

each polypeptide chain is called a protein SUBUNIT

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42
Q

the pH at which a given a.a. has no net charge

A

isoelectric point (pI)

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43
Q

an electrically neutral but dipolar molecule that contains both positive and negative charges

A

zwitterion

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44
Q

molecules with the same molecular formula and atomic connectivity, but different 3D orientation of their atoms

A

stereoisomers

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45
Q

stereoisomers that are mirror images of each other and whose structures cannot be superimposed

A

enantiomers

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46
Q

enzyme that catalyzes the hydrolysis of a peptide bond

A

protease

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47
Q

refers to the a.a. sequence, which determines how the polypeptide backbone folds into an energetically stable 3D structure

A

primary (1°) structure

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48
Q

refers to the regular repetitive arrangement of local regions of the polypeptide backbone

A

secondary (2°) structure

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49
Q

what are the 3 major secondary structures in proteins?

A
  • α helices
  • ß strands
  • ß turns
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50
Q
  • a graphical representation of the polypeptide backbone associated with a protein’s secondary strcuture
    • can use this diagram to depict common folds and patterns in proteins
A

(cartoon) ribbon diagram

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51
Q

includes the spatial location (complete arrangement) of all the atoms in the polypeptide chain

A

tertiary (3°) structure

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52
Q

the structure of a protein complex containing more than one polypeptide chain

A

quaternary (4°) structure

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53
Q

collections of secondary structures that describe the spatial arrangement of a polypeptide chain

A

protein folds

think of folds as a description of the path the polypeptide follows in 3D space

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54
Q

what are the different ways to view 3D structures of proteins?

A
  • space-filling model
  • ball-and-stick model
  • backbone model
  • cartoon ribbon diagram
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55
Q
  • each atom is shown as a solid sphere
  • shows the overall shape of the protein and the surface exposed to aqueous solvent
  • excellent to show surface ligand binding
A

space-filling model

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56
Q

an excellent model to show bonding arrangement in proteins

A

ball-and-stick model

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57
Q
  • model that shows the general course of the polypeptide chain
  • difficult to see secondary structures
A

backbone model

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58
Q
  • model that concentrates on the backbone of the polypeptide chain
  • a.a. side chains are eliminated
  • can see into interior of the protein
  • can be used to depict common folds and patterns in protein
A

cartoon ribbon diagram

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59
Q
  • a right-handed helical conformation of a polypeptide chain
  • one of the most common elements of protein secondary structure
A

α helix

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60
Q

a 2° structure of proteins consisting of an extended polypeptide chain with side chains positioned above and below it

A

β strands

61
Q

a common secondary structure of proteins formed from β strands hydrogen-bonded together (b/w backbone NH and CO groups on separate strands)

A

β (pleated) sheets

62
Q

where is the H-bond found in α-helices?

A
  • intrastand H-bond found b/w residues n & n+4
  • b/w carbonyl oxygen (n) and H atom attached to nitrogen in peptide bond located 4 a.a. away (n + 4)
63
Q

hydrogen bonds in α helix: measurements

A
  • length of H-bonds b/w N and O: 2.8 Å
  • 3.6 residues per turn
  • pitch of 5.4 Å
64
Q

which a.a. can’t be a side chain in an α-helix structure? why?

A

PROLINE

nitrogen in ring lacks a hydrogen and does not contribute to H-bonding; rigid ring also restricts confirmations that can be adopted

65
Q

when is an amphipathic α helix generated?

A

when a.a. with hydrophilic or hydrophobic properties are positioned every 3-4 residues along the polypeptide backbone

66
Q

a β sheet structure in which adjacent β strands are oriented in opposite directions with regard to amino to carboxyl termini

A

antiparallel β sheet

67
Q

a β sheet structure in which β strands lie in the same amino to carboxyl orientation

A

parallel β sheets

68
Q

the hydrogen bond arrangement is more stable for _____ β sheets than for _____ β sheets

A

the hydrogen bond arrangement is more stable for ANTIPARALLEL β sheets than for PARALLEL β sheets

*why antiparallel β sheets are more common in proteins

69
Q

a turn or a loop in a polypeptide chain that connects 2 β strands in an antiparallel β sheeet

A

β turn

70
Q

what is the difference b/w type I and type II β turns?

A

type I: carbonyl oxygen b/w 2nd and 3rd residues is oriented inward

type II: carbony oxygen faces outward

71
Q
  • irregular segments that connect elements of secondary structures
  • usually range from 6 to 20 residues in length
A

loops

72
Q

why are secondary structures common in proteins?

hint: think angles

A

secondary structures are common because they minimize the steric hindrance of the side chains

73
Q

which a.a. have the highest propensity to occur in α helices?

A

AH: Eat Ass Like My Queen/King/Royal Highness Is Watching for Fun

alpha helices
E (glutamate)
A (alanine)
L (leucine)
M (methionine)
Q (glutamine)
K (lysine)
R (arginine)
H (histidine)
I (isoleucine)
W (tryptophan)
F (phenylalanine)

74
Q

which a.a. have the highest propensity to occur in β strands?

A

BS: Lil Matt Vader Is Your Cousin? Word! Fun Times

beta strands
L (leucine)
M (methionine)
V (valine)
I (isoleucine)
Y (tyrosine)
C (cysteine)
W (tryptophan)
F (phenylalanine)
T (threonine)

75
Q

which a.a. have the highest propensity to occur in β turns?

A

BuT: Each King Got New Pants Sent Down

beta turns
E (glutamate)
K (lysine)
G (glycine)
N (asparagine)
P (proline)
S (serine)
D (aspartate)

76
Q

what are the 4 general classes of protein structures?

A
  • predominantly α helix
  • predominantly β sheets
  • α/β combined (Intermixed helices and strands)
  • α + β (helical regions adjacent to sheets)
77
Q

an independent folding module within a polypeptide chain

A

domain

78
Q

a small but distinct structural unit of a protein fold

A

motif

79
Q

contains 4 α-helices linked together (one of the most common protein folds)

A

four-helix bundle

80
Q

consists of 4 or more β strands linked together to form β-sheet structures

A

Greek key fold/motif

81
Q
  • consists of 2 regions of alternating α helices and β strands that fold together into a compact structural domain
  • found in several proteins that bind nucleotides
A

Rossmann fold

82
Q

an alternating α helix/β strand fold first identified in the glycolytic enzyme triose phosphate isomerase

A

TIM barrel fold

83
Q
  • compact domain of about 200 a.a. residues
  • contains eight or more radial β strands that form interior of protein (surrounded by eight α helices that face outward)
A

TIM Barrel fold

84
Q

a large protein fold (300 a.a.) containing 3 distinct structural components that are found in some proteins that bind to membrane-associated biomolecules

A

FERM Domain fold

85
Q

what are the structural components of the FERM domain fold?

A

FA/FC: mostly β sheets

FB: contains only α helices

86
Q

what are the 4 proteins where the FERM domain fold is found?

A
  • Band 4.1
  • ezrin
  • radixin
  • moesin
87
Q

tertiary structures can be stabilized by _____ and _____

A

tertiary structures can be stabilized by DISULFIDE BONDS and METAL IONS

88
Q

the number and overall arrangement of the polypeptide chains w/in multi-subunit protein complexes

A

quaternary structure

89
Q

a protein complex containing two identical protein subunits encoded by the same gene

A

homodimer

90
Q

a protein complex with 2 subunits derived from distinct polypeptides (different gene products)

A

heterodimer

91
Q

how do multiple protein subunits (4º) provide increased functional to proteins?

A
  • by providing structural properties not present in individual subunits
  • by providing a mechanism for regulation of protein function through conformational changes that alter the protein subunit interface
  • significantly increasing the efficiency of biochemical processes by bringin linked functional components into close proximity
92
Q

a homodimer of 2 helical polypeptides wrapped around each other to form a coiled coil

A

keratin

(a fibrous protein)

93
Q

a fibrous protein consisting of 3 subunits (2 heavy chain, 1 light), one of which consists entirely of β sheets

A

silk fibroin

94
Q

a protein complex consisting of long helical subunits that are intertwined to form a right-handed triple-helix fiber

A

collagen

95
Q

a protein that facilitates the formation of stable 3D structures through the process of protein folding

A

chaperones

96
Q

what are the 3 main functions of chaperone proteins?

A
  • help newly synthesized proteins fold properly
  • rescue misfolded proteins
  • disrupt protein aggregates
97
Q

a denaturing condition in which 50% of the proteins are fully folded and 50% are fully unfolded (no partially folded/unfolded proteins)

A

transition curve midpoint (Tm)

98
Q

an enzyme that cleaves RNA, also the first protein shown to be capable of denaturing and refolding in vitro

A

ribonuclease A (RNAaseA)

99
Q

an intermediate stage in a model of globular protein folding in which hydrophobic residues first form the interior of the protein

A

molten globule

100
Q

a protein folding model which proposes that hydrophobic residues first form the interior of the protein through loosely defined tertiary structures (molten globules)

A

hydrophobic collapse model

101
Q

a protein folding model which proposed that local 2° structures form independently in the 1st phase, leading to the formation of 3° structures in 2nd phase

A

framework model

102
Q

a protein folding model which proposes that local 2° structures form before 3° structures, driven by localized interactions b/w 2° structures

A

nucleation model

103
Q

the two most common type of chaperone proteins are the _____ and the _____, which bind to misfolded proteins and use ATP hydrolysis as an energy source to facilitate correct folding

A

the two most common type of chaperone proteins are the CLAMP-TYPE and the CHAMBER-TYPE, which bind to misfolded proteins and use ATP hydrolysis as an energy source to facilitate correct folding

104
Q

a group of proteins that provide a way for the cell to recover from heat denaturing by helping proteins refold when the temperature returns to normal

A

heat shock family (clamp-type chaperone proteins)

105
Q

a well-characterized clamp-type chaperone protein

A

Hsp70

named from Its molecular mass of 70 kDa

106
Q

consists of 14 identical polypeptide subunits arranged in 2 rings of 7 subunits each that houses a protein folding chamber

A

GroEL component of chaperonins (Hsp60)

107
Q

what are the 3 protein domains of the GroEL component of chaperonins/Hsp60?

A

substrate binding domain: form walls of protein folding chamber

intermediate domain: form walls of protein folding chamber

ATP binding domain: separates upper and lower chamber; controls opening and closing of chamber

108
Q
  • 7 identical subunits that functions as the cap for the chaperonin/Hsp60 complex
  • binds to only one end of the chaperone complex at a time
A

GroES component of the GroEL-GroES complex

109
Q

what are the possible causes for protein folding diseases?

A
  • due to mutations in the protein-coding sequence of the gene
  • accumulated misfolded proteins that contain no a.a. changes
110
Q

an enzyme found in bioluminescent organisms that catalyzes a reaction of luciferin to generate visible light (one of the earliest biochemical assays)

A

luciferase

111
Q

an isotonic suspension of lysed cells, used for protein isolation and identification

A

cell extract/cell homogenate

112
Q

what are the most commonly used homogenization techniques?

A

sonication: disrupts cell membranes through vibrational effects of ultrasonic waves

shearing: forcing cells through a small opening

incubation of cell sample with mild detergents: disrupts cell membranes

113
Q
  • a process that separates particles of different sizes or densities by spinning solution samples in a rotor at high speeds
  • separates large molecules into fractions called pellet and supernatant
A

centrifugation

114
Q

the total amount or activity of a target protein, divided by the total amount of protein in the sample

A

specific activity

115
Q

what are the four fractions that can (possibly) be obtained from a eukaryotic cell extract after centrifugation?

A

nuclei
mitochondria
plasma membrane components
cytosol

116
Q

a protein separation method that involves adding increasing amounts of a saturated ammonium sulfate solution to the protein solution

A

salting out

117
Q

a diffusion-based process that uses a semipermeable membrane to allow small molecules to cross the membrane but not large molecules (usually proteins)

A

dialysis

118
Q

a technique that separates proteins on the basis of differential physical or chemical interactions with a solid gel matrix

A

column chromatography

119
Q

what are the 3 types of column chromatography?

A

gel filtration

ion-exchange

affinity

120
Q

a column chromatography method that uses porous hydrocarbon beads to separate proteins on the bases of size

A

gel filtration chromatography (aka size-exclusion)

121
Q

a protein purification method that exploits charge differences b/w proteins

A

ion-exchange chromatography

122
Q

what are the 2 commonly used ion exchange matrices in ion-exchange chromatography?

A

(+) charged anion-exchange matrix called DiEthylAminoEthyl (DEAE) cellulose

(-) charged cation-exchange matrix called CarboxyMethylCellulose (CMC)

123
Q

a buffer solution with a high [] of an appropriate competing ion to dispalce the bound protein (used in ion-exchange chromatography)

A

elution buffer

124
Q

a column chromatography method that exploits specific binding properties of the target protein to separate it from other cellular proteins that lack this binding function

A

affinity chromatography

125
Q

a biochemical technique that separates proteins on the basis of charge and size

A

gel electrophoresis

126
Q

a gel electrophoresis technique that uses a solid-support molecular sieve made of polyacrylamide to separate molecules in an electric field on the basis of charge and size (on the basis of their mass)

A

polyacrylamid gel electrophoresis (PAGE)

127
Q
  • an amphipathic molecule used in gel electrophoresis to give protein a net negative charge (and migrate toward anode (+ charge) at bottom of buffer tank)
  • denatures the protein
A

sodium dodecyl sulfate (SDS)

128
Q

_____ proteins migrate faster through the buffer-saturated polyacrylamide gel matrix than _____ proteins

A

SMALL proteins migrate faster through the buffer-saturated polyacrylamide gel matrix than LARGE proteins

129
Q

_____ proteins resolve well in gels with low percentage of polyacrylamide, while _____ proteins resolve best in high percentage polyacrylamide gels

A

LARGE proteins resolve well in gels with low percentage of polyacrylamide, while SMALL proteins resolve best in high percentage polyacrylamide gels

130
Q

a type of polyacrylamide gel electrophoresis that separates proteins on the basis of charge as a function of pH

A

isoelectric focusing

131
Q

for isoelectric focusing, at a pH below its isoelectric point, the protein has a net _____ charge, while at a pH above its isoelectric point, the protein has a net ____ charge

A

for isoelectric focusing, at a pH below its isoelectric point, the protein has a net POSITIVE charge, while at a pH above its isoelectric point, the protein has a net NEGATIVE charge

132
Q

a protein separation technique that combines isoelectric focusing and SDS-PAGE to separate proteins on the basis of both pI and molecular mass

A

2D PAGE

133
Q

uses the fluorescent dyes Cy3 and Cy5 to distinguish 2 protein samples run on the same 2D PAGE gel

A

2D differential in-gel electrophoresis (2D DIGE)

134
Q

a protein sequencing method that modifies the N-terminal acid tagging reaction by using phenylisothiocyanate (PITC)

doesn’t disrupt the rest of the polypeptide chain

A

Edman degradation

135
Q

how is Edman degradation better than Sanger’s old method?

(for protein sequencing)

A

Edman degradation does not require the input of additional protein after each round of cleavage

136
Q

what is a limitation of Edman degradation?

A

it is not possible to obtain the sequence of a polypeptide longer than 50 a.a. in a single set of reactions

137
Q

protease enzymes that cleaves a polypeptide chain on the carboxyl side of lysine or arginine

A

trypsin

138
Q

protease enzyme that cleaves a polypeptide chain on the carboxyl side of tyrosine, tryptophan, or phenylalanine

A

chymotrypsin

139
Q

trypsin cleaves polypeptide chain on carboxyl side of which a.a.?

A

lysine and arginine

140
Q

chymotrypsin is a protease enzyme that cleaves the polypeptide chain on the carboxyl side of which a.a.?

A

aromatics (tyrosine, tryptophan, and phenylalanine)

141
Q

protease enzyme that cleaves polypeptide chain on carboxyl side of methionine

A

cyanogen bromide

142
Q

cleaves the carboxyl side of aspartate and glutamate

A

S. aureus

143
Q

a method of measuring the mass-to-charge ratio of molecules, which is then used to deduce the molecular mass

A

mass spectrometry

144
Q
  • a method for preparing proteins for mass spec and releases polypeptides that have been cleaved by trypsin
  • generates a highly charged molecule in the gas phase
A

elctrospray ionization (ESI)

145
Q

a method for generating peptide ions for mass spec in which tryptic fragments are released as charged molecules after exposure to laser flash

A

matrix-assisted laser desorption/ionization (MALDI)

146
Q
  • a method of structure determinataion that detects nuclear spin properties of certain atoms (1H, 13C, 15N) to deduce their relative locations
  • gathers info on relative positions of certain atoms in a protein solution
A

NMR spectroscopy

147
Q

provides a snapshot in time of protein structure because it gives atomic positions in a static protein crystal lattice

A

X-ray crystallography

148
Q

a procedure that determines the phases of diffracted X-rays by comparing the to X-ray diffraction from a crystal containing an electron-rich element

A

isomorphous element

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