BIOC12: BIOCHEM (Midterm) Flashcards
(148 cards)
1
Q
what are the 4 groups of macromolecules?
A
- nucleic acids
- proteins
- carbohydrates
- lipids
2
Q
a group of molecules that are largely hydrophobic and only sparingly soluble in water
A
lipids
3
Q
what does in vitro mean?
A
outside a living cell
4
Q
protein or RNA biomolecules that function as reaction catalysts to increase the rates of biochemical rxns
A
enzyme
5
Q
sequences of biochemical reactions coordinated and controlled by a cell in response to available energy
A
metabolic pathway(s)
6
Q
mechanisms that facilitate communication b/w cells, often initiated through the binding of small molecules to proteins called receptors
A
signal transduction
7
Q
nitrogen-containing molecules that function primarily as the building blocks for proteins
A
amino acids
8
Q
what are nucleotides made of?
A
- a nitrogenous base
- a 5-membered sugar (ribose / deoxyribose)
- 1-3 phosphate groups
9
Q
what are the 5 nucleotide bases?
A
adenine
guanine
cytosine
thymine
uracil
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)
11
Q
when polar and non-polar chemical properties are contained within the same molecule
A
amphipathic
12
Q
a molecule consisting of a polar carboxyl group (COOH) covalently linked to a non-polar extended hydrocarbon chain
A
fatty acid
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
14
Q
any of a group of small biomolecules that serve as reactants and products in biochemical reactions within cells
A
metabolite
15
Q
the rate at which reactants and products are interconverted in a metabolic pathway
A
metabolic flux
16
Q
metabolite/hormone/peptide that binds to target proteins and alters their structure and function to control biochemical processes
A
ligand
17
Q
a set of metabolic processes and reactions that uses oxygen to generate ATP
A
aerobic respiration
18
Q
the process of oxidizing water to capture chemical energy and generate oxygen
A
photosynthesis
19
Q
the conversion of carbon dioxide to organic compounds (particularly glucose)
A
carbon fixation
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)
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
22
Q
a system in which matter and energy are freely exchanged with the surroundings
A
open system
23
Q
a system in which energy is exchanged with the surroundings but matter is not
A
closed system
24
Q
a system in which neither matter nor energy are exchanged with the surroundings
A
isolated system
25
what is the 1st law of thermodynamics?
1st law: energy cannot be created or destroyed, only converted from one form to another
ΔE = Efinal − Einitial = q − w
26
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 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
27
what is the 2nd law of thermodynamics?
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
28
a measure of the spontaneity of a rxn
Gibbs free energy (G)
ΔG = ΔH − TΔS
29
a weak non-covalent bond in which hydrogen is shared b/w 2 electronegative atoms
hydrogen bond
30
what is the bond strength of a single H-bond?
20 kJ/mol
31
weak interactions b/w oppositely charged atoms or groups
ionic interactions
32
weak interactions b/w the dipoles of nearby electrically neutral molecules
van der Waals interactions
33
a type of weak interaction due to the tendency of hydrophobic molecules to pack close together away from water
hydrophobic effects
34
a difference in pressure across a semipermeable membrane caused by osmosis across the membrane
osmotic pressure
35
the diffusion of solvent molecules from a region of lower solute [] to one of higher solute []
osmosis
36
molecules are attracted to both polar and nonpolar environments
amphiphilic molecules
37
an aqueous solution that resists changes in pH because of the protonation or deprotonation of an acid-base conjugate pair
buffers
38
a weak acid with more than one dissociable H+
polyprotic acid
39
a.a. within a polypeptide chain
residues
40
short polypeptides that contain less than 40 a.a.
oligopeptides/peptides
41
each polypeptide chain is called a protein \_\_\_\_\_
each polypeptide chain is called a protein **SUBUNIT**
42
the pH at which a given a.a. has no net charge
isoelectric point (pI)
43
an electrically neutral but dipolar molecule that contains both positive and negative charges
zwitterion
44
molecules with the same molecular formula and atomic connectivity, but different 3D orientation of their atoms
stereoisomers
45
stereoisomers that are mirror images of each other and whose structures cannot be superimposed
enantiomers
46
enzyme that catalyzes the hydrolysis of a peptide bond
protease
47
refers to the a.a. sequence, which determines how the polypeptide backbone folds into an energetically stable 3D structure
primary (1°) structure
48
refers to the regular repetitive arrangement of local regions of the polypeptide backbone
secondary (2°) structure
49
what are the 3 major secondary structures in proteins?
* α helices
* ß strands
* ß turns
50
* 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
(cartoon) ribbon diagram
51
includes the spatial location (complete arrangement) of all the atoms in the polypeptide chain
tertiary (3°) structure
52
the structure of a protein complex containing more than one polypeptide chain
quaternary (4°) structure
53
collections of secondary structures that describe the spatial arrangement of a polypeptide chain
protein folds
think of folds as a description of the path the polypeptide follows in 3D space
54
what are the different ways to view 3D structures of proteins?
* space-filling model
* ball-and-stick model
* backbone model
* cartoon ribbon diagram
55
* 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
space-filling model
56
an excellent model to show bonding arrangement in proteins
ball-and-stick model
57
* model that shows the general course of the polypeptide chain
* difficult to see secondary structures
backbone model
58
* 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
cartoon ribbon diagram
59
* a right-handed helical conformation of a polypeptide chain
* one of the most common elements of protein secondary structure
α helix
60
a 2° structure of proteins consisting of an extended polypeptide chain with side chains positioned above and below it
β strands
61
a common secondary structure of proteins formed from β strands hydrogen-bonded together (b/w backbone NH and CO groups on separate strands)
β (pleated) sheets
62
where is the H-bond found in α-helices?
* 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
hydrogen bonds in α helix: measurements
* length of H-bonds b/w N and O: **2.8 Å**
* **3.6 residues** per turn
* pitch of **5.4 Å**
64
which a.a. can't be a side chain in an α-helix structure? why?
**PROLINE**
nitrogen in ring lacks a hydrogen and does not contribute to H-bonding; rigid ring also restricts confirmations that can be adopted
65
when is an amphipathic α helix generated?
when a.a. with hydrophilic or hydrophobic properties are positioned every 3-4 residues along the polypeptide backbone
66
a β sheet structure in which adjacent β strands are oriented in opposite directions with regard to amino to carboxyl termini
antiparallel β sheet
67
a β sheet structure in which β strands lie in the same amino to carboxyl orientation
parallel β sheets
68
the hydrogen bond arrangement is more stable for _____ β sheets than for _____ β sheets
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
a turn or a loop in a polypeptide chain that connects 2 β strands in an antiparallel β sheeet
β turn
70
what is the difference b/w type I and type II β turns?
**type I:** carbonyl oxygen b/w 2nd and 3rd residues is oriented inward
**type II:** carbony oxygen faces outward
71
* irregular segments that connect elements of secondary structures
* usually range from 6 to 20 residues in length
loops
72
why are secondary structures common in proteins?
hint: think angles
secondary structures are common because they minimize the steric hindrance of the side chains
73
which a.a. have the highest propensity to occur in α helices?
**AH: E**at **A**ss **L**ike **M**y **Q**ueen/**K**ing/**R**oyal **H**ighness **I**s **W**atching for **F**un
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
which a.a. have the highest propensity to occur in β strands?
**BS: L**il **M**att **V**ader **I**s **Y**our **C**ousin? **W**ord! **F**un **T**imes
beta strands
L (leucine)
M (methionine)
V (valine)
I (isoleucine)
Y (tyrosine)
C (cysteine)
W (tryptophan)
F (phenylalanine)
T (threonine)
75
which a.a. have the highest propensity to occur in β turns?
**B**u**T**: **E**ach **K**ing **G**ot **N**ew **P**ants **S**ent **D**own
beta turns
E (glutamate)
K (lysine)
G (glycine)
N (asparagine)
P (proline)
S (serine)
D (aspartate)
76
what are the 4 general classes of protein structures?
* predominantly α helix
* predominantly β sheets
* α/β combined (Intermixed helices and strands)
* α + β (helical regions adjacent to sheets)
77
an independent folding module within a polypeptide chain
domain
78
a small but distinct structural unit of a protein fold
motif
79
contains 4 α-helices linked together (one of the most common protein folds)
four-helix bundle
80
consists of 4 or more β strands linked together to form β-sheet structures
Greek key fold/motif
81
* 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
Rossmann fold
82
an alternating α helix/β strand fold first identified in the glycolytic enzyme triose phosphate isomerase
TIM barrel fold
83
* 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)
TIM Barrel fold
84
a large protein fold (300 a.a.) containing 3 distinct structural components that are found in some proteins that bind to membrane-associated biomolecules
FERM Domain fold
85
what are the structural components of the FERM domain fold?
**FA/FC:** mostly β sheets
**FB:** contains only α helices
86
what are the 4 proteins where the FERM domain fold is found?
* Band 4.1
* ezrin
* radixin
* moesin
87
tertiary structures can be stabilized by _____ and \_\_\_\_\_
tertiary structures can be stabilized by **DISULFIDE BONDS** and **METAL IONS**
88
the number and overall arrangement of the polypeptide chains w/in multi-subunit protein complexes
quaternary structure
89
a protein complex containing two identical protein subunits encoded by the same gene
homodimer
90
a protein complex with 2 subunits derived from distinct polypeptides (different gene products)
heterodimer
91
how do multiple protein subunits (4º) provide increased functional to proteins?
* 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
a homodimer of 2 helical polypeptides wrapped around each other to form a coiled coil
keratin
(a fibrous protein)
93
a fibrous protein consisting of 3 subunits (2 heavy chain, 1 light), one of which consists entirely of β sheets
silk fibroin
94
a protein complex consisting of long helical subunits that are intertwined to form a right-handed triple-helix fiber
collagen
95
a protein that facilitates the formation of stable 3D structures through the process of protein folding
chaperones
96
what are the 3 main functions of chaperone proteins?
* help newly synthesized proteins fold properly
* rescue misfolded proteins
* disrupt protein aggregates
97
a denaturing condition in which 50% of the proteins are fully folded and 50% are fully unfolded (no partially folded/unfolded proteins)
transition curve midpoint (Tm)
98
an enzyme that cleaves RNA, also the first protein shown to be capable of denaturing and refolding *in vitro*
ribonuclease A (RNAaseA)
99
an intermediate stage in a model of globular protein folding in which hydrophobic residues first form the interior of the protein
molten globule
100
a protein folding model which proposes that hydrophobic residues first form the interior of the protein through loosely defined tertiary structures (molten globules)
hydrophobic collapse model
101
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
framework model
102
a protein folding model which proposes that local 2° structures form before 3° structures, driven by localized interactions b/w 2° structures
nucleation model
103
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
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
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
heat shock family (clamp-type chaperone proteins)
105
a well-characterized clamp-type chaperone protein
Hsp70
named from Its molecular mass of 70 kDa
106
consists of 14 identical polypeptide subunits arranged in 2 rings of 7 subunits each that houses a protein folding chamber
GroEL component of chaperonins (Hsp60)
107
what are the 3 protein domains of the GroEL component of chaperonins/Hsp60?
**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
* 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
**GroES component** of the GroEL-GroES complex
109
what are the possible causes for protein folding diseases?
* due to mutations in the protein-coding sequence of the gene
* accumulated misfolded proteins that contain no a.a. changes
110
an enzyme found in bioluminescent organisms that catalyzes a reaction of **luciferin** to generate visible light (one of the earliest biochemical assays)
luciferase
111
an isotonic suspension of lysed cells, used for protein isolation and identification
cell extract/cell homogenate
112
what are the most commonly used homogenization techniques?
**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
* 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**
centrifugation
114
the total amount or activity of a target protein, divided by the total amount of protein in the sample
specific activity
115
what are the four fractions that can (possibly) be obtained from a eukaryotic cell extract after centrifugation?
nuclei
mitochondria
plasma membrane components
cytosol
116
a protein separation method that involves adding increasing amounts of a saturated ammonium sulfate solution to the protein solution
salting out
117
a diffusion-based process that uses a semipermeable membrane to allow small molecules to cross the membrane but not large molecules (usually proteins)
dialysis
118
a technique that separates proteins on the basis of differential physical or chemical interactions with a solid gel matrix
column chromatography
119
what are the 3 types of column chromatography?
gel filtration
ion-exchange
affinity
120
a column chromatography method that uses porous hydrocarbon beads to separate proteins on the bases of size
gel filtration chromatography (aka size-exclusion)
121
a protein purification method that exploits charge differences b/w proteins
ion-exchange chromatography
122
what are the 2 commonly used ion exchange matrices in ion-exchange chromatography?
(+) charged anion-exchange matrix called **DiEthylAminoEthyl (DEAE)** cellulose
(-) charged cation-exchange matrix called **CarboxyMethylCellulose (CMC)**
123
a buffer solution with a high [] of an appropriate competing ion to dispalce the bound protein (used in ion-exchange chromatography)
elution buffer
124
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
affinity chromatography
125
a biochemical technique that separates proteins on the basis of charge and size
gel electrophoresis
126
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)
polyacrylamid gel electrophoresis (PAGE)
127
* 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
sodium dodecyl sulfate (SDS)
128
\_\_\_\_\_ proteins migrate faster through the buffer-saturated polyacrylamide gel matrix than _____ proteins
**SMALL** proteins migrate faster through the buffer-saturated polyacrylamide gel matrix than **LARGE** proteins
129
\_\_\_\_\_ proteins resolve well in gels with low percentage of polyacrylamide, while _____ proteins resolve best in high percentage polyacrylamide gels
**LARGE** proteins resolve well in gels with low percentage of polyacrylamide, while **SMALL** proteins resolve best in high percentage polyacrylamide gels
130
a type of polyacrylamide gel electrophoresis that separates proteins on the basis of charge as a function of pH
isoelectric focusing
131
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
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
a protein separation technique that combines isoelectric focusing and SDS-PAGE to separate proteins on the basis of both pI and molecular mass
2D PAGE
133
uses the fluorescent dyes Cy3 and Cy5 to distinguish 2 protein samples run on the same 2D PAGE gel
2D differential in-gel electrophoresis (2D DIGE)
134
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
Edman degradation
135
how is Edman degradation better than Sanger's old method?
(for protein sequencing)
Edman degradation does not require the input of additional protein after each round of cleavage
136
what is a limitation of Edman degradation?
it is not possible to obtain the sequence of a polypeptide longer than 50 a.a. in a single set of reactions
137
protease enzymes that cleaves a polypeptide chain on the **carboxyl side** of **lysine or arginine**
trypsin
138
protease enzyme that cleaves a polypeptide chain on the **carboxyl side** of **tyrosine, tryptophan, or phenylalanine**
chymotrypsin
139
trypsin cleaves polypeptide chain on carboxyl side of which a.a.?
**lysine** and **arginine**
140
chymotrypsin is a protease enzyme that cleaves the polypeptide chain on the carboxyl side of which a.a.?
aromatics (**tyrosine**, **tryptophan**, and **phenylalanine**)
141
protease enzyme that cleaves polypeptide chain on carboxyl side of **methionine**
cyanogen bromide
142
cleaves the carboxyl side of aspartate and glutamate
S. aureus
143
a method of measuring the mass-to-charge ratio of molecules, which is then used to deduce the molecular mass
mass spectrometry
144
* 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
elctrospray ionization (ESI)
145
a method for generating peptide ions for mass spec in which tryptic fragments are released as charged molecules after exposure to laser flash
matrix-assisted laser desorption/ionization (MALDI)
146
* 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
NMR spectroscopy
147
provides a snapshot in time of protein structure because it gives atomic positions in a static protein crystal lattice
X-ray crystallography
148
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
isomorphous element
