Unit One Flashcards
1
Q
The rate of absorptions of nutrients is determined by:
A
The cell’s surface area
2
Q
True or False: As cell size increases, its surface area to volume ratio decreases.
A
True
3
Q
Select the equation that describes surface area to volume ratio for a sphere
A
3/r
4
Q
Select the equation that describes surface area for a sphere
A
4 x Pi x r^2
5
Q
Consider four spherical cells, with radius of r1 = 0.05 micrometer; r2 =1.3 micrometers ; r3 =2.5 micrometers; r4 = 0.75 micrometers
Which cell has the largest surface area to volume ratio?
A
1
6
Q
Consider the surface area to volume ratio for the following spherical cells:
A. ratio: 0.5
B. ratio: 3.8
C. ratio: 0.03
D. ratio: 4.5
Which cell has the worst diffusion rate?
A
c
7
Q
As a cell grows larger, its:
A
volume increases faster than its surface area
8
Q
High surface area to volume ratio allows cells to do what quickly?
A
move material in and out of the cell
9
Q
Calculate the surface-to-volume ratio for a spherical bacterium with a diameter of 0.6
micrometers and compare it with the surface-to-volume ratio for a globular eukaryotic cell with a cell diameter of 100 micrometers. surface area of a sphere 4pir^2
A
10 and 0.06 micrometers, respectively
10
Q
Conceptually, a chemical equilibrium is the same as a cellular steady state.
A
false
11
Q
In a chemical equilibrium the concentration of reactants is always equal to the concentration of products.
A
false
12
Q
Cells of the intestinal lining have small protrusions known as microvilli that increase cellular surface area. What purpose might that serve?
A
to increase absorption
13
Q
Calculate the surface-to-volume ratio for a spherical bacterium with a diameter of 0.8mm and compare it with the surface-to-volume ratio for a spherical eukaryotic cell with a cell diameter of 150 micrometers. surface area of a sphere 4pir^2
A
0.0075 and 0.04 micrometers, respectively
14
Q
elect the option that best describes a chemical equilibrium:
- All of the options represent characteristics of chemical equilibrium
- Temperature remains constant when the system is at equilibrium
- Concentration of reactants and products remain constant when the system is at equilibrium
- Volume remains constant when the system is at equilibrium
A
all of the options represent characteristics of chemical equilibrium
15
Q
In a chemical equilibrium the concentration of reactants is always equal to the concentration of products.
A
false
16
Q
Which of the following statements about equilibrium is FALSE?
- At equilibrium, there is no net change in the system
- At equilibrium, the concentration of reactants and products remains the same
- At equilibrium, the forward and backwards reactions cease to occur
A
At equilibrium, the forward and backwards reactions cease to occur
17
Q
A Keq = 10 tell us what about where the equilibrium stands?
A
The reaction equilibrium lies to the right
18
Q
Consider the binding of oxygen to haemoglobin (protein without oxygen): Hb + O2 –> Hb-O2. If the pressure of the system decreases, predict what is the effect on the equilibrium shown?
A
The equilibrium shifts to the left
19
Q
How do we call a system that can exchange energy in the form of heat but not matter?
A
a closed system
20
Q
Entropy (S) is a thermodynamic measure of:
A
molecular randomness and disorder
21
Q
The change in enthalpy of a system is due to heat supplied at
A
constant pressure
22
Q
In which direction does heat energy move spontaneously
A
from hot to cold objects
23
Q
A system that increases in temperature at constant pressure is
A
gaining energy from its surroundings
24
Q
Select the option that best describes what will happen when the mass-action ratio is Q=3.5 and the equilibrium constant is Keq = 1.0
A
The reaction will proceed to the left in order to achieve equilibrium
25
what are the cellular dimensions of a cell limited by? how do parameters like volume, surface area, and size affect diffusion rate?
cellular size is limited by rate of diffusion of nutrients and waste
- upper limit of the cell is limited by rate of transport and need to deliver O2 to all parts of the cell
- lower limit of cell is determined by number of molecules needed to sustain living state of the cell
- larger surface area to volume ratio results in faster rates of diffusion
26
does volume increase faster or slower than surface area?
volume increases faster than surface area increases
27
draw, recognize, and name different functional groups (COME BACK TO DO THESE CARDS)
28
what are the four major building blocks for biological macromolecules and what do they look like
1. amino acids of proteins
2. some components of nucleic acids (nitrogenous bases and five-carbon sugars)
3. some components of lipids
4. the parent sugar
29
know the terminology and be able to identify structures that are: configurational isomer, conformational forms, enantiomers, diastereomers, chiral centers
- conformation: spatial arrangement of substituent groups that are free to assume different positions in space
- geometrical isomers (or cis trans isomers) differ in the arrangement of substituents groups with respect to the double bond
- chiral centers are asymmetric carbons. A molecule can have 2^n stereoisomers (n is the number of chiral centers)
- enantiomers: stereoisomers that are mirror images of each other. These have nearly identical chemical reactivities but differ in optical activity
- diastereomers: stereoisomers that are not mirror images of each other
30
why is molecular spatial distribution important in biomolecules?
spatial distribution influences molecules interactions and physical interplay with its surroundings.
31
why are thermodynamics an important aspect of biochemistry?
it deals with the energy output of chemical reactions and helps us understand how energy flows in biological cells, how large molecules assemble into complex structures, etc.
32
what are the definitions of an isolated system, a closed system, and an open system?
isolated system: system exchanges neither matter nor energy with its surroundings
closed system: system exchanges energy but not matter with its surroundings
open system: system exchanges both energy and matter with its surroundings
33
what is the first law of thermodynamics?
In any physical or chemical change, the total amount of energy in the universe remains constant, although the form of the energy may change
34
what are oxidation-reduction reactions?
One reactant is oxidized (loses electrons) as another is reduced (gains electrons) there is no with out reduction. This describes reactions involved in electron flow
35
what is the second law of thermodynamics
the randomness in the universe is constantly increasing
36
what is entropy? what kind of function is it? what is a favorable/unfavorable entropy? what is the formula of entropy
Entropy represents the randomness or disorder of the components of a chemical system. It is a state function meaning it depends only on the initial point and final point of a reaction. positive delta s is favorable negative delta s is not favorable, however delta s alone is not enough to determine spontaneity
37
what is enthalpy? what kind of function is it? what is a favorable/unfavorable enthalpy? what is the formula of enthalpy
enthalpy is the heat content roughly reflecting the number and kinds of chemical bonds. It is a state function measured by h final- h initial. It is a state function. A positive delta h indicates the final state has a greater amount of potential energy. A negative delta h means energy is released to the surroundings and this is favorable.
38
what is Gibbs free energy? what sign determines if it is favorable or unfavorable? what is the formula for gibbs free energy? under what conditions (s, h, and t) is gibbs free energy favored and not favored?
Gibbs free energy the amount of energy available to do work. It relates to the change in enthalpy and entropy that take place during a reaction at a specific temperature. A positive delta G is unfavorable. A negative delta G is favorable. When delta G=0 a system is at equilibrium.
39
what is the change of free energy in a spontaneous reaction and what is the change in a nonspontaneous reactions
spontaneous reactions have a negative change in free energy. Nonspontaneous reactions have a positive change in free energy
40
how do you make an unfavorable reaction favorable
couple it with a favorable reaction
change concentration? change temp?
41
what is energy coupling? give an example of a well known energy coupling reaction
energy coupling is when when an endergonic reaction is paired with an exergonic reaction so the overall reaction becomes favorable
42
what is Keq? how is it measured and what does it mean in terms of delta G
Keq is the equilibrium content. It is concentration of the products at equilibrium /concentration of the reactants at equilibrium. When Keq>1 the reaction favors the products at equilibrium. When Keq<1 the reactants are favored. When Keq=1 the concentrations of reactants and products are equal at equilibrium. It is used in the equation to find delta g
43
what is le chateliers principle and how does this apply to biochem reactions
When a system is at equilibrium if an external agent disrupts the equilibrium, the system will spontaneously move in the direction that diminishes the disruption. This maintains the equilibrium without having to add additional energy to the system. For unfavorable reactions we can couple the reaction or alter concentration to make it favor the direction of the products.
44
what is the mass-action ratio? how is it calculated and what does it mean in terms of Keq and delta G
The mass-action ratio (Q) is the ratio of product concentrations to reactant concentrations at a given time. This can be calculated to tell how far the reaction is from equilibrium.
45
what is the formula for standard free energy change
delta G= delta G (standard condition) +RTlnKeq
46
what do enzymes do and how do they work. Include what this does to transition state and activation energy
enzymes greatly enhance reaction rates of specific chemical reactions without being consumed in the process. Enzymes do NOT change activation energy of favorability of a reaction, they only increase the speed at which a reaction occurs.
47
what are pathways? how does this relate to catabolism and anabolism? what is catabolism and anabolism?
Pathways are sequences of consecutive reactions in which the product of one reaction becomes the reactant in the next.
Catabolism is degradative, free energy- yielding reactions. This drives ATP synthesis and produces the reduced electron carriers NAD(P)H
anabolism are synthetic pathways that require the input of energy. They take simple matter and create complex matter. The energy input used comes from catabolic pathways
48
what is metabolism and the what is the unity of life
Metabolism is the overall network of enzyme-catalyzed pathways, both catabolic and anabolic.
Unity of life: pathways of enzyme-catalyzed reactions that act on the main constituents of cells and its nearly identical in all living organisms
49
what is feedback inhibition
it keeps the production and utilization of each metabolic intermediated in balance. Pathways are usually controlled by feedback inhibition loops
50
what is systems biology
understanding complex interactions among intermediates and pathways in quantitative terms
51
what are hydrogen bonds? why are they biologically relevant?
weak electrostatic attraction between one electronegative atom and a hydrogen atom covalently linked to a second electronegative atom. Hydrogen bonds are found within the structure of DNA molecules. They are main reason for the folded shape structure for enzymes that allows biological reactions to occur.
they are individually weak but collectively strong interactions
52
what are the other noncovalent interactions that occur (everything except hydrogen bonds)
ionic interactions: electrostatic - permanently charged species, or between the ion and a permanent dipole.
dipole interactions: electrostatic - uncharged but polar molecules
van der Waals interactions: weak interactions between all atoms, regardless of polarity
Hydrophobic interactions: complex phenomenon associated with the ordering of water molecules around nonpolar substances
53
why is water such a good solvent
it dissolves salts and charged biomolecules by screening electrostatic interactions. The increase in entropy of the system is largely responsible for the ease of dissolving salts in water
54
why is polarity and solubility so important in biochemistry?
polarity allows you to predict whether or not a solute will be soluble to a solvent (like dissolves like)
55
what is the hydrophobic effect? why is this so important to our proteins
the tendency of nonpolar substances to aggregate in aqueous solutions and exclude water molecules. It is one of the major driving forces behind the proper folding of proteins
56
what is pH?
measures how acidic or basic a solution is. Low ph is acidic high ph is basic. pH=-log[H+]
57
what is the principle behind the dissociation of weak electrolytes
weak electrolytes only slightly dissociate in water. The extent they dissociate is dependent on the Ka
58
what is the henderson-hasselbalch equation? how is this used in biohchemistry?
the henderson-hasselbalch equation can predict the state of ionization of a molecule
59
what does pka measure and what is its formula
pKa measures acidity. pKa= -logKa
60
what is the buffering region
the flat zone of a titration curve. It is +/- one unit from the pH. In this zone a buffer can neutralize an acid or a base but not both
61
know all 20 amino acids by name and one letter code and be able to draw them (come back to do these cards)
62
what amino acids are essential?
histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine
63
classification of each amino acid based on r group
nonpolar aliphatic: glycine, alanine, proline, valine, leucine, isoleucine, methionine
Aromatic R groups: phenylalanine, tyrosine, tryptophan
Polar, uncharged R groups: serine, threonine, cysteine, asparagine, glutamine
Positively charged R groups: lysine, histidine, arginine
Negatively charged R groups: aspartate and glutamate
64
what types of modifications lead to uncommon amino acids? how do these modifications occur?
they can be modified after protein synthesis, during protein synthesis, or modified transiently to change a proteins function (e.g. phosphorylation.
Free metabolites
65
what is the acid/base chemistry of amino acids? how do you find small oligopeptide charge and and pI
amino groups can act as acid or bases due to their amino groups, carboxyl groups, and ionizable R groups (weak acids and bases). Amino acids function as buffers. A zwitterion is a dipolar ion that occurs at neutral pH.
The pH at which the net electric charge is zero is the isoelectric point (pI)
The net charge of the amino acid changes as the pH changes.
pHpKa the base form dominates
66
what is the reaction that leads to amino acid polymerization and BE ABLE TO DRAW OLIGOPEPTIDES
67
fundamentals of each purification/seperation technique (use comparison table)
68
know how to purify a protein based on data provided in a question
69
what are the levels of protein structure
Primary structure: the peptide bond and protein backbone
Secondary structure: describes the local and spatial arrangement of a segment in a polypeptide. Disregard the positions of R groups interactions with other segments. Stable secondary structures include the alpha helix, the beta conformation, and the beta turn
Tertiary structure: overall spatial arrangement of all atoms in a protein
Quaternary level of structure: spatial arrangement of two or more polypeptide chains to form a functional protein
70
why is primary structure of a protein important?
Drives the folding and intramolecular bonding of the linear amino acid chain, which ultimately determines the protein's unique three-dimensional shape. shape determines function
71
how does mass spectrometry work?
atoms or molecules are ionized using a high-energy electron beam and then separated based on their mass-to-charge ratios (m/z).
72
what information can you gain from mass spectrometry and tandem mass spectrometry
Mass spectrometry provides information concerning the molecular structure, atomic mass of whole molecules, molecular fragments, and atoms.
tandem ms: two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. First round sorts peptides produced by cleavage, second step, second round measures m/z ratios of charged fragments.
73
how are samples introduced for mass analysis?
Step 1: ionize analytes into a vacuum
Step 2: introduce charged molecules to electric and/or magnetic fields
Step 3: charged molecules move through field as function of the mass to charge ratio, m/z
Step 4: deduce mass of analyte
74
what are the limitations of tandem MS?
cannot be applied for single-cell analyses as it is insensitive to analyze such small amounts of a cell
75
What is the Ramachandran principle and how is it used to determine protein and secondary structures
The Ramachandran plot visualizes all of the phi and psi angles observed in different proteins. It can reveal potential secondary structures for an unknown protein. Glycine is the only amino acid that doesnt fall in the expected range
76
what is the chemical nature of a polypeptide bond and how does it influence protein folding
covalent bonds between alpha carbons. The are three types of covalent bonds alpha C-N, alpha C-C, and C-N. The C-N bonds have partial double bond character so they can't rotate freely (resonance). The resonance forces the peptide bond to conform within a plane
77
which bonds can rotate in a proteins backbone?
Only in bonds containing the alpha carbon
78
what limits the rotation of bonds in a proteins backbone?
the partial double bond character of C-N bonds
79
why does secondary level of structure have such low diversity?
the C-N bonds force the peptide backbone to have a planar structure
80
what are the levels of structure for fibrous proteins
- filaments or elongated form
- provide support, shape, and external protection
- formed by a single repeating secondary element of structure
- insoluble in water
- high concentrations of hydrophobic amino acid residues (to favor how they fold and feeds into their hydrophobic nature)
81
what are the levels of structure for globular proteins
- compact shape
- wide array of functions due to structural diversity
- function as enzymes, transport proteins, receptors, motor proteins, regulators, and more
- soluble in water or bound to membranes (hydrophilic amino acid on exterior)
- may contain a combination of secondary level strucures
82
what experimental data supports the principles of protein folding
83
what are the principles of protein folding
- the hydrophobic effect is a major contributor to stability of folded proteins. Burial of hydrophobic R groups requires 2+ layers of secondary structure
- alpha helixes and beta sheets are found in different layers
- adjacent amino acids segments are usually stacked adjacent
- the beta conformation is most stable with right-handed connections
84
what are the characteristics of collagen and keratin? what kind of protein are they?
They are fibrous proteins.
Collagen: found in cartilage, bones, tendons, and skin.
- primary: repeating tripeptide sequence (gly-pro-hyp)
- secondary: left handed helix with 3 aa residues per turn. Glycine is always in the 3rd position. Left handed turn is a result of steric hinderance from proline
tertiary and quaternary: structure stabalized by h-bonds and covalent bonds (lys, HyLys, His)
our body is able to withstand the forces of life due to the secondary and quaternary structure
Keratin: found in hair, nails, feathers, and skin
- primary: sequence of aa. 7aa psuedorepeat (rich in ala, val, leu, ile, met, phe)
- secondary: right handed alpha helix
- tertiary: spatial arrangement of all atoms in the right-handed alpha helix
- quaternary: two alpha helixes arranged in a left handed coiled coil.
The super twisting of the 4 structure increases the strength of the fiber because the counterspinning prevents stretching
85
what is the experimental evidence behind the different types of denaturation/ renaturation
denaturation:
- temperature: low temps- protein become too rigid to perform substrate binding but 3D structure is NOT lost. High temps- any weak interaction that is not covalent level primary structure in nature will break with high temp
- pH extremes: causes certain R groups to protonate/deprotonate (alters h-bonds) changing the amino acid sequence, thus function of the protein
- organic solvents: can replace h-bonds in the protein (examples include urea and guanidine). The interaction with organic solvents rather than h-bonds causes denaturation. They also cause denaturing due to the hydrophobic effect, they change the polarity of the environment the protein is in (decreases hydrophobic effect which is really important for protein folding)
- Detergents: detergents have a polar head and nonpolar aliphatic tail which alters the hydrophobic effect. (SDS is a detergent)
86
what is melting temperature and what info can be gained from a proteins melting temperature
melting temperature is the temperature needed to have 50% of denaturation in a protein. Once a protein has reached its melting temp it can't refold itself
87
what is the folding funnel model and how is it used to explain why proteins acquire a single native structure
88
what kind of system is a living organism
open system
89
Which of the following is a reflection of the total energy change in a chemical reaction, a measure of the number and kinds of bonds that are made and broken?
- delta G
- delta H
- delta S
- delta T
delta H
90
if under a given set of conditions, the reaction A --> B occurs with a delta G=-14 kj/mol and the reaction C-->B occurs when delta G= +16 kj/mol then:
A) the conversion of A to C is reversible
B) the conversion of A to C is exergonic
C) A and C can never be at equilibrium, even under different reaction conditions
D) The conversion of A to C is entropically driven
The conversion of A to C is exergonic
91
Which component is absolutely necessary for the purification of a protein?
A) column chromatography
B) the gene sequence of the protein
C) a means of detecting the protein
D) a centrifuge
a means of detecting the protein
92
The specific activity of a protein in crude cellular extract is 15 units/mg. Following a purification process, involving precipitation with ammonium sulfate and multiple chromatography steps, the specific activity of the protein is 12,000 units/mg. What is the purification factor?
A) 180,000
B) 800
C) 0.00125
D) 15
E) 12,000
800
the ratio of the final specific activity (12000) to the starting specific activity (15) gives the ratio 800. 12000/15= 800
93
denaturing gel electrophoresis separates proteins based on differences in:
A ) size and shape
B) molecular mass
C) charge
D) amino acid content
size and shape
94
What measurement increases during purification of an enzyme:
A) activity
B) total protein
C) specific activity
D) fraction volume
specific activity
specific activity is the number of enzyme units per mg of total protein. The specific activity is a measure of enzyme purity: it increases during purification of an enzyme and becomes maximal and constant when the enzyme is pure
95
what is the highest level of protein structure in human insulin, which has two polypeptides of different mass linked by several disulfide bonds?
A) primary
B) secondary
C) tertiary
D) quaternary
quaternary
when a protein has 2+ polypeptide subunits, their arrangement in space is referred to as quaternary structure
96
which statement is true about mass spec?
A) mass spec can be performed on analytes in the liquid phase
B) mass spec can obtain the sequences of multiple polypeptide segments of 100 residues each
C) the mass (m) of an analyte is used to deduce the mass to charge ratio with high precision
D) MALDI MS requires treatment of proteins with a protease before injection into a mass spec
E) mass spec can monitor changes in the cellular proteome as a function of metabolic state
mass spec can monitor changes in the cellular proteome as a function of metabolic state
- when coupled to peptide separation protocols, mass spec can document a complete cellular proteome. Changes in the cellular proteome can be monitored as a function of metabolic state or environmental conditions
97
Which statement is false
A) protein structure is commonly defined at four levels between organisms
B) the function of a protein is a result of its amino acid sequence
C) orthologs are homologs found in the same species
D) it is possible to change the amino acid sequence of a protein and have no effect on its function
C) orthologs are homologs found in the same species
Homologs from different species are called orthologs
98
The amino acid sequences of proteins:
A) can be used to establish evolutionary relationships between organisms
B) are an example of tertiary structure
C) are similar within a given organism
D) are also referred to as "consensus sequences"
can be used to establish evolutionary relationships between organisms
- protein sequences are a rich source of information about protein structure and function. Bioinformatics can analyze changes in the amino acid sequences of homologous proteins over time to trace the evolution of life on earth and establish evolutionary relationships between organisms
99
Which amino acid would most likely be found in the interior of a globular protein
A) Ala
B) D
C) glutamate
D) cysteine
E) Lys
Ala
- CH3 as a functional group wont dissolve in aqueous solutions
100
Which statements are true about the formation of a peptide bond:
A) a peptide bond forms when the carboxylic acid groups, R-COOH, of the two amino acids react together
B) a molecule of water links the amino acids together during peptide bond formation
C) amino groups amino acids act as electrophiles to remove the OH from alpha carboxyl groups
D) the amino group of one amino acid works as a nucleophile to displace the hydroxyl group of another amino acid
E) an OH group is removed from the alpha carboxyl group of one amino acid and an H from the alpha amino group of another amino acid
D) the amino group of one amino acid works as a nucleophile to displace the hydroxyl group of another amino acid
E) an OH group is removed from the alpha carboxyl group of one amino acid and an H from the alpha amino group of another amino acid
101
which statement is correct about peptides?
A) peptides have no alpha carboxyl groups
B) peptides have their amino acid sequences written from the N-terminus
C) peptides do not have isoelectric points
D) peptides are not biologically active
E) peptide bonds are broken through condensation reactions
peptides have their amino acid sequences written from the N-terminus
102
the cytoskeletal component filamentous actin is made of many subunits, all of which are globular action. Which term refers to globular actin in this context?
A) prosthetic group
B) protomer
C) ligand
D) cofactor
E) polymorphism
protomer
identical units in a multisubunit protein are referred to as protomers
103
which statement is correct about proteins?
A) proteins can consist of more than one polypeptide chain
B) proteins consist solely of polymerized amino acids
C) proteins all have similar amino acid compositions
D) proteins can, by definition, consist of no more than 2,000 amino acid residues
E) proteins do not have ionizable groups
proteins can consist of more than one polypeptide chain
- multisubunit proteins have two or more polypeptide chains that are noncovalently associated
104
which item is the predominant factor in protein stability?
A) disulfide bonds
B) hydrophobic effect
C) salt bridges
D) nonpeptide covalent bonds
hydrophobic effect
- this only requires protein to be in contact with solution, they are then brought into closer proximity due to the hydrophobic effect which then allows other things to occur like hydrogen bonding
105
why is there very little allowable rotation around the peptide bond?
A) peptide bonds are amide bonds
B) the R group prevents rotation about the peptide bond, except in glycine
C) the C-N bond is shorter
D) peptide bonds are only formed in the cis configuration
E) the partial double bond character makes the peptide bond planar
the partial double bond character makes the peptide bond planar
106
which amino acid would destabilize an amphipathic alpha helix if placed in the middle of one?
A) glycine
B) proline
C) glutamate
D) valine
E) all of these amino acids would potentially destabilize an amphipathic alpha helix
all of these amino acids would potentially destabilize an amphipathic alpha helix
107
the beta sheet:
A) can be either parallel or perpendicular
B) has strands in which the R groups of the amino acids are all on the same side of the sheet
C) is composed of amino acid residues all very near each other in the primary structure
D) is primarily stabilized by hydrogen bonds
is primarily stabilized by hydrogen bonds
108
ramachandran plots measure which dihedral angles?
A) phi and psi angles
B) psi and omega angles
C) phi and omega angles
D) phi, psi, and omega angles
phi and psi angles
omega is a peptide bond and peptide bonds dont rotate so they'll never be represented on the plot
109
which statement regarding the tertiary structure of proteins is FALSE?
A) amino acid residues far apart in primary structure may interact with each other in the tertiary structure
B) the tertiary structure of a protein is destabilized by the hydrophobic effect
C) many proteins can be classified as either globular or fibrous but not both
D) quaternary structure is the description of how the tertiary structures in a multisubunit protein are arranged with respect to each other
the tertiary structure of a protein is destabilized by the hydrophobic effect
110
Select the option that best describes what happens when the pH of a solution is neutral:
A) The concentration of protons is greater than the concentration of hydroxyl ions
B)The concentration of protons is equal to the concentration of hydroxyl ions
C)The concentration of protons is lower than the concentration of hydroxyl ions
The concentration of protons is equal to the concentration of hydroxyl ions
111
true or false: Temperature does not affect the ionization constant of a molecule
false
112
The predominant non-covalent interaction seen in alpha-helices and beta-sheets is ___.
A) electrostatic interactions
B) hydrogen bonds
C) dipole-dipole interactions
D) hydrophobic interactions
E) all of these choices
hydrogen bonds
113
alpha-helices and beta-sheets are examples of ___ structure.
A) 1
B) 2
C) 3
D) 4
E) none of the above
2
114
Which of the following best describes the peptide backbone in a beta-sheet?
A) coiled
B) compacted
C) highly extended
D) rigid
E) none of these choices
highly extended
115
Which of the following is most critical for maintaining the tertiary structure of a protein?
A) hydrogen bonding
B) hydrophobic effect
C) disulfide bonds
D) salt bridges
E) none of these choices
hydrophobic effect
116
Which of the following interactions would be involved in quaternary structure?
A) hydrogen bonds
B) hydrophobic effect
C) disulfide bonds
D) salt bridges
E) all of these choices
all of these choices
117
Which one of these characteristics is NOT true for alpha helix?
A) There are 3.6 amino acids per turn
B) There is a requirement for glycine every third amino acid residue
C) A hydrogen bond forms between the carbonyl oxygen of the n-th amino acid residue and the -N nitrogen in the amide bond of the (n + 4)th amino acid residue.
D) Proline is typically not found within the alpha helix structure
E) It is right-handed
There is a requirement for glycine every third amino acid residue
118
For beta-sheets, the terms ‘parallel’ and ‘antiparallel’ refer to ___________.
the direction of the associated peptide strands
119
Noncovalent forces that stabilize protein structure include all of the following except __________.
A) the hydrophobic effect
B) salt bridges
C) electrostatic interactions with metal ions
D) hydrogen bonding
E) disulfide bridges
disulfide bridges
120
The first step in the folding of disordered polypeptides into ordered functional proteins is the formation of ______.
A) Primary structure
B) Secondary structure
C) Tertiary structure
D) Quaternary structure
E) hydrogen bonds
Secondary structure
121
Molecular chaperones assist proteins in the formation of ___.
tertiary structure
122
Which of the following amino acids is generally absent from an alpha helix?
A) Trp
B) Ser
C) Ile
D) Pro
E) none of these choices
Pro
123
true or false: Alpha-helixes have torsional angles that range between -170 to -60 for Phi and -40 to -70 for Psi
true
124
true or false: Based on the Ramachandran principle, Phi and Psi torsional angles that adopt zero degrees are stable torsional angles.
false
125
In a protein, the most conformationally restricted amino acid is ______; the least conformationally restricted amino acid is ______.
pro, gly
126
What observation about protein refolding or renaturation helped to solidify the connection between primary amino acid sequence and 3-D structure?
A) Spontaneous refolding of proteins into their native state under physiologic conditions
B) Assisted refolding of proteins into their native state under laboratory conditions.
C) Identification of thermostable proteins than maintain their native state in adverse temperatures.
D) A and B
E) B and C
Spontaneous refolding of proteins into their native state under physiologic conditions
