Unit 1 Flashcards
(132 cards)
1
Q
DNA nucleotides
A
adenine, guanine, cytosine, thymine
2
Q
unbranched polymer that, when folded into its three dimensional shape, performs much of the work of the cell
A
Proteins
3
Q
of hydrogen bonds formed between A and T
A
2
4
Q
of hydrogen bonds formed between C and G
A
3
5
Q
transfer of info from DNA to RNA
A
transcription
6
Q
__________ are cells which are composed of multiple specialized compartments.
A
Eukaryotes
7
Q
Broad class of biological macromolecules which serve as a barrier, signaling component and performs several other duties
A
Lipids
8
Q
Highly organized region of the cell where protein glycosylation occurs
A
Golgi
9
Q
Responsible for protein processing and xenobiotic metabolism
A
Endoplasmic Reticulum
10
Q
Filled with proteases and other digestive enzymes
A
Lysosomes
11
Q
Four key classes of biomolecules
A
proteins, nucleic acids, lipids, carbs
12
Q
Eukaryotic vs Prokaryotic
A
Eukaryotic have membrane-bound compartments, prokaryotes do not.
13
Q
Intracellular, membrane-bounded compartments
A
organelles
14
Q
What is the role of the Endoplasmic Reticulum?
A
Rough ER: synthesizes proteins
Smooth ER: chemical processing
15
Q
Which macromolecule class is chiefly responsible for catalysis of cellular processes?
A
Proteins
16
Q
DNA and RNA are composed of what basic biochemical compounds
A
nucleotides
17
Q
What are the important functions of carbs
A
fuel and information; cell to cell communication
18
Q
Type of bond between oxygen and hydrogen in water
A
Hydrogen bond
19
Q
Electric _________ is the result of an electronegative atom in a covalent bond with a non-electronegative bond.
A
dipole
20
Q
Electrostatic interaction between atoms with opposite electrical charges are also called _______.
A
ionic
21
Q
Water shields the electrostatic interaction of ions due to its high ____________.
A
dielectric constant
22
Q
The distance when two atoms no longer repulse each other yet have a strongest attractions is known as the _________ radii or contact distance.
A
Van der Waals
23
Q
Thermodynamic force that drives hydrophobic interactions
A
Entropy
24
Q
A molecule with two distinctive chemical properties or characteristics
A
amphiphatic
25
Using Coulomb's Law, describe how water is an ideal solvent for the ions found in cells
Water has a high dielectic constant
26
What is the significance of hydrogen bonding in biochemical structures such as DNA?
Hydrogen bonding allows bonds to be broken and rebuilt.
27
What is an electrostatic interaction?
Interaction between ions, Na+ Cl-
28
What is the net effect of many van der Waals interactions?
stability in numbers
29
If most proteins are found surrounded by water in the cell, what type of functional groups would you expect to find on the surface of a water soluble protein?
Hydrophillic/Polar
30
What is the second law of thermo?
Entropy must always increase.
31
How do hydrophobic interactions aid in protein folding?
They force the nonpolar sidechains to come together.
32
Henderson-Hasselbach Equation
pH = pKa +log_10 (A-/HA-)
33
Chiral type of amino acids found in proteins
L-amino acid
34
Another name for dipolar molecules
Zwitter ions
35
Disulfide bonds are formed by pairs of which amino acid?
Cysteine
36
The amino acid with a pKa near neutral
Histidine
37
The amino acid with whose side group leads to a less flexible peptide bond
Proline
38
The amino acid with an imidazole side chain
Histidine
39
An amino acid which must be supplied by the diet
Essential
40
The amino acid with a negative charged sidechain at neutral pH.
Aspartate or Glutamate
41
Amino acid with sulfide side chains
Cysteine
42
The amino acid with the abbreviation Ser.
SErine
43
Amino acid that contains a weakly acidic "phenolic" group
Tyrosine
44
Amino acid with the smallest sized chain allowing great flexibility in a protein
Glycine
45
Charge of alanine when the pH is 2.0
+1
46
Amino acid with an iodine ring
Tryptophan
47
General structure of amino acid
NH3, COOH, H, R
48
What is the importance of the central carbon on an amino acid?
alpha-carbon
49
When a peptide bond is formed, what molecule is also made?
H2O
50
According to convention, _____________ is the terminus drawn on the left side of a peptide.
alpha amino group
51
Where are proteins with extensive disulfide links likely to be found?
extra-cellular
52
This amino acid disrupts the alpha helix
Proline
53
Name of the plot that shows the possible phi and psi angles in proteins.
Ramachandran
54
Why are all the theoretical combinations of phi and psi not possible?
steric clashes between atoms
55
Type of structure to which alpha helices, beta sheets, and turns are referred to
Secondary Structure
56
Overall 3D structure of a protein is referred to as its __________________.
Tertiary Structure
57
These reagents disrupt protein dislufide bonds
BME DTT
58
Almost all peptide bonds are this due to side group steric clash
Trans
59
__________ is a fibrous protein and is the primary component of wool and hair.
Alpha Keratin
60
Every third residue in the protein collagen is ________. Collagen contains _____________, a modified amino acid.
glycine; hydroxyproline
61
The _________ beta-sheet structure occurs when the two strands are oriented in opposite directions.
anti-paralllel
62
A protein is considered to be _________ when it is converted into a random coil structure without its normal activity.
denatured
63
__________ refers to the spatial arrangement of polypeptide subunits and the nature of their interactions.
Quaternary
64
How does a protein's amino acid sequence influence the tertiary structure?
The side chains of the amino acids affect the way in which the protein folds.
65
Name two methods that can be used to disrupt/break cells and tissues for protein purification
enzymatic; mechanical
66
A type of protein chromatography that is based on the attraction of the protein for a particular chemical group.
?
67
________ is added prior to protein gel electrophoresis to coat proteins with negative charges and to denature the proteins
SDS (Sodium ______ Sulfate)
68
Proteins with different sedimentation coefficients can be separated by _________.
centrification
69
Protein primary sequence can be determined by ________ and __________.
Edman Degredation; Mass spec
70
2D protein gel electrophoresis is separation of proteins based on _______ and ________.
isoelectric point (pi); size
71
Proteins can be separated from small molecules, ions, or buffers through a semi-permeable membrane by a method known as ________.
Dialysis
72
Chromatic method that separates proteins based on their charges
Gel filtration
73
__________ is a chemical reagent that is often used to detect the presence of amino acids
Ninhydrin
74
Chromatographic method that separates proteins based on their sizes
ion exchange
75
A nickel column used in purifying proteins will bind proteins that contain a ________ tag.
Hystine
76
In the Edman method for protein sequencing, phenyl isothiocyanate is used to selectively remove the _________ residue.
N-terminus
77
Disulfide bonds in proteins are readily oxidized by _______ or ________
BME; DTT
78
Polypeptides can be fragmented into smaller peptides by cleavage with trypsin, which hydrolyzes the peptide bond at the C-terminal side of ___________ residues
Lysine; Arginine; Histidine
79
_________ gels are often used media for electrophoretic techniques such as SDS-PAGE and isoelectric focusing.
Poly Acrylamine
80
The mobility of proteins in SDS-PAGE is inversely proportional to their _______.
mass
81
Websites where you can find published literature about proteins
PubMed
82
Websites where you can find published literature about protein primary sequence
Swiss Prot
83
Website where you can find published literature about protein 3D structures
Protein Data Bank
84
Determines protein tertiary structures at atomic resolution through diffraction of protein crystals
X-ray crystallography
85
Determines protein tertiary structures at atomic resolution through the use of atoms in the protein's magnetic properties
NMR
86
The site on the enzyme where the reaction occurs.
Active Site
87
The substance that the enzyme binds and converts to product
Substrate
88
Enzymes that do not have the required cofactor bound
Apoenzyme
89
A tightly bound cofactor (heme) might be called a ____________.
prosthetic group
90
Enzymes will decrease the energy of activation but does not change the ________ of a chemical reaction.
delta G
91
The enzyme active site amino acids facilitate a lower ___________.
activation energy
92
The two methods in which enzymes bind to a substrate
Lock and key; induced fit
93
Enzymes accelerate the rate of a chemical reaction by ________ the free energy of activation of the reaction.
lowering
94
An enzyme which loosely binds substrate will have a ________ level of specificity.
lower
95
Organic cofactors are referred to as _______.
coenzymes
96
A reaction can occur spontaneously only if delta G is __________.
negative
97
When delta G for a system is zero, the system is at __________.
equilibrium
98
The total change of free energy in a reaction depends on __________ and _________.
free energy product; substrate
99
Competitive inhibitors which mimic the substrate while in the transition state are called _________ inhibitors.
transition state
100
How do enzymes facilitate the formation of the transition state?
Enzymes lower the activation energy by bringing A closer to B.
101
Cooperativity
sigmoidal; allsoteric enzyme
102
Michaelis-Menten enzyme
hyperbolic curve with Vmax
103
_______ is the study of chemical reactions.
Kinetics
104
A reaction that is directly proportional to the concentration of reactant is a ________.
first order reaction
105
An enzyme reaction with two substrates is considered to be a _________ reaction.
second order reaction
106
At __________ there will be no net change of substrate or product.
steady state
107
The value _______ is called the initial velocity.
V_0
108
The k_cat/K_M is often referred to as the _________.
catalytic efficiency
109
An enzyme's affinity for its substrate is measured by what constant
K_M
110
________ Enzymes do not obey Michaelis-Menten kinetics
Allosteric
111
The type of inhibition by a product of one enzyme on another enzyme in an earlier protein in a metabolic pathway is a ________ inhibitor.
feedback
112
The straight-line kinetic plot of 1/V_0 versus 1/S is called a ___________.
double reciprocal
113
Aspartic Acid
Asp, D, Polar Acidic
114
Glutamic Acid
Glu,E, Polar Acidic
115
Histidine
His, H, Polar Basic pKa ~7
116
Arginine
Arg, R, Polar Basic
117
Lysine
Lys, K, Polar Basic
118
Serine
Ser, S, Polar Uncharged
119
Threonine
Thr, T, Polar Uncharged
120
Tyrosine
Tyr, Y, Polar Uncharged
121
Asparagine
Asn, N, Polar Uncharged
122
Cysteine
Cys, C, Polar Uncharged
123
Glutamine
Gln, Q, Polar Uncharged
124
Tryptophan
Trp, W, Hydrophobic
125
Phenylalanine
Phe, F, Hydrophobic
126
Proline
Pro, P, Hydrophobic
127
Methionine
Met, M, Hydrophobic
128
Leucine
Leu, L, Hydrophobic
129
Isoleucine
Ile, I, Hydrophobic
130
Glycine
Gly, G, Hydrophobic
131
Alanine
Ala, A, Hydrophobic
132
Valine
Val, V, Hydrophobic
