Test One Flashcards
(179 cards)
1
Q
electropositive atoms
A
atoms with tendency to give away electrons
2
Q
characteristic of polar, uncharged R group
A
interact with H2O, or other atoms on other side chains with H bonds,
3
Q
a function protein may be formed by
A
one polypeptide chain or from several
4
Q
van der waals interactions rely on
A
distance between the interacting atoms, attraction and repulsion is balanced out, has to have right fit on molecule
5
Q
what is in a nucleoside
A
base and sugar
6
Q
characteristics of nonpolar aromatic r groups
A
hydrophobic
7
Q
nucleotides are linked together by
A
phosphodiester bonds
8
Q
what aa are polar neg charge
A
aspartate, glutamate
9
Q
what is quaternary structure
A
connections between two or more polypeptide chauins
10
Q
what is resonance
A
single and double bonds adjacent to each other can have multiple structures
11
Q
what aa has an indole group
A
tryptophan
12
Q
what connection is the peptide bond that joins two aa
A
C-N
13
Q
what is tertiary structure
A
3-d orientation of all the different secondary structures and the turns and loops that connect them
14
Q
How does modification of RNA help
A
affect the ability of RNA molecules to fold into their correct 3-D structure and to interact with proteins
15
Q
what 2 aa carry a neg charge at ph of 7
A
aspartate and glutamate
16
Q
what is secondary structure
A
regularly repeating elements within a protein, in which h bonding forms between polar atoms in the backbone chain
17
Q
what binds in a beta turn
A
carbonyl oxygen of first residue forms h bond with amide H of 4th residue
18
Q
proline is known as
A
helix breaking residue
19
Q
methionine has what type of group
A
thioether, cluster in protein and stabilize structure through hydrophobic effects
20
Q
methylation of DNA in bacteria helps with
A
protection of DNA from degradative enzymes
21
Q
what aromatic aa can form h bonds to make them somewhat polar
A
tyrosine (OH) and tryptophan (N)
22
Q
the strength of ionic bonds vary based on
A
salt concentration and hydrophobicity of the environment
23
Q
what causes alpha helix to lose structure
A
bulky side chains, polar side chains forming h bond with backbone,
24
Q
parallel b sheet
A
n to c terminal same direction
25
characteristic of nonpolar, aliphatic r group
composed of hydrocarbon chains, nonpolar, hyrdrophobic,
26
function of proteins
catalyzing biochemical rxns, structural roles, receiving and transmitting chemical signals, transporting specific ions and molecules across membranes
27
what is electronegativity
the propensity of an atom within a molecule to attract electrons to itself
28
what can stabilize alpha helix
opposite charge side chains forming ion pair, aromatic side chain creating hydrophobic effect, aa with charge opposite to partial charge of helix dipole
29
what aa do you find in beta sheet
large aromatic and proline,
30
what is the covalent link between two aa
peptide bond
31
a nucleotide molecule has three components
nitrogenous base, five C sugar, phosphate group
32
what polar uncharged aa can act as both donor and acceptor
asparagine and glutamine (amide group)
33
what is stereochemistry
the spatial arrangement of atoms within a molecule
34
which is stronger covalent or ionic
covalent
35
what are the two main secondary structures
alpha helix and beta strand
36
where is the OH group on RNA
2'
37
a right handed spiral for alpha helix is what direction
clockwise
38
DNA and RNA are composed of building blocks known as
nucleotides
39
what aa are polar, uncharged r groups
serine, threonine, cysteine, asparagine, glutamine
40
methylation of DNA in eukaryotes help with
activating or silencing gene expression
41
do ionic bonds restrict the orientation of bonded atoms
no
42
what aa are found less frequently in alpha helices
serine, asparagine, aspartate, and threonine, glycine, proline
43
nonpolar molecules are
no effective dipole moment
44
the h bond in alpha helix bonds with what
hydrogen on amide nitrogen h bonds with carbonyl oxygen on 4th reside towards n terminus
45
what positions in gamma turn form h bond
carbonyl of 1 and amide of 3
46
beta turn usually has what in position 2
proline
47
all h bonds of alpha helix point in what direction
same direction which sets up electric dipole that gives partial pos charge to n term and partial neg charge to c terminus
48
what bond connects N-C alpha
phi
49
what is an H bond
an attractive intermolecular force between two partial electrical charges of opposite polarity
50
does glycine contribute to hydrophobic effects
no, only contains Hydrogen
51
how is beta sheet formed
h bonds between backbone amide and carbonyl groups, structure needs more than one beta strand
52
what bond connects C alpha- carbon
psi
53
what aa are non polar, aliphatic
glycine, alanine, proline, valine, leucine, isoleucine and methionine
54
antiparallel b sheet
n to c terminal opposite directions
55
what is a primary structure
the sequence of amino acids that make up the polypeptide chain
56
what are the three weak chemical interactions
van der waals forces, hydrophobic interaction, and h bonding, sometimes even use weak ionic interactions
57
what is the hydrophobic effect
strong tendency of water to exclude nonpolar groups, forcing these groups to aggregate in contact with one another
58
what donor groups of the polar uncharged aa are there
serine (OH), threonine (OH) and Cysteine (sulfhydryl group)
59
what is a gamma turn
3 amino acids, reversal turn
60
what is pi stacking
attractive, noncovalent interactions resulting from overlap between electrons of neighboring aromatic rings
61
are the last four residues of alpha helix h bonded
no and causes dipole charge to be spread out and confirmation is irregular at the end
62
electronegative atoms
atoms with tendency to gain electrons
63
what is a covalent bond
2 atoms share a pair of electrons between their positively charged nuclei
64
beta turn usually has what in position 3
glycine
65
what are the two main types of protein shape
globular proteins, fibrous structural proteins
66
which configuration in favorite for peptide bonds
trans, alpha carbons lie on opposite sides
67
pi stacking with nucleotides help with
nucleic acid's helical structure
68
amino acids are joined together by
peptide bonds
69
two cys aa can form a
disulfide bond
70
peptide bonds can have what configurations
cis or trans
71
what is an ionic bond
complete transfer of one or more electrons from one atom to another
72
what is a polar covalent bond
the electrons are shared between the atoms but biased toward one pole of the two atom bond
73
how is DNA and RNA read
5' to 3'
74
what is the most common beta sheet
anti then mix then parallel
75
what is molecular biology
study of molecules that store and process genetic info
76
what is the portion of secondary structure that does not have alpha or beta
contains loops and turns allowing secondary structure to reverse direction to form folded, globular proteins
77
b strands are connected how
covalently in a single polypeptide
78
what makes up a protein
amino acids
79
what three aa carry a positive charge at ph of 7
lysine, arginine, histidine
80
how are the R groups of alpha helix
protrude outwards
81
what aa are polar pos charge
histidine, lysine, arginine
82
is water polar or nonpolar
polar
83
how are r groups on beta sheets
on opposite sides of each other, alternating to prevent interaction
84
what aa are non polar aromatic
phenylalanine, tyrosine, tryptophan
85
what is the primary modification of DNA nucleotides is
addition of methyl group to C, A and G bases
86
how many aa in alpha helix per turn
3.6
87
what is an electric dipole moment
separated positive and negative charges
88
uracil is similar to
thymine except absence of methyl group
89
what is a beta turn
complete reversal of direction using 4 residues
90
what are the ways RNA can be modified
methyl group added to bases or 2'-OH, substitution of less common bases for A,C,G, and U
91
what aromatic aa is most hydrophobic
phenylalanine
92
proline contains what
aliphatic side chain, creates steric henderance
93
characteristic of antiparallel b sheet
form nearly straight H bonds and are slightly more stable than parallel
94
characteristics of polar, charged R groups
positive charge at ph of 7, or neg charge at ph of 7, side chains form h bonds and ionic interactions with aa of opposite charge
95
can b sheets be a mixture of anti and parallel
yes
96
a left handed spiral for alpha helix is what direction
counterclockwise
97
bonding is what type of process
exothermic
98
what is a common quaternary structure
association of two identical subunits
99
what is a dimer
a protein consisting of two polypeptide subunits
100
what are domains
protein with 150 to 200 aa residues, polypeptide chain usually folds into two folding units
101
the larger the protein, what about domain
more domains it contains
102
do the domains have same function
not always but they sometimes interact with each other
103
function of zinc finger domain
bind dna
104
function of individual domain
catalyze a reaction ( nuclease activity)
105
supersecondary structures are also known as
structural motifs
106
what makes up a structural motif
beta sheets, alpha helices or combo of both
107
what is the smallest motif containing a beta sheet
beta hairpin
108
what is a beta hairpin
two antiparallel beta strands are connected, often by beta or gamma turn
109
beta sheets tend to follow what type of twist
right handed
110
if beta sheet contains hydrophobic r groups at every 2nd residue what happens
groups lie on same side of the sheet, facilitating layer formation in the folded state
111
what is a beta barrel
when beta sheet of 8 or more stands and with one surface that is hydrophobic can form a cylinder, first strand h bonds with last strand, hydrophob side chains inside cylinder
112
what is a greek key motif
common b motif, 4 antiparallel beta strands
113
what is a beta alpha beta motif
consists of two parallel beta strands connected by an alpha helix
114
what is an alpha/beta barrel
alpha helix linker connects two beta strand that are adjacent and H bonded together, 8 beta strands surrounded by 8 alpha helices
115
what is a rossmann fold
b-a-b, no circularization, central parallel beta sheet that contains alpha helices on both sides of the sheet
116
what is the helix turn helix
contains only alpha helices (2), used for transcription factors
117
what is the four helix bundle
4 alpha helices, parallel or anti, or mixture,
118
what is the coiled coil motif
two alpha helices pack against each other at an angle of 18 degrees and twwist around one another in left handed supercoil
119
how do alpha helices interact
interact using hydrophobic surfaces that face one another
120
what is an amphipathic helix
hydrophobic on one side and hyrdophillic on other
121
what is a leucine zipper motif
4 to 5 heptad repeats of leucine
122
what is an oligomer
protein composed of multiple polypeptide chains
123
what are protomers
individual polypeptide chains
124
what is an homooligomers
oligomer with identical subunits
125
what is an heterooligomer
oligomer with nonidentical subunits
126
purpose of oligomer
if one subunit misfolds it does not affect rest of protein
127
what are purines
a and G
128
what are pyrimidines
C, T, and U
129
where is the glycosidic bond on DNA or RNA
1' c and N9 of purine and N1 of pyrimidines
130
what are the type of pentoses in DNA or RNA
b-furanose
131
are the pentose rings planar
no they are puckered
132
where is the phosphodiester bond in RNA or DNA
5'-CH2 phosphate group linked with 3'-OH of next nucleotide, which gives directionality and polarity
133
is the backbone of DNA or RNA hydrophilic or phobic
philic
134
what on DNA or RNA backbone form h bonds with water
hydroxyl groups of sugar residues
135
what is an oligonucleotide
nucleic acid containing 50 or fewer nucleotides
136
what is a polynucleotide
more than 50 nucleotides
137
what is hydrophobic stacking
bases stack on each other to minimize the contact with water which help stabilize structure
138
what are the bonds with base stacking
van der waals and electrostatic interactions
139
what are the activated precursors of DNA and RNA synthesis
nucleoside triphosphates
140
what phosphate is needed to transfer to provide chemical energy for rxn
gamma phosphate from a nucleoside 5'triphosphate
141
cAMP is formed from
ATP
142
what enzyme is used to form cAMP from ATP
adenylyl cyclase
143
what are secondary messengers
cAMP and cGMP
144
direction of DNA
right handed
145
the pentose ring of each deoxyribose is in what conformation
c-2 endo
146
stability of double helix comes from
hydrophobic base stacking with dipole and pi orbital
147
purines have two conformations called
syn and anti
148
pyrimidines have what conformation
anti
149
what is the most common dna structure
b dna
150
a-dNA is favored when
no water present
151
turn of A-DNA
right
152
diameter of A-DNA is
wider
153
how many bp in helical turn for A-DNA
11
154
B-DNA has what turn
right
155
diameter of B-DNA is
narrower
156
how many BP per turn of B-DNA
10.5
157
turn of Z-DNA
left
158
diameter of Z-DNA
narrowest
159
how many BP per turn for Z-DNA
12
160
what is special about Z-DNA
alternating purines and pyrimidines
161
what can cause bend in DNA
4 to 6 A and T residues separated by C and G rich segments, allow for transcription factors to bind
162
palindromes
same seq read 5 to 3 and 3 to 5
163
what are inverted repeats
complementary sequences that occur on the same strand of a DNA or RNA molecule but in inverse directions, with seq separation between repeats
164
inverted repeats have ability to
form hairpin or cruciform
165
what is a mirror repeat
the inverted repeat seq is nonpalindromic
166
function of palindromic repeats and inversion seq
slowing or blocking protein synthesis, form recognition sites for restriction enzymes,
167
what is a tetraplex or quadruplex
four DNA strands associated together, need high G residues,
168
function of RNA secondary structure
enables RNA molecules to fold into many different shapes that lend themselves to many different biological functions
169
what are some other base pairing in RNA
A-A and G-U
170
RNA structure with -oh
extra site for H bonding, stabilizing 3d folding, influence sugar puckering, more compact A helical form
171
mismatch base pairs in RNA cause
bulges or internal loops
172
what is the most common secondary structure of RNA
hairpin allowing for thermodynamic stability
173
what else binds to RNA
metal ions and help shield the neg charge of backbone allowing molecule to pack closely together
174
what is a ligand
molecule bound by a given protein
175
what is a binding site
ligand binding to specific site on protein, specific
176
what is an induced fit
conformational change in the protein alters a binding site so it becomes more complimentary to ligand
177
what is cooperativity
conformational change in one subunit can affect the conformation of other subunits
178
DNA binding proteins function
protect DNA, organize DNA, regulate genes or groups of genes, alter conformation of DNA, metabolism of DNA, and ensure proper segregation of chromosomes
179
DNA binding proteins bind to
specific or non specific sites on DNA
