Molecular Bio Midterm #1 Flashcards
Lectures 1-11
1
Q
what is a local energy minimum
A
a state with less energy than its surrounding neighbours in protein folding
2
Q
what Is a chaperone
A
proteins that assist in proper folding of other proteins
3
Q
what is a homodimer
A
two of the same proteins
4
Q
what is a heterodimer
A
two different proteins
5
Q
what is kinase
A
an enzyme used to add a phosphate group to an amino acid
6
Q
what is a phosphatase
A
an enzyme used to remove phosphate groups from certain amino acids
7
Q
5 post-translational modifications
A
methylation, acetylation, phosphorylation, glycosylation, hydroxylation
8
Q
primary structure does what
A
encodes all information needed for proper protein folding
9
Q
what are the two forces driving protein folding
A
hydrophobic and van der waals interactions
10
Q
what does extreme electronegativity allow you to predict?
A
the type of bond that will form
11
Q
what is separation of positive and negative charges called
A
electric dipole moment
12
Q
how does electronegativity on the periodic table increase
A
left to right and bottom to top
13
Q
what is the separation of positive and negative charges called
A
electric dipole moment
14
Q
what are the three weak non-covalent bonds
A
hydrogen bonds, van Der Waals forces, hydrophobic interactions
15
Q
hydrogen bond (of H-bond) is primarily what the of force?
A
an electrostatic force of attraction between a hydrogen atom which is covalently bonded to a more electronegative “donor” atom or group (Dn), and another electronegative atom bearing a lone pair of electrons – the hydrogen bond acceptor (Ac)
16
Q
order the bond strength strongest to weakest
A
covalent, ionic, hydrogen and hydrophobic, van der waals
17
Q
polar compounds are water soluble so they are…?
A
hydrophilic
18
Q
non-polar compounds are not water soluble so they are..?
A
hydrophobic
19
Q
do proteins have hydrophobic or hydrophilic regions and why
A
have both hydrophobic and hydrophilic regions due to structure and function once folded
20
Q
5 functional groups
A
hydroxyl, amino, methyl, carboxyl, phosphate
21
Q
why is cysteine chemically unique
A
cysteine is the only amino acid that can form covalent bonds
22
Q
why is proline conformationally unique
A
part of essential things like collagen
23
Q
why is glycine conformationally unique
A
R group is H- nothing else can fit and it is flexible (can fit in many different spots)
24
Q
alpha carbons have what type of group
A
R- groups
25
what type of bond is formed between the c-terminus and the n-terminus
covalent peptide (C-N) partial double bond
26
is the peptide bond between the C-terminus and the N-terminus rotatable? why?
non-rotatable because carbon and oxygen are stuck at there respective sides
27
can other bonds rotate
the single bonds around the molecule are all rotatable
28
what is life
a chemical system capable of darwinian evolution
29
evolutionary processes depend on what
changes in genetic variability and allele frequencies over time
30
what are the three properties of life
multiplication, mutation, heredity
31
what we know about DNA
it is not the origin of like but provides stability and storage
32
RNA
reactive in a way DNA is not, capable of diversity, storage, and catalysis
33
which biomolecules are capable of diversity and storage but not catalyst?
RNA
34
life requires chemicals capable of what
storing information, replicating information, modifiability
35
what is RNA structure
highly evolved ribozyme
36
what is a ribozyme
RNA molecule that catalyzes things
37
p generation
parents used in a cross
38
F1 generation
progeny resulted from a cross in p gen
39
F2 generation
progeny resulting from a cross in the f1 generation
40
purebred
individual homozygous for a given trait or set of traits
41
hybrid
progeny resulting from a cross of parents with different genotypes
42
gene
section of DNA encoding a protein or functional RNA
43
allele
variant of the gene encoding a trait
44
phenotype
outward appearance of an organism
45
genotype
alleles contained in an organism
46
homozygous
having two identical copies of a allele for a gene
47
heterozygous
having two different alleles for a gene
48
dominant allele
allele expressed in the phenotype of a heterozygous organism
49
recessive allele
allele masked in the phenotype of a heterozygous organism
50
what does an atomic number stand for
number of proteins in its nucleus
51
how many bonds does H, O, N, and C need
H - 1
O - 2
N - 3
C - 4
52
what happens in a covalent bond
electrons are shared
53
what happens in ionic bond
electrons transferred
54
what is electronegativity
different affinities of the bonded atoms for electrons
55
what scale is electronegativity measured on
pauling scale
56
structural isomer
molecules with the same molecular formulas (number and type of atoms), but different bonding arrangements of atoms. They have different properties
57
what happens in extreme electronegativity
atom loses electron, and one becomes positive whereas the other becomes negative and forms an ionic bond
58
stereoisomers
molecules with the same molecular forms and bonding of atoms but different spatial arrangement. They have different properties
59
chiral molceule vs chiral molecule
a chiral molecule cannot be superimposed on its mirror image whereas an achiral molecule can be superimposed
60
what are the 4 unique amino acids
glycine, cystein, histamine, proline
61
how is a dihedral angle between two planes defined
defined by atoms 1,2, and 3 and atoms 2, 3, and 4 respectively
62
how are amide or peptide bond planes joined
joined by the dihedral bonds of the alpha carbon
63
how is a dihedral angle determined
between lines perpendicular to each plane
64
why are many possible conformations of an alpha carbon between two peptide planes are forbidden
few combinations are possible because of steric crowding/ hindrance
65
in an alpha helix, where does the hydrogen bond form
hydrogen on amide N forms a hydrogen bond with the carbonyl O of the 4th residue towards the N-terminus
66
amino acid residues in an alpha helix have conformations with what
ψ = -60° and ∅ = -45 to -50°
67
what is the N terminus
the nitrogen of the first amino group
68
what do helices exploit
maximum hydrogen bonding among groups
69
what is the N terminus
the nitrogen of the first amino group
70
when making a peptide bond where would you never add a new amino group
H2N
71
how are bonding strands in an antiparallel strand shown
straight
72
when making a peptide bond where would you add a new amino group
the OH of the first alpha carbon
73
how are bonding strands in a parallel strand shown
oblique (diagonal)
74
where does the R group of the helix pop out
towards the axis not outside
75
how do R groups alternate
up and down
76
how many angstroms are there per residue
3.5
77
how many angstroms are between R groups on the same side
7
78
where is the Phi angle around
the -N-CA- bond (where 'CA' is the alpha-carbon)
79
where is the psi angle around
around the -CA-C- bond.
80
what is a motif
particularly stable and common arrangements of multiple secondary structural elements (aka super secondary structures). motifs are structural but not necessarily functional characteristics
81
what is a domain
independent folding units with a defined function a domain can have one or more motifs
82
what is a protein
a functional polypeptide. it can have one or more domains
83
helical structures have R residues facing what way
outside
84
beta sheets (sheet motifs) have R residues facing what way
both inside and outside
85
what does a zinc finger motif do
reads DNA and shows alpha and beta
86
what is protein folding
the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil
87
all information needed for proper protein folding is encoded by what
primary structure
88
what are molten globules
compact, partially folded conformations of proteins that have near-native compactness, substantial secondary structure, dynamic tertiary structure and increased solvent-exposed hydrophobic surface area relative to the native state
89
what collapses during protein folding
postulated hydrophobic collapse
90
what is a local energy minimum
a dip that has less energy than its surrounding neighbours
91
what does a massive dip mean
protein has misfolded
92
what is methylation
addition of a methyl group
93
what is acetylation
addition of an acetyl group
94
what is phosphorylation
addition of a phosphate group
95
what is glycoslation
addition of a sugar molecule
96
what is hydroxylation
addition of a hydroxide (OH) group
97
what electronegativity range is non polar covalent
<0.4
98
what electronegativity range is polar covalent
0.4 - 1.8
99
what electronegativity range is ionic
>1.8
100
what is alpha-keratin
key structural material making up scales, hair, nails, feathers, horns, claws, hooves, and the outlet layer of skin among vertebrates.
101
what is alpha-keratin found in
vertebrates
102
what is beta-keratin found in
birds and reptiles
103
what is collagen
a fibrous structural protein with modified amino acids. it is the main structural protein in the extracellular space in the various connective tissues in animal bodies
104
what percent of whole body protein does collagen make up
25% - 35%
105
what three consistencies can collagen tissues be
depending on degree of mineralization, can be rigid (bones), compliant (tendon), or have a gradient from rigid to compliant (cartilage)
106
how many amino acid residues does each collagen helix consist of
~1000
107
what post-translational modification needs vitamin C as a reactant
hydroxylation of Pro and Lys
108
what can cause wrinkles
collagen levels decreasing and cross linking not being rebuilt properly
109
what happens at carbon 1'
the carbon that leads to the base – the pyrimidine or purine base is linked here
110
what happens at carbon 2'
tell you if it’s a ribonucleotide or deoxynucleotide
- ribonucleotide will have one hydroxy and one hydrogen
- deoxy will have two hydrogens
111
what happens at carbon 3'
it has a hydroxy which in involved in the phosphodiester bond – related to the 3’ molecule of DNA
112
what happens at carbon 4'
nothing
113
what happens at carbon 5'
the phosphate is attached here
- bond between the phosphate of the 5’ and the hydroxy of the 3’ is formed here
114
what are the purine bases
adenine and guanine
115
what are the pyrimidine bases
cytosine, thymine (DNA), uracil (RNA)
116
what does a nucleoside have
base and a sugar
117
what does a nucleotide have
base, sugar, and phosphate
118
what are the base names
adenine, guanine, cytosine, thymine, uracil
119
what are the nucleoside RNA names
adenosine, guanosine, cytidine, thymidine, uridine
120
how do the nucleoside DNA names differ from the RNA names
"deoxy" is added onto the front the names but the names stay the same as in RNA
121
what are the three-letter abbreviations for nomenclature of bases
adenosine - AMP
guanosine - GMP
cytidine - CMP
thymidine - TMP
uracil - UMP
122
how do the three letter abbreviations change when talking about DNA
a "d" is added in front of the three letter abbreviations which stay the same
123
what is the orientation of the DNA molecule
5' to 3'
124
why is DNA helical
protect the hydrophobic bases from water while exposing the backbone of the phosphodiester bonds
125
antiparallel orientation
one strand going 5' - 3' and the other going 3' to 5'
126
what is the secondary structure of DNA
two antiparallel polynucleotide chains wound around the same axis with a sugar-phosphate backbone wrapped around the outside
