Proteins and DNA Flashcards
1
Q
Where does DNA –> RNA occur
A
nucleus
2
Q
what is it called for DNA to be converted to RNA
A
transcription
3
Q
where does RNA convert to protein
A
cytoplasm
4
Q
what is it called for RNA to be converted to protein
A
translation
5
Q
what is the primary structure of proteins composed of
A
amino acids
6
Q
how are amino acids in primary structures held together
A
peptide bonds
7
Q
what kind of bonds are peptide bonds
A
covalent
8
Q
what is the chain of amino acids called
A
polypeptide chain
9
Q
how do secondary structure proteins come about
A
polypeptide chains fold into sheets
10
Q
what are secondary structures due to
A
H-bonds
11
Q
what makes the backbone of a protein
A
primary structure proteins
12
Q
what are the 2 types of secondary structure proteins
A
A helix and B sheets
13
Q
what is a shape characteristic of alpha helixes
A
corkscrew
14
Q
what is a shape characteristic of beta sheets
A
parallel or antiparallel
15
Q
where does C=O bind to N-H in alpha helixes
A
4 AA residues ahead
16
Q
where does C=O bind to N-H in beta sheets
A
side by side sheets
17
Q
which way do R groups point in beta sheets
A
in
18
Q
which way do R groups point in alpha helixes
A
out
19
Q
are tertiary structure proteins hydrophobic or hydrophilic
A
hydrophobic
20
Q
what determines the shape of tertiary structure proteins
A
polar/nonpolar R groups
21
Q
what 3 things determine protein shape
A
type of amino acid, order of amino acid, and bonds between amino acid
22
Q
what are prion proteins
A
bad proteins
23
Q
what is an amyloid
A
PRPsc enters protein and makes it defective
24
Q
where is DNA located
A
in the nucleus
25
what kind of RNA leaves the nucleus
fully modified
26
is euchromatin or heterochromatin loose
euchromatin
27
is DNA accessible in euchromatin
yes
28
is DNA accessible in heterochromatin
no
29
what is a nucleotide
phosphate and sugar
30
what is a nucleoside
just sugar
31
what are the two types of nitrogen bases
purines and pyrimidines
32
what are the purines nitrogen bases
adenine and guanine (pure silver - Ag)
33
what are the pyrimidines nitrogen bases
cytosin, thymine, and uracil
34
what is the nitrogen base that is only found in RNA
uracil
35
what is pentose
a 5 carbon sugar (penthouse has 5 floors)
36
what does carbon 1 do
links bases
37
what does carbon 2 do
identifies sugar
38
what does carbon 3 and 5 do
phosphodiester bond
39
what is called when the hydrogen on carbon 2 contains a oxygen
ribose
40
what is it called when the hydrogen on carbon 2 doesn't contain a oxygen
deoxyribose
41
what kind of bond is between carbon 3 and 5 on a pentose
phosphodiester bond
42
what is the 1st nucleotide on a pentose
OH on 3' carbon
43
what is the 2nd nucleotide on a pentose
phosphate group of 5' carbon
44
what does the OH on 3' carbon bind to
phosphate group of 5' carbon
45
what does the binding of OH to phosphate cause on a pentose
3rd phosphate of ATP is cut off to form backbone
46
what kind of bond are base pairs
H bonds
47
what is needed for base pairs to bond
optimal distance
48
how many copies of DNA does the nucleus contain
1
49
what does helicase do
breaks H bonds
50
what does primase do
create RNA primer
51
which way does polymerase read
3'-5'
52
what way does polymerase write
5'-3'
53
what is called when the polymerase writes the protein in segments
ozaki fragments
54
what happens to the ozaki fragments
they are ligated
55
what is ligation
to be put together
56
what is the base of the promoter region called
TATA box
57
what does the TATA box recruit
transcription factors
58
what do the transcription factors on the TATA box recruit
RNA polymerase
59
what is another function of RNA polymerase
unwinds DNA
60
what does U replace in RNA
T
61
what does A pair with
T
62
what does C pair with
G
63
what is the type of RNA for polymerase 1
rRNA
64
what is the type of RNA for polymerase 2
mRNA and snRNA
65
what is the type of RNA for polymerase 3
rRNA, tRNA, and snRNA
66
where on the pentose is RNA found
OH on 2' carbon group
67
is RNA or DNA more stable
DNA
68
what is the main structure for RNA
single stranded but can fold
69
what is the function of rRNA
core of ribosomes
70
what is the function of mRNA
protein synthesis template
71
what is the function of tRNA
carries AA to ribosomes for protein synthesis
72
what is the function of snRNA
processes DNA and RNA
73
what is 5' capping
attaching a nucleotide on the 5' end
74
what is 3' poly adenylation
adding a lot of A nucleotides to 3' end
75
what is splicing
removing the intron, exons join together
76
which way is mRNA read
5' - 3'
77
what is the word for 3 bases
codon
78
what is a codon
a specific amino acid
79
what is the wobble
3rd base that differs/varies
80
what is a point mutation
single base changed
81
what is a frameshift mutation
all codons after mutation are different
82
what is a missense mutation
changed base --> 1 changed codon
83
what is a nonsense mutation
stop codon made
84
what is a silent mutation
base change doesn't result in anything
85
what do ribosomes translate mRNA to
proteins
86
what do rRNA bundles make
subunits
87
what does the small subunit do
read mRNA
88
what does the large subunit do
docking site for tRNA
89
what is the order of the initiation sites
E P A (APE)
90
where is tRNA found
ribosomes
91
what does tRNA contain
anticodons
92
what happens when tRNA binds to codon
it releases its amino acid
93
what charges empty tRNA
tRNA synthetase
94
in charging tRNA, what does ATP cleavage link together
amino acids and tRNA
95
what does tRNA drop at the ribosome
amino acids
96
what is elongation in translation initiation
addition of amino acid
97
what happens when the subunit makes a stop codon in translation initiation
proteins releases and ribosomes dissociates from mRNA
98
where are proteins with a signal sequence moved to
rough endoplasmic reticulum
99
what does the ERAD do
degrades troubled proteins
100
what causes ERAD to start
the cell recognizes misfolded protein
101
what is added to protein in the ERAD process
ubiqudin
102
where does ubiqudin cause the protein to move to
cytosol to cytoplasm
103
what degrades the protein once it moves to the cytoplasm
proteasome
104
what does unfolded protein response (UPR) stop
translation
105
what do chaperons do
folds and unfolds protein
106
what does UPR create more of in response to misfolded protein
chaperons
107
where are chaperons found
endoplasmic reticulum
108
what is the last resort for misfolded proteins
autophagy
109
what is autophagy
cell death
110
what does the Golgi apparatus sort
ER products
111
how do vesicles enter the golgi
cis face or trans face
112
what is cis face
part of golgi closest to nucleus
113
what is trans face
part of golgi furthest to nucleus
114
what part of the cell is the "road"
cytoskeleton
115
what part of the cell is the "vehicle"
motor proteins
116
where does the + end send stuff toward
membrane
117
where does the - end send stuff toward
nucleus
118
do microtubules carry stuff short or long distances
long distances
119
does f-actin carry stuff short or long distances
short distances (this man is so f-ing short)
120
which way does kinesin carry stuff
+ end
121
which was does dynein carry stuff
minus end
122
what is the way to remember what motor proteins carry stuff which direction
(+)K5 - D6
123
what is endocytosis
moving things into cytoplasm
124
what is phagocytosis
big particles get eaten
125
what is pinocytosis
fluid gets drunk (Pino like the wine)
126
where does COP2 carry stuff in receptor mediated endocytosis
ER --> golgi
127
where does COP1 carry stuff in receptor mediated endocytosis
golgi --> ER (the L in golgi looks like a 1)
128
where does clathrin carry stuff in receptor mediated endocytosis
to and from plasma membrane
129
what separates vesicle and membrane in receptor mediated endocytosis
dynamin (dynamite causes stuff to break apart)
130
what happens to the cage at the docking site in receptor mediated endocytosis
it sheds
131
what happens when V-snare binds to T-snare
water is squeezed out
132
what is V-snare
the vesicle
133
what is T-snare
the target/membrane
134
what are the V-snare(s)
VAMP
135
what are the T-snare(s)
syntaxin and snap-25 (Taylor swift) (sin and snap)
136
what is the calcium binding protein
synaptotagmin (tags the membrane because it's on the vesicle)
137
what activates the SNARE complex
calcium binding
138
what is formed when V and T snares wind together
A helices
