DNA and Proteins Flashcards
1
Q
What is the Central Dogma?
A
The process by which DNA is converted to mRNA and then to a protein
2
Q
d: genome
A
the entire genetic material that makes up an organism
3
Q
d: allele
A
each of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome
4
Q
d: nucleotides
A
are organic molecules that serve as the monomer units for forming DNA and RNA
5
Q
name the two nucleotides that transcription occurs between
A
DNA
RNA
6
Q
what is a nucleoside compared to a nucleotide?
A
nucleotides without a phosphate group
7
Q
composition of nucleoside
A
base
sugar
8
Q
composition of a nucleotide
A
base
sugar
phosphate group
9
Q
eg of a nucleoside
A
adenosine
10
Q
d: nucleic acid
A
a complex organic substance present in living cells, especially DNA or RNA, whose molecules consist of many nucleotides linked in a long chain
11
Q
name the two classes of nucleic acids
A
purines
pyrimidines
12
Q
name the two purines
A
Adenine
Guanine
13
Q
name the three pyrimidines
A
uracil
thymine
cytosine
14
Q
are purine or pyrimidines larger molecules
A
purines are larger
15
Q
Name the bases present in DNA
A
Guanine
Cytosine
Adenine
Thymine
16
Q
Name the bases present in RNA
A
Uracil
Adenine
Cytosine
Guanine
17
Q
What are the components of AMP? (C present etc)
A
5 C 1 phosphate group adenine 1 oxygen in centre 2 hydroxyl groups 6 hydrogens in centre
18
Q
what does AMP stand for?
A
Adenosine 5’-monophosphate
19
Q
d: chromosome
A
a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.
20
Q
how is the polymer DNA formed?
A
through a condensation reaction of many nucleotides
21
Q
f: DNA
A
code for polypeptides
22
Q
Where is DNA found?
A
nucleus
23
Q
what is the bond called that forms during the condensation reaction of DNA nucleotides which holds them together?
A
phosphodiester bond
24
Q
f: phosphodiester bond
A
holds the sugar phosphate backbone of DNA together
25
d: purines
bases with a double ring structure
26
d: pyrimidines
bases with a single ring structure
27
What type of bonds form between adenine and thymine and how many?
Hydrogen bonds
| 2
28
What type of bonds form between cytosine and guanine and how many?
hydrogen bonds
| 3
29
How are the two DNA strands described motion wise? Why?
Antiparallel
| run in opposite directions to one another
30
What is the end of the DNA strand with the phosphate group attached called?
5' end
31
What is the end of the DNA strand without the phosphate group attached called?
3' end
32
Why does DNA have to be replicated (duplicated) before cell division?
so that the daughter cells have a complete complement of the genome
33
d: semiconservative
denoting replication of a nucleic acid in which one complete strand of each double helix is directly derived from the parent molecule
34
how is DNA replication described?
as semi-conservative
35
why must DNA polymerase enzyme only go in one direction?
its active site can only bind to nucleotides at one end
36
what does DNA polymerase require and where is it placed before it starts building up the backbone?
Primase ( RNA primer)
| 3' end
37
how many sights of origin do eukaryotic cells have for DNA replication?
multiple
38
why does replication start simultaneously at several points in the genome and bidirectionally?
ensures that replication can be finished in a reasonable time
39
what is the only end nucleotides can be added to?
3'
40
how do you know if its the leading strand?
always has a free 3’ end
41
d:lagging strand
the strand of forming DNA whose direction of synthesis is opposite to the direction of the growing replication fork
42
which DNA strand is replicated in short fragments? what are they called?
lagging strand
| Okazaki fragments
43
why is lagging strand replicated in fragments?
Copying lagging strand template is more complex
44
what separates the h-bonds in DNA replication?
DNA helicase enzyme
45
how are the free nucleotides joined together?
by forming phosphodiester bonds via DNA polymerase enzyme
46
incorporating the wrong type of nucleotide during DNA replication can cause which type of mutation?
deleterious
47
DNA polymerase has 3’ to 5’ exonuclease activity, how does this improve replication?
removes incorrect nucleotide
48
name the 3 main classes of RNA
ribosomal
messenger
transfer
49
f: rRNA
combines with proteins to form ribosomes where protein synthesis takes place
50
f: tRNA
carries the amino acids to be incorporated into the protein
51
f: mRNA
carries the genetic information for protein synthesis
52
name the stable RNAs
ribosomal
| transfer
53
describe the structure of RNA
| strands, loops, bases
single stranded
stem loops
contains Uracil (U)
54
what is a stem loop in RNA?
local stretches of intramolecular base-pairing
55
which RNA type has the highest % of total cellular RNA?
rRNA
56
which RNA type has the LOWEST % of total cellular RNA?
mRNA
57
d: anticodon
sequence of three nucleotides forming a unit of genetic code in a tRNA molecule, corresponding to a complementary codon in mRNA.
58
what type of structure do tRNA molecules have?
3D
59
describe the structure when tRNA is flattened into 2D
cloverleaf structure
60
what end is the specific AA attached to in tRNA? what does this depend on?
3'
| anticodon sequence
61
What makes RNA?
RNA polymerases
62
How many types of RNA polymerase do prokaryotic cells have?
1
63
How many types of RNA polymerase do Eukaryotic cells have? and names
3
POL I
POL II
POL III
64
How can the 3 POL's be distinguished?
by their sensitivity to toxins eg alpha-amanitin
65
What POL synthesises all mRNA?
POL II
66
describe the steps of transcription (5)
RNA polymerase binding
detection of initiation sites (promoters) on DNA
DNA chain separation
local unwinding of DNA
to gain access to the nucleotide sequence
Transcription initiation
selection of the first nucleotide of the growing RNA
Elongation
addition of further nucleotides to the RNA chain
Termination
67
What is the promoter of RNA?
Pol II
68
Where does transcription start?
at nucleotide +1
69
Where is the TATA box present?
about 25 nucleotides before the transcriptional start
70
How does RNA polymerase know where to start transcription?
promoter shows it
71
What does TBP stand for?
TATA box binding protein
72
f: TATA box
regulates gene expression by providing a binding site for enzymes involved in transcription
73
What does TFIID stand for?
transcription Factor II D
74
f: TBP
Introduces kink into DNA
determines transcriptional start and direction
Provides a binding site for further transcription factors and for RNA polymerase
75
What does transcription require to be initiated?
additional general transcription factors
76
What allows transcription to occur at low basal rates?
TFIID remains at promoter, a new initiation complex can assemble
77
d:elongation (transcription)
elongation is the stage when the RNA strand gets longer, due to the addition of new nucleotides.
78
describe the termination step in transcription
Newly synthesised RNA makes a stem-loop structure
followed by a stretch of Us
A specific enzyme cleaves the (now finished) RNA
and the RNA is released
79
What happens to the RNA polymerase II after transcription?
it dissociates
80
What is required for regulation of transcription?
Requires ‘specific’ transcription factors that
Bind to specific DNA sequences in the vicinity of a promoter
Regulating transcription positively or negatively
81
name the two functional domains which can be physically separated in specific transcription factors in the regulation of transcription
DNA-binding domain
| transcriptional activation domain
82
How do specific transcription factors bind to DNA sequences in regulation of transcription?
via enhancers
83
d: transcription factor
a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence
84
give two egs of transcription factors which control gene expression
Steroid receptors
| glucocorticoid receptor
85
where are steroid receptors found?
cell cytoplasm
86
How do steroids enter target cells?
by diffusion
87
what is the name for a coding region in eukaryotic cell?
exon
88
what is the name for a non-coding region in eukaryotic cell?
intron
89
what has to happen to introns before mRNA is translated to a protein? why?
spliced out
| introns and exons are transcribed together
90
How are the ends of mRNAs processed?
Addition of poly(A) tail
| Addition of 5’ cap
91
What is mRNA called before and after regulation?
pre-mRNA
| mature mRNA
92
d: codon
a sequence of 3 bases that code for 1 AA
93
how many different combinations of bases?
64
94
d: reading frame
one of three possible ways of reading a nucleotide sequence, depending where translation starts
95
how is the AA attached to tRNA molecule?
via Aminoacyl-tRNA synthetase enzyme
96
what are the sources of energy for translation?
ATP and GTP
97
what is the energy source for formation of bond that binds tRNA and AA?
ATP
98
what bond forms between tRNA and AA?
covalent
99
how many rRNA molecules does a ribosome contain? What else do ribosomes contain?
4
| protein components
100
Name the 3 tRNA binding sites in Ribosomes
exit
peptidyl
aminoacyl
101
what provides energy for translation initiation?
hydrolysed GTP
102
What is required for initiation of translation?
Initiation factors
103
describe initiation of translation
Small ribosomal subunit binds to 5’ end of mRNA
Moves along the mRNA until AUG (start codon) is found (ATP-dependent)
Special ‘initiator’ tRNA with UAC anticodon base-pairs with the start codon
carries methionine
Large subunit joins assembly and initiator tRNA is located in P site
104
what codon is for methionine?
AUG
105
What is the start codon in translation?
methionine
106
f: elongation factor in translation
brings the next aminoacyl-tRNA to the A site
107
describe elongation process translation
An elongation factor (EF-1a), brings the next aminoacyl-tRNA to the A site
GTP is hydrolysed, EF is released from tRNA
A second elongation factor (EFbg) regenerates EF1a to pick up the next aminoacyl-tRNA
108
What is the name of the enzyme which catalyses peptide bond formation between AA and what sites are these AA between?
peptidyl transferase
| P and A
109
Which site is the peptide located after it is formed?
A
110
Describe peptide bond formation and translocation process
Peptidyl transferase catalyses peptide bond formation
Elongation factor EF-2 moves ribosome along the mRNA by one triplet
‘Empty’ tRNA moves to E site and can exit and become reloaded with an amino acid
tRNA with the growing peptide moves from the A to the P site
A site is free for the next aminoacyl-tRNA
111
When does termination of translation occur?
when the A site of the ribosome encounters a stop codon
112
give 3 stop codons
UAA, UAG or UGA
113
describe termination of translation process
No aminoacyl-tRNA base-pairs with stop codons
Release factor RF binds stop codon
GTP hydrolysis
Finished protein is cleaved off tRNA
The components – rRNA, mRNA and tRNA – dissociate from one another
Whole process starts all over again with small subunit being bound by IF ready for translation of a new protein
114
d:polysome
a cluster of ribosomes held together by a strand of messenger RNA that each ribosome is translating.
115
name the 5 types of mutations of protein synthesis
```
point
missense
nonsense
silent
frameshift
```
116
d:point mutation
change in a single base in DNA
117
d: missense mutation
results in a change of amino acid sequence
can change protein function,
118
d: nonsense mutation
creates a new termination codon
changes length of protein due to premature stop of translation
119
d: silent mutation
no change of amino acid sequence
due to degeneracy of the genetic code
no effect on protein function
120
d: frameshift mutation
addition or deletion of a single base (or two!)
| changes reading frame of translation into protein
121
give 4 chromosome mutations
deletions
duplications
inversions
translocations
122
give three things that happen to the finished protein
targeting
modification
degradation
123
describe targeting of protein
moving a protein to its final cellular destination
many possible locations within a cell
depends on the presence of specific amino acid sequences within the translated protein
124
d: modification of a protein
addition of further functional chemical groups
125
d: degradation
unwanted or damaged proteins have to be removed
126
where free ribosomes found?
cytosol
127
what do free ribosomes make proteins destined for?
cytosol
nucleus
mitochondria
translocated post-translationally
128
what do bound ribosomes make proteins destined for?
```
plasma membrane
ER
Golgi apparatus
secretion
translocated co-translationally
```
129
where are bound ribosomes found?
rough endoplasmic reticulum
130
d: co-translationally
happens during synthesis
131
d:post-translationally
happens after translation
132
list some post-translational modifications (3)
Glycosylation
Formation of disulfide bonds in the ER
Folding and assembly of multisubunit proteins in the ER
Specific proteolytic cleavage in the ER, Golgi, and secretory vesicles
133
d: glycosylation
addition and processing of carbohydrates in the ER and the Golgi
134
what does the hereditary form of emphysema result from?
misfolding of the protein a1-antitrypsin in the ER
135
name a disease that originates from inherited recessive disorder of protein targeting
I-cell disease (mucolipidosis II)
