Mid Term 1 reveiw Flashcards
(170 cards)
1
Q
What are the 4 nucleotide bases for dna
A
A T C G
2
Q
What are the 3 building blocks of dna
A
Phosphate, Sugar, Base
3
Q
What section of DNA is the 3’ end
A
the oxygen on the sugar
4
Q
WHat section of DNA is the 5’ end
A
THe phosphate group
5
Q
WHat are the 2 categories of Nucleotides
A
Pyrimidines and Purines
6
Q
What nucleotide bases are Purines
A
A G
7
Q
WHat nucleotide bases are Pyrimidines
A
C T
8
Q
What type of bonds hold together Nucleotide subunits
A
Phosphodiester Bonds
9
Q
What way does DNA strand Run
A
5’ to 3’
10
Q
What Type of bonds are nucleotides bonded by
A
Covalent bonds
11
Q
What gives rise to DNA Polarity
A
3’-hydroxyl
group (-OH) of one sugar and the 5’ phosphate group
12
Q
How many Hydrogen bonds connect A T
A
2
13
Q
How many Hydrogen bonds hold together C G
A
3
14
Q
What % of a typical chromosome does Heterochromatin make up
A
40
15
Q
What % of a typical chromosome does Euchromatin make up
A
60
16
Q
When was the first genome draft complete
A
1999
17
Q
When was the first genome sequence complete
A
2021
18
Q
WHat percentage of the genone is protein-coding exons
A
less than 1 %
19
Q
How many NT are required for an average size protein
A
1300
20
Q
WHat is the average length of a human gene
A
26000
21
Q
How many possible reading frames are there
A
3
22
Q
WHat is the length of a Open reading frame
A
less than 10,000 codons that lack stop codon
23
Q
What is a SNP
A
Single-nucleotide polymorphisms
24
Q
WHat is the chance of a SNP
A
single-base changes that are present in at
least 1% of the populations
25
Which base pairs with adenine in DNA?
C) Thymine
26
What is the basic unit of eukaryotic chromosome structure?
Nucleosome
27
In which phase of the cell cycle is chromatin least condensed?
Interphase
28
How many chromosomes do humans typically have?
46
29
Which method of DNA sequencing involves enzymatic extension with dideoxynucleotides?
Sanger method
30
Which region of chromatin is more condensed and contains silenced genes?
Heterochromatin
31
What is the flow of genetic information according to the central dogma of molecular biology?
DNA → RNA → Protein
32
What proteins help package DNA into chromosomes?
Histones
33
In what phase is chromatin most condensed
Metaphase
34
The human genome contains approximately how many protein-coding genes
20,000
35
DNA replication is said to be:
Semiconservative
36
What enzyme unwinds the DNA double helix during replication?
Helicase
37
When does DNA Replication occur
occur before a cell can
divide
38
What phase in dna replicated
synthesis phase
39
How was semiconservative dna found
using heavy and light Nitrogen. Heavy sank, and light floated. DNa with both sat in the middle. TRANSFERED TO LIGHT MEDIUM
40
WHat 2 methods can open DNA double helix
thermal energy or initiator protein
41
Where does DNA synthesis occur
y shaped junction called the Replication fork
42
How many replication Forks are there
2
43
What is it called when replication works in 2 directions
bidirectional replication
44
What are the rates of dna replication
1,000 nt/s bacteria 100 nt/s humans
45
What direction does DNA polymerase Function
5 to 3
46
What is the purpose of DNA polymerase
catalyzes the formation of phosphodiester bond. Addition of nucleotides
47
How often does DNA polymerase make errors
1 error in 107
nucleotide pairs it copies
48
How is the Nucleotide error from DNA Polymerase fixed
Fixed by proof reading
49
How many sites does DNA Polymerase contain
2
p: Polymeration
E: editing( Proof Reading)
50
What is the Aprox length of the RNA primer needed for DNA Polymerase
10 nt
51
How can DNA SYnthesis from the lagging strand be desribed as
discontinuous DNA synthesis
52
WHat is Nuclease
degrades RNA primer
53
What is repair polymerase
proofreading activity
replaces RNA primer
with DNA
54
What is DNA ligase
joins the 5’-phosphate end of one DNA fragment
to the adjacent 3’-hydroxyl end of the next
joins together Okazaki fragments on the lagging
strand during DNA synthesis
55
What is DNA helicase
ATP dependent
unwinding of the parent DNA double helix
56
What is Single-strand DNA binding proteins
latch onto ssDNA
* prevent reforming of double helix and
keeping them in elongated form
57
What is the Sliding Clamp
keeps
DNA pol
attached to
DNA template
58
What is the clamp loader
locks sliding
clamp around
newly formed
DNA double helix
* ATP dependent
59
What causes DNA ahead of thr replication fork to get wounded more tightly
helicase moves forward
60
What is DNA Topoisomerases
enzymes that relieve the tension that builds
up in front of a replication fork
produce a transient, single-stranded break
in the DNA backbone, which releases the
build-up tension
* reseals the nick before falling off the DNA
61
What is a Telomeres
long, repetitive nucleotide sequences
present at the ends of every chromosome
provide replication machinery with “extra”
DNA to complete the lagging strand
62
What is Telomerase
carries its own RNA template
* uses the RNA primer to add multiple copies
of the same repetitive DNA sequence to the
lagging-strand template
63
What is xeroderma pigmentosum
cannot mend the damage done to DNA by
UV radiation
* inherit defective gene for one of the proteins
involved in the DNA repair
64
What are the three types of major chemical changes in DNA
depurination
deamination
thymine dimer
65
What is Depurination
* does not break the phosphodiester backbone
* removes purine bases from a nucleotide
66
What is the causes of lesions in DNA
Depurination
67
What is Deamination
* conversion of cytosine to uraci
spontaneous loss of an amino group
does not break the phosphodiester backbone
NH2 converts to O
68
What is a Thymine Dimers
covalent linkages between two adjacent
pyrimidine bases
produce permanent mutations
69
When Deamination occurs, how do the new strands of dna differ
1 strand will have "A" where C is ment to be
2 strand will not be mutated
70
When Depurination occurs, how do the new strands of dna differ
1 strand will be shorted due to the loss of A or G
2nd Strand will be normal
71
What is Step 1 in the basic pathway for repairing damaged dna
DNA damage is recognized
and removed by a variety of
nucleases. small gap is one strand of dna
72
What is Step 2 in the basic pathway for repairing damaged dna
a repair DNA polymerase binds
to the 3’-OH end of the cut
DNA strand
enzyme fills the gap
by making a complementary
copy
73
What is Step 3 in the basic pathway for repairing damaged dna
DNA ligase seals the break
left in the sugar-phosphate
backbone
74
What will happened if errors during
replication are not corrected?
uncorrected errors will lead to permanent
mutation
75
How does the mismatch pepair system work
rely on the genetic redundancy build into
every DNA double helix
* nucleotide damage on one strand can
be repaired using the information in the
complementary strand
76
What can cause double-stranded DNA breaks
radiation
* mishaps at the replication fork
* various chemical assaults
77
What can happen when there is a double-stranded DNA breaks
can lead to
* fragmentation of chromosomes
* loss of genes
78
How can double-stranded DNA breaks be repaired
nonhomologous end joining
homologous recombination
79
What is nonhomologous end joining
quickly stick the broken ends together
carried out by specialized group of enzymes
* nucleases
* DNA ligases
breaks are rapidly sealed, but nucleotides
are often lost at the site of repair
80
What is homologous recombination
error-free strategy for repairing double-strand
breaks
81
When does homologous recombination occur
shortly after DNA has been replicated
* double-strand damaged DNA
* undamaged dsDNA template
82
What is the first step of Homologous recombination
often occurs when
duplicated helices
are still physically
close to each other
recombination specific
nuclease
* specialized enzymes
* recA bacteria
* rad52 eukaryotes
83
What is the Second step of Homologous recombination
once an extensive,
accurate match is
made, the invading
strand is elongated
uses complementary
undamaged strand
as a template
complementary
base-pairing within
damaged duplex
84
What is the Third step of Homologous recombination
repair is then completed
by additional DNA
synthesis at the
3’ ends of both strands
of the broken double
helix
the net result is two
intact DNA helices
genetic info from one
helix was used to
repair the other
85
What is the result of Failure to repair DNA damage
allow mutations to arise
in protein coding genes particular position
within DNA sequence
86
What is the first step of Nucleotide excision repair
UvrB and C endonucleases
nick the strand containing
the dimer
damaged fragment is
released from DNA
87
What is the second step of Nucleotide excision repair
damaged fragment is
released from DNA
DNA polymerase fills
the gap with new DNA
DNA ligase seals the
repaired strand
88
What is a Pyrimidine dimers
molecular lesions induced by UV radiation
89
What are the 2 common Pyrimidine dimers
cyclobutene
pyrimidine dimer
(CPDs)
* 6-4 photoproduct
90
what are the 4 Ribonucleic Acid
A U C G
91
How many Hydrogen Bonds occur between A and U
2
92
How many strands is RNA
single-stranded
93
What is RNA conventional base pairs
When RNA has folded shape, A and U or C and G line up when folded
94
What is RNA nonconventional base pairs
When RNA has folded shape, A and C/G or U and G/C line up when folded
95
What 3 roles can RNA have
structural,
regulatory, or catalytic roles
96
What is a gene
a segment of DNA that directs the production
of a particular protein or functional RNA
molecule
97
What strand of DNA does RNA come from
Coding strand of DNA
98
What is RNA polymerase
catalyzes
formation of
phosphodiester
bond
* moves stepwise
along the DNA
99
What direction does RNA polymerase work
5’-to-3’ direction
100
What is the difference between DNA and RNA Polymerase
can start an RNA chain without a primer
does not accurately proofread its work
* makes about 1 mistake in every 10,000nt
minor consequences of mistakes
in RNA transcript for a cell
101
What is messenger RNA (mRNA)
RNA molecules that ultimately direct
synthesis of proteins
102
What is ribosomal RNAs (rRNAs)
* form the structural and catalytic core
of the ribosome
103
What is transfer RNAs (tRNAs)
serve as adaptors between mRNA and
aa during protein synthesis
104
What is microRNAs (miRNAs)
regulate gene expression
105
What is small interfering RNAs (siRNAs)
provide protection from viruses and
proliferating transposable elements
106
What is long noncoding RNAs (lncRNAs)
act as scaffolds and serve other diverse
functions, many of which are still being
discovered
107
How does Transcription initiation in bacteria occur
RNA polymerase recognizes specific nucleotide
sequence which lies immediately upstream
of the transcription start site, a gene region
called a promoter
108
What is a sigma factor
RNA polymerase contains a subunit
called sigma factor – recognizes the promoter
109
How is the double helix opened in transcription
RNA polymerase opens up the DNA double helix
immediately in front of the promoter
110
What happens to the Sigma factor when Rna synthesis starts
Sigma factor is reduced
111
What type of dna contains promotor and terminator
bacteria dna
112
How many DNA Polymerases are used for eukaryotic cells
3
113
What is RNA polymerase I
Most rRNA genes
114
What is RNA polymerase II
All proteins-coding genes, miRNA genes, plus genes for other noncoding RNAs
mRNA
115
What is RNA Polymerase III
tRNA, 5S rRNA,
116
What RNA polymerase is used to make mRNA
RNA polymerase 2
117
What does eukaryotic RNA polymerases require the
assistance of
general transcription factors
118
What is a Elongation factors
allow the RNA pol II to move through DNA
that is packed into nucleosomes
119
What is located at the -35 of a Eukaryotic promoters contain
sequences
TFIIB
120
What is located at the -30 of a Eukaryotic promoters contain
sequences
TBP
121
What is located at the transcription start site of a Eukaryotic promoters contain
sequences
TFIID
122
What is located at the +30 of a Eukaryotic promoters contain
sequences
TFIID
123
Where in the cell is a Eukaryotic mRNAs are processed
in the nucleus
* capping, splicing, and polyadenylation
* carried out by enzymes bound to
phosphorylated tail of RNA pol II
124
What is RNA capping
* modifies the 5’ end
of the RNA transcript
introduces atypical nt
methyl-guanine
125
What is polyadenylation
special structure
at the 3’ end
* series of repeated
adenines
126
What is the purpose of Capping and polyadenylation of
eukaryotic mRNA
increase the stability of the mRNA molecule
facilitate export from the nucleus to the
cytosol
* mark the RNA molecule as mRNA
127
What is an intron
non coding sequence of nucleotides
128
How are Introns removed from Pre RNA
RNA splicing
129
When does RNA Splicing occur
after capping and as the RNA pol II continues
to transcribe the gene, RNA splicing begins
130
In what form are Introns cut out by the splicing machine
lariat” structure
this structure is
produced when an
adenine nucleotide
within the intron reacts
with the beginning of
the intron
131
What is required at each RNA splicing reaction
5 snRNPs and about 200 additional
proteins
132
What is the function of the U1 protein in RNA splicing
U1 recognized 5’
splice site
133
What is the function of the U2 protein in RNA splicing
U2 recognizes the
lariat branch-point site
134
What is the function of the U1 protein in RNA splicing
U6 rereads the 5’ splice
site by displacing U1
135
What is a spliceosome
arge assembly of RNA and protein
molecules that carry out splicing in
the nucleus
136
What protein partners do export ready mRNA molecule require
cap-binding protein
* poly-A binding protein
* exon junction complex
137
Where does mRNA molecules become degraded
becomes degraded in the cytosol by the ribonucleus
138
how many different types of amino acids are there
20
139
how many different triplets possibilities are there
64
140
What is the start codon
MET
AUG
141
how many stop codons are there
3
UAA
UAG
UGA
142
What acts as intermediaries
between the codons of mRNA and aa
tRNA
143
What is the shape of tRNA
a cloverleaf
144
What is tRNA
* ~ 80nt long
* 4 short segments form
double helical structures
* each region plays
important function
* anticodon region
* aa binding region (3’-end)
145
What is a anticodon
form by a set of three consecutive nt
that bind, through base-pairing, to the
complementary codon in an mRNA
molecule
146
What is aminoacyl-tRNA synthetase
enzyme that recognizes and attaches the correct Amino acid to tRNA
Needs ATP
147
What are the 2 sub units of a ribosome
one large subunit
* one small subunit
148
What makes up the weight of a ribosome
2/3 RNA
* 1/3 protein
149
What is the function of a small ribosomal subunit
matches the tRNA to the codon of the mRNA
150
What is the function of a large ribosomal subunit
atalyzes the formation of the peptide bonds
that covalently link the aa together into
a polypeptide chain
151
What are the 3 binding sites of a ribosome
A site - aminoacyl-tRNA
* P site - peptidyl-tRNA
* E site - exit
152
What are the 4 steps of translation
1 a charged tRNA enters
at the A site by base-
pairing with the
complementary codon
on the mRNA molecule
2 C-term of the polypeptide
chain is uncoupled from
the tRNA at the P site and
joined to the free aa
linked to tRNA in A site
3 large ribosomal subunit
shifts relative to small subunit
* moves the two bound tRNAs
* P site → E site
* A site → P site
4 small ribosomal subunit moves
exactly three nt along the mRNA
* ejects the spent tRNA
* resets the A site for new
incoming charged tRNA
153
At what rate do eukaryotic ribosome add amino acids
adds about 6 amino acids to
a polypeptide chain each second
154
At what rate do bacterial ribosome add amino acids
adds about 20 amino acids to
a polypeptide chain each second
155
What is the first step in Initiation of protein synthesis
initiator tRNA binds tightly
to the P site on the small
ribosomal subunit
the small ribosomal subunit
scans the mRNA until it
encounters the first AUG
156
What is the second step in Initiation of protein synthesis
binding of large ribosomal
subunit and completion of
ribosomal assembly
157
What is the Third step in Initiation of protein synthesis
tRNA binds to the A site, the first peptide bond is formed.
158
What binds to the stop codon in the ribosome
release factors
159
What happens when a release factor binds to a stop codon
alters
the activity of peptidyl
transferase in the ribosome
160
How far away can ribosomes be on a mrn strand
ribosomes may be as
close as 80nt apart
161
What is the function of an antibiotic
inhibitors of prokaryotic protein synthesis
162
WHat is Tetracycline
Blocks binding of aminoacly-tRNA site of Ribosomes
163
What is Streptomycin
prevents the transition from initiation complex to chain elongation
164
What is Chloramphenicol
Blocks the peptidyl transferase reaction on ribosomes
165
What is Erythromycin
Binds in the exit channel of the ribosome and inhibits elongation of the peptide chain
166
What is Rifamycin
Block initiation of Transcription by binding to and inhibiting RNA Polymerase
167
What is proteases
enzymes responsible for degrading proteins
hydrolyze the peptide bond between aa
168
What is proteosomes
large protein machines responsible for
breaking down proteins
in eukaryotes, proteins marked for destruction
are modified by small protein – ubiquitin
169
What is post-translational modification
covalent modification
* more than 100 types
* most common:
* phosphorylation
and glycosylation
170
