Molecular Exam Flashcards
lectures (219 cards)
1
Q
what is a palindromic/ inverted repeat
A
a single stranded sequence of nucleotides followed downstream by its reverse compliment
2
Q
on its own what is a palindrome
A
a sequence that is read the same way in either direction
3
Q
what is non palindromic inverted repeat
A
a repeat that is not palindromic because it is interrupted
4
Q
what is another name for a mirror repeat?
A
hairpin loop or cruciform
5
Q
what forces does a cruciform repeat have
A
hydrophobic interactions (double stranded)
6
Q
what type of duplex is not possible for RNA. why
A
B-type duplex because of steric crowding
7
Q
what helical structure does RNA form
A
A form
8
Q
what does a RNA sequence encode for
A
protein to serve as a binding site for single-stranded binding proteins or interacting RNAs
9
Q
what are secondary structures
A
helices that create functional motifs on their own and function as switches that alter the accessibility of constituent sequences
10
Q
what are tertiary structures
A
multiple secondary structures that form higher-order (tertiary) motifs that function as catalysts, ligand-binding domains, switches, and environmental sensors
11
Q
what is the secondary structure of tRNA
A
partially double helical single-stranded regions with loops that form complicated structures
12
Q
what functions do the loops have in tRNAs
A
contains anti-codons and carries amino acids
13
Q
what is a pseudoknot
A
an element where the first and third bond and the second and fourth bond
14
Q
what happens more frequently in RNA than in DNA
A
non-watson-crick base pairing
15
Q
what are very modifiable
A
ribonucleosides
16
Q
what is a genome
A
the complete haploid genetic complement of the typical cell
17
Q
what is genomics
A
the study of DNA at the genome level
18
Q
what is the E. coli genome like
A
has 4.6x10^6 base pairs and codes for 3,000 different proteins
19
Q
how mant sets of chromosomes are in haploid, diploid, and polyploid
A
haploid - 1 set
diploid - 2 sets
polyploid - many sets of the same chromosomes
20
Q
what does the c-value refer to
A
the total amount of DNA in an unreplicated haploid or gametic nucleus of an organism (refers to the haploid size)
21
Q
what does the g value refer to
A
the number of protein-coding genes
22
Q
what is complexity
A
the number of instructions necessary to have an organism
23
Q
what is the c-value paradox
A
genome size does not correlate with the organismal complexity in eukaryotes
24
Q
what is the number of protein-coding genes in Homo sapiens
A
19,900 (~20,000)
25
what is the number of protein-coding genes in S. cerevisiae
6,600
26
what is the number of protein-coding genes in E. coli
4,300
27
what are tandem clusters
long DNA regions with short sequences that repeat in tandem
28
what are transposable genetic elements
described DNA sequence that can occasionally move (transpose) from one position on a chromosome to another
29
who discovered transposable elements
Barbara McClintoele in 1940's from corn study
30
what are the two basic types of transposable elements in the human genome
class 1 - retrotransposons
class 2 - dna transposons
31
what is a retrovirus
a retrotransposons RNA based virus
32
what type of polymerase do retroviruses possess
RNA-dependant DNA polymerase with reverse transcriptase (allows them to synthesize DNA from RNA transcript)
33
what is the difference between DNA and RNA
DNA -> DNA = DNA polymerase
DNA -> RNA = RNA polymerase
34
how are retrotransposons transposed
through an RNA intermediate
35
what do retrotransposons and retroviruses have in common
they both have the gene to make DNA from RNA (no longer a virus)
36
what retrotransposons are currently transpositionally active
Li line and ALV sine retrotransposons
37
what is a gene
the locatable region of genomic sequence, corresponding to unit of inheritance
38
what is a locus
specific location of gene/ DNA sequence on chromosome
39
what is an allele
variant of DNA sequence at given locus
40
what are genes like in prokaryotes
regular coding sequences where transcript happens at same time as transcription
41
what do most eukaryotic genes have their coding info interrupted by
non-coding sequences called introns. coding sequences are then called exons
42
what is an intron present in and absent from
present in gene, absent from mRNA
43
introns have to be removed for what to occur
for mRNA to be translated to produce protein
44
what is the genome size in humans
3.1648 x 10^9 bp
45
what is the average size gene
~50,000 bp
46
what is the size of the average intron
~3,330 bp
47
what is the size of exons
~100 bp
48
what is the size of coding sequences
~2,000 bp
49
how long is human DNA
~1.8m
50
how long is the largest human chromosome
~3x10^8 bp
51
what is a chromatin
the complex of DNA and protein found in eukaryotic cells
52
what is the H1 unit of DNA packaging
linker histone outside the nucleosome
53
in a cell at the mitotic stage, right before cell division, how many copies of any particular gene except for the sex chromosome in men?
4 - homologous chromosomes
54
what is the structure of nucleosome core particles
146 bp of DNA wrapped in 1.67 left-handed superhelical turns around the histone octamer, consisting of 2 copies each of the core histones
55
how are adjacent nucleosomes joined
stretch of free DNA termed "linker DNA" (rage of 20-100 bp)
56
what do N-terminal histone tails do
contact DNA in the phosphodiester backbone and minor grooves
57
how many pairs of chromosomes do women have
23
58
what is the structure of eu chromatin
chromosomes are outside and are organized into factors
59
what is heterochromatin
regions of chromatin that remain highly condensed and transcriptionally inactive during interphase
60
what is karyotyping
looking to see if you have any abnormalities in your genome
61
how do you see large mutations in kayrotyping
banding
62
what is metaphase
two identical copies of one chromosome
63
what chromosomes are homologous and which one are not
sex chromosomes are NOT homologous and the other 22 pairs are homologous
64
what is a karyotype
the number, sizes, and shapes of the metaphase chromosomes
65
how is DNA packaged in eukaryotic cells
in the form of chromatin
66
what do deletions of histone tails result in
transient unwrapping of DNA, an increase in nucleosome sliding rate, and a decrease in nucleosome stability
67
what are the core domains of histones formed by
three a-helices connected by short loops, mainly composed of positively charged residues
68
how many histone tails are there per nucleosome
ten histone tails which contain approx. 30% of total histone mass
69
what does the flexibility of glycerines do
facilitates change in the local curvature of nucleosomal DNA
70
what is nucleosome sliding
a process in which DNA gradually repositions itself around histones, while maintaining contact with the histone core.
71
what do histone tails have a high degree of
conformational flexibility
72
what is one of the most prevalent modes of interaction between histone tails and DNA
insertion of arginine and, in some cases, lysine side chains into the DNA minor and major grooves serving as anchors
73
what does ATP-dependant chromatin remodelling complexes do
move, eject, or restructure nucleosomes
74
what does trans regulations mean
there is an outside regulating factor that is not in the chromatin
75
what does cis regulations mean
the process is intrinsic to the chromatin
76
what are the three processes that histones can go through at numerous sites
acetylated, methylated, and ubiquitylated
77
where are modifications most common
N-terminal
78
what is acetylation associated with
gene activation
79
what is neutralized upon acetylation
positive charge on lysine
80
what does not eliminate the positive charge on lysine
mono-, di-, or trimethylation
81
what 4 amino acids are histone tails particularly rich in
G (glycine), K (lysine), S (serine), R (arginine)
82
what happens when dna is methylated
inactivation
83
what happens when histone proteins are methylated
activation
84
what is genomic imprinting
an epigenetic phenomenon in which a segment of DNA is imprinted, or marked during egg or sperm formation in a way that results in the monoallelic expression of a gene depending on the parental origin of throughout the life of the individual who inherits that DNA
85
who is always silenced in dwarf genes
the mother
86
what are glucocorticoids (GCs)
steroid hormones widely used for treatment of inflammation, autoimmune diseases, and cancer
87
what does histone acetylation influence
chromatin structure and transcription through recruitment proteins
88
what is a histone code
different patterns of histone modifications are ‘read” by various proteins to produce an effect on gene expression
89
what is a bromodomain
an approximately 110 amino acid protein domain that recognizes acetylated lysine residues, such as those on the N-terminal tails of histones
90
what is type 1 topoisomerase activity
catalyze changes in DNA topology via transient single-stranded breaks in DNA
91
what is type 2 topoisomerase
catalyze changes in DNA topology via transient double-stranded breaks in DNA. ex, Gyrase
92
what is SSB activity
single-stranded DNA binding protein
93
what is the SSB activity complex for DNA replication of eukaryotes called
replication protein A (RPA)
94
what is a primosome
a complex where DnaG is bonded to DNA helicase
95
how is primase activated
by the helicase where it then synthesizes a short RNA primer
96
what do polymerase detect
whether or not a mistake was made in DNA replication
97
what happens when polymerase detects a mistake
a different type of domain is invoked where the polymerase can go in reverse
98
how is proofreading in exonuclease activity is read
3' - 5'
99
can a ligase produce phosphates
no
100
what is a klenow fragment
– a proteolytic product of E. coli DNA Polymerase I which retains polymerization and 3'→ 5' exonuclease activity, but has lost 5'→ 3' exonuclease activity
101
how many nucleotides in distributive synthesis
ten nucleotides
102
how many nucleotides in processive synthesis
thousands nucleotides
103
what are internal RNA primers removed by
exonuclease
104
what is a telomere
tandem repetitive sequence at the ends of linear chromosomes in humans
105
what is telomerase
reverse transcriptase. RNA dependant DNA polymerase
106
what does telomerase do
carry its own template and copies that instead of other templates.
107
what is a template
template is something that codes for a specific pattern
108
what does a reverse transcriptase carry
its own RNA sequence with it and copies that when it extends the end of the 3’ hydroxy.
109
what subunit of Core POL III has polymerase activity
α subunit (encoded by the dnaE gene)
110
what Core POL III subunit has 3'-5' exonuclease activity
ε subunit (dnaQ)
111
what does the θ subunit of Core POL III do
stimulates the ε subunit’s proofreading and maintains the heterodimer structure
112
how many subunits does 3 B clamps have and what are the function(s)
2 subunits - sliding clamp(s)
113
what is Pol α responsible for
the initiation of DNA at origins of replication (on both the leading and lagging strands) and during the synthesis of Okazaki fragments on the lagging strand
114
what are the 4 subunits in pol α
catalytic subunit POLA1
regulatory subunit POLA2
small primase subunit PRIM1
large primase subunit PRIM2
115
what happens once primase has created the RNA primer
pol α starts replication elongating the primer with ~20 nucleotides
116
eukaryotes do not have what type of clamp and what is it replaced with
do not have beta clamps, have PCNA instead
117
what are mutations
changes in the genetic material (sequence) that can be irreversibly passed from cell to cell and/ or from parent to offspring
118
what are mutagens
a physical or chemical agent that permanently changes genetic material, usually DNA, in an organism
119
what are the two types of mutations
point (gene level) mutations and large scale (chromosomal level) mutations
120
what is a point mutation
small-scale mutation that causes nucleotic substitutions, insertions, or deletions in DNA or RNA sequence
121
what does the term frameshift mutation indicate
the addition or deletion of nucleotides (that change the reading frame)
122
what is a transition
a pyrimidine to a pyrimidine or a purine to a purine
123
what is a transversion
a switch in base pairs or pyrimidine to pyrimidine/ purine to purine
124
what is a mutation
two strands separate and the incorrect pairing is fixed in the second generation. this second generation is the mutation
125
what is a lesion
a mismatch in base pairing that causes a mutation (ex. A - G)
126
what are the 3 stop codons
UAA, UAG, UGA
127
what are the three types of point mutations
silent, missense, nonsense
128
what is a frameshift
change of reading frames
129
what is the start codon that allows us to figure out what three bases give us a codon
AUG
130
what do insertions of 3 do
they do not change the reading frame
131
what is a missense
a change in amino acids
132
what is a nonsense
a base substitution mutation that changes the codon for the amino acid into a stop codon
133
what do you call the mutations that convert a codon for an amino acid into a stop codon?
nonsense
134
what are the three types of single chromosome mutation
deletion, duplication, inversion
135
which one of our chromosomes has more telomeres than it should and has telomeric sequences in the middle where a centromere has atrophied
chromosome 2
136
what are the 4 damage repair pathways
mismatch repair
base excision repair
nucleotide excision repair
recombination repair
137
what is a molecular lesion
damage to the structure of a biological molecule such as DNA, RNA or protein
138
what is a mutagen
chemical or physical agent capable of inducing changes in DNA called lesions and ultimately mutations
139
what is a mutation
changes in the genetic material (sequence) that can be irreversibly passed from cell to cell and-or from parent to offspring
140
what can mutagens be
physical, chemical, or biological
141
what does methylation of cytosine give
uracil and damage to the base
142
what is deprivation
if you hydrolyze the base out, there is nothing there anymore
143
what is ROS
reactive oxygen species
144
what is alkylation
addition of CnH2n+1
145
what is an adduct
a product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components
146
what does cross linking do
links 2 bases together
147
what is difference between genotoxic and cytotoxic
cytotoxic is used to kill cells and genotoxic is used to kill genomes
148
what initiates melanin production
fragment of DNA with the crosslink
149
what does a tan mean
tan means your system is repairing the damaged crosslinked region
150
what does CH3 mark
the parental strand in bacteria
151
what is the function of MutS
binds mismatch
152
what is the function of MutL
links MutH and MutS
153
what is the function of MutH
binds 7-meGACT
154
what is the function of DNA ligase
binding DNA fragments together to form 2 new daughter DNA strands. It does so by facilitating the formation of a phosphodiester bond between two DNA monomers at a time
155
what does AP endonuclease do
enzyme that breaks phosphodiester bonds in DNA to repair damage and is found in both prokaryotic and eukaryotic organisms:
156
function of UrvA
processes and recognizes DNA lesions
157
function of UvrB
interacts with both the UvrA and UvrC proteins in addition to binding, bending, and incising DNA.
158
functions of UvrC
cleaving the nucleotides either side of the DNA damage
159
function of UvrD
functions within the TCR by using its inherent ATPase activity for backtracking the stalled RNAP without displacing it altogether
160
what is a consensus sequence
a nucleotide or amino acid sequence consisting of the residues that most commonly occur at each position in a set of similar sequences
161
what happens during the initiation phase of transcription
RNAP/ σ recognizes the promoter and starts the transcription
162
what happens during the elongation phase of transcription
the RNA strand is continuously growing (50-70rNTPs /s)
163
what do RNAP core enzymes do
carries out all steps of transcription except promoter-specific initiation that requires an accessory σ factor
164
what happens during the termination phase of transcription
the rNAP stops synthesis and the nascent RNA is separated from the DNA template
165
what is the ρ factor (Rho factor)
a hexameric helicase involved in the termination of transcription of some genes
166
what are the 5 RNA polymerases in eukaryotes and what do they do
1) RNAP I: makes rRNA in the nucleolus
2) RNAP II: makes mRNA and sRNA in nucleoplasm
3) RNAP III: makes rRNA and tRNA in nucleoplasm
4) mRNAP: mitochondria
5) cRNAP: chloroplast
167
how much of each type of RNA are contained in a cell?
- about 75% rRNa
- about 15% tRNA
- less than 10% mRNA
168
what does tRNA code for
methionine and its start codon
169
can you only base pair with one thing at a single time
no, possible to base pair with two things at once
170
what is the wobble hypothesis
codon variation for a particular amino acid is greatest in the third position
171
what did crick and brenner propose about a single tRNA molecule
can recognize codons with different bases at the 3’- end owing to non-Watson-crick base pair formation with the third base in the codon-anticodon interaction
172
what does the term wobble hypothesis indicate
that a certain degree of flexibility or “wobbling” is allowed at this position in the ribosome
173
how many tRNAs recognize how many codons
~40 tRNAs recognize 61 codons
174
in order for translation to happen what do we need
polypeptides, tRNA with amino acid, ribosomes, and aminoacyl-RNA-synthetase
175
what does aminoacyl-RNA-synthetase do
catalyzes attachment of amino acids to tRNA
176
what is called the second genetic code
the ability of aminoacyl-tRNA synthetase to recognize appropriate tRNA
177
what is a ribosome
the site where translation takes place
178
what are ribosomes a mixture of
RNA and proteins on the end
179
in E. coli, how much of its dry weight is ribosomes
25% (around 15,000)
180
what is a polyribosome (polysome)
a complex of an mRNA molecule and is translated by multiple ribosomes to form polypeptide chains during translation.
181
when does translation of mRNA begin
on ribosomes that are free in the cytosol
182
where does a lot of synthesis happen
in the rough endoplasmic reticulum
183
what are the three sites on a ribosome and what do they do
- A.site (acceptor site): holds the newest tRNA carrying the next amino acid to be added to the chain
- P.site (peptidyl-tRNA site): holds tRNA carrying growing polypeptide chain
- E.site (exit site): empty tRNA leaves ribosome
184
what is the transcription factor II D (TFIID)
a general transcription factor that participates in the RNA polymerase II preinitiation complex
185
what does the TFID complex do before the start of transcription
binds to the TATA box in the core promoter of the gene
186
what is TFIID composed of
TBP and several subunits called TATA-binding proteins associated factors (TBP-associated factors (TAFs))
187
what is TATA-binding proteins (TBP)
is a general transcription factor that binds specifically to a DNA sequence called the TATA box
188
what is BRE
TFIIB recognition element
189
what percent of human promoters have TATA boxes
10-20%
190
what occurs concurrently
transcription and translation
191
where does transcription happen
in the cytoplasm
192
what is heterogeneous nuclear RNA (hnRNA)
primary transcript - what comes out of the transcript machinery
193
what happens due to heterogenous nuclear RNA (hnRNA)
puts on a 5' cap, removes introns and splices together exons, then puts on poly-A this
194
where does transcription happen in eukaryotes
nucleus
195
what does 5' capping (Pol II) do
cap blocks the 5' end of mRNA and can be methylated at several positions
196
what does 7-methylguanylate residue do
attaches to the first nucleotide of the pre-mRNA by a 5'-5' linkage
197
what are the 4 functions of 7-methylguanylate residue
- enable transport of mRNAs out of the nucleus
- protect mRNA from degradation
- enhance efficiency of splicing mRNAs
- enhance translatability of mRNAs
198
what do most eukaryotic mRNAs have
chain of AMP residues about 250 nucleotides long at their 3' ends
199
what is polyadenylation
the process of adding poly (A) to RNA
200
when is poly (A) is added and by what
added post-transcriptionally by polyadenylate (poly (A)) polymerase
201
what is the polyA signal and what does it do
5'-AAUAAA-3'
signal to remove part of the transcript
202
what is the function of poly(A)
protects from degradation and is involved in the translation of mRNA
203
the ends of nuclear introns are defined by what
the GU-AG rule
204
introns often begin and end with what
begin with GU and end with AG (GU 5', AG 3')
205
what is a lariat
a form that an intron is removed in
206
what is a splicosome
a large complex molecular machine found primarily within the cell nucleus of eukaryotic cells
207
what are spliceosomes composed of
5 small nuclear RNAs (snRNAs) and a range of associated protein factors
208
what creates a snRNP
an RNA-protein complex where snRNAs and protein factors are combined
209
what does snRNP so
identify splice site, branch site and 3' splice site. the 3' gets cut and lariat is made
210
what does DNA polymerase need to work and why
Mg - extremely important and can change the fidelity
211
what will DNA polymerase never get
base pairing or phosphodiester bonds
212
what can DNA polymerase never do
initiate a new strand
213
what is the easiest genome to replicate
a circular genome found in mitochondria
214
what is an origin of replication
a bubble formed due to circular DNA duplex having no beginning or end
215
what happens in DNA replication in a circular genome
both strands are replicated and at the end, ligase joins the newly synthesized strands
216
what is an Okazaki fragment
a short segment of DNA that is synthesized discontinuously during DNA replication on the lagging strand:
217
what does helicase do
melts DNA and opens up DNA duplex
218
what does topoisomerases do
untying knots and unwinding DNA
219
what is helicase activity
will load leading or lagging strands and will use ATP hydrolysis to break up H bonds
