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Study Cards > Molecular Exam > Flashcards

Molecular Exam Flashcards

lectures

1
Q

what is a palindromic/ inverted repeat

A

a single stranded sequence of nucleotides followed downstream by its reverse compliment

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2
Q

on its own what is a palindrome

A

a sequence that is read the same way in either direction

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3
Q

what is non palindromic inverted repeat

A

a repeat that is not palindromic because it is interrupted

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4
Q

what is another name for a mirror repeat?

A

hairpin loop or cruciform

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5
Q

what forces does a cruciform repeat have

A

hydrophobic interactions (double stranded)

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6
Q

what type of duplex is not possible for RNA. why

A

B-type duplex because of steric crowding

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7
Q

what helical structure does RNA form

A

A form

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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

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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

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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

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11
Q

what is the secondary structure of tRNA

A

partially double helical single-stranded regions with loops that form complicated structures

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12
Q

what functions do the loops have in tRNAs

A

contains anti-codons and carries amino acids

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13
Q

what is a pseudoknot

A

an element where the first and third bond and the second and fourth bond

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14
Q

what happens more frequently in RNA than in DNA

A

non-watson-crick base pairing

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15
Q

what are very modifiable

A

ribonucleosides

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16
Q

what is a genome

A

the complete haploid genetic complement of the typical cell

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17
Q

what is genomics

A

the study of DNA at the genome level

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18
Q

what is the E. coli genome like

A

has 4.6x10^6 base pairs and codes for 3,000 different proteins

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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

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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)

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21
Q

what does the g value refer to

A

the number of protein-coding genes

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22
Q

what is complexity

A

the number of instructions necessary to have an organism

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23
Q

what is the c-value paradox

A

genome size does not correlate with the organismal complexity in eukaryotes

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24
Q

what is the number of protein-coding genes in Homo sapiens

A

19,900 (~20,000)

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25
Q

what is the number of protein-coding genes in S. cerevisiae

A

6,600

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26
Q

what is the number of protein-coding genes in E. coli

A

4,300

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27
Q

what are tandem clusters

A

long DNA regions with short sequences that repeat in tandem

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28
Q

what are transposable genetic elements

A

described DNA sequence that can occasionally move (transpose) from one position on a chromosome to another

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29
Q

who discovered transposable elements

A

Barbara McClintoele in 1940’s from corn study

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30
Q

what are the two basic types of transposable elements in the human genome

A

class 1 - retrotransposons
class 2 - dna transposons

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31
Q

what is a retrovirus

A

a retrotransposons RNA based virus

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32
Q

what type of polymerase do retroviruses possess

A

RNA-dependant DNA polymerase with reverse transcriptase (allows them to synthesize DNA from RNA transcript)

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33
Q

what is the difference between DNA and RNA

A

DNA -> DNA = DNA polymerase
DNA -> RNA = RNA polymerase

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34
Q

how are retrotransposons transposed

A

through an RNA intermediate

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35
Q

what do retrotransposons and retroviruses have in common

A

they both have the gene to make DNA from RNA (no longer a virus)

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36
Q

what retrotransposons are currently transpositionally active

A

Li line and ALV sine retrotransposons

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37
Q

what is a gene

A

the locatable region of genomic sequence, corresponding to unit of inheritance

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38
Q

what is a locus

A

specific location of gene/ DNA sequence on chromosome

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39
Q

what is an allele

A

variant of DNA sequence at given locus

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40
Q

what are genes like in prokaryotes

A

regular coding sequences where transcript happens at same time as transcription

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41
Q

what do most eukaryotic genes have their coding info interrupted by

A

non-coding sequences called introns. coding sequences are then called exons

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42
Q

what is an intron present in and absent from

A

present in gene, absent from mRNA

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43
Q

introns have to be removed for what to occur

A

for mRNA to be translated to produce protein

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44
Q

what is the genome size in humans

A

3.1648 x 10^9 bp

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45
Q

what is the average size gene

A

~50,000 bp

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46
Q

what is the size of the average intron

A

~3,330 bp

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47
Q

what is the size of exons

A

~100 bp

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48
Q

what is the size of coding sequences

A

~2,000 bp

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49
Q

how long is human DNA

A

~1.8m

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50
Q

how long is the largest human chromosome

A

~3x10^8 bp

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51
Q

what is a chromatin

A

the complex of DNA and protein found in eukaryotic cells

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52
Q

what is the H1 unit of DNA packaging

A

linker histone outside the nucleosome

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53
Q

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?

A

4 - homologous chromosomes

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54
Q

what is the structure of nucleosome core particles

A

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

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55
Q

how are adjacent nucleosomes joined

A

stretch of free DNA termed “linker DNA” (rage of 20-100 bp)

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56
Q

what do N-terminal histone tails do

A

contact DNA in the phosphodiester backbone and minor grooves

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57
Q

how many pairs of chromosomes do women have

A

23

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58
Q

what is the structure of eu chromatin

A

chromosomes are outside and are organized into factors

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59
Q

what is heterochromatin

A

regions of chromatin that remain highly condensed and transcriptionally inactive during interphase

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60
Q

what is karyotyping

A

looking to see if you have any abnormalities in your genome

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61
Q

how do you see large mutations in kayrotyping

A

banding

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62
Q

what is metaphase

A

two identical copies of one chromosome

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63
Q

what chromosomes are homologous and which one are not

A

sex chromosomes are NOT homologous and the other 22 pairs are homologous

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64
Q

what is a karyotype

A

the number, sizes, and shapes of the metaphase chromosomes

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65
Q

how is DNA packaged in eukaryotic cells

A

in the form of chromatin

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66
Q

what do deletions of histone tails result in

A

transient unwrapping of DNA, an increase in nucleosome sliding rate, and a decrease in nucleosome stability

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67
Q

what are the core domains of histones formed by

A

three a-helices connected by short loops, mainly composed of positively charged residues

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68
Q

how many histone tails are there per nucleosome

A

ten histone tails which contain approx. 30% of total histone mass

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69
Q

what does the flexibility of glycerines do

A

facilitates change in the local curvature of nucleosomal DNA

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70
Q

what is nucleosome sliding

A

a process in which DNA gradually repositions itself around histones, while maintaining contact with the histone core.

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71
Q

what do histone tails have a high degree of

A

conformational flexibility

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72
Q

what is one of the most prevalent modes of interaction between histone tails and DNA

A

insertion of arginine and, in some cases, lysine side chains into the DNA minor and major grooves serving as anchors

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73
Q

what does ATP-dependant chromatin remodelling complexes do

A

move, eject, or restructure nucleosomes

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74
Q

what does trans regulations mean

A

there is an outside regulating factor that is not in the chromatin

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75
Q

what does cis regulations mean

A

the process is intrinsic to the chromatin

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76
Q

what are the three processes that histones can go through at numerous sites

A

acetylated, methylated, and ubiquitylated

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77
Q

where are modifications most common

A

N-terminal

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78
Q

what is acetylation associated with

A

gene activation

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79
Q

what is neutralized upon acetylation

A

positive charge on lysine

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80
Q

what does not eliminate the positive charge on lysine

A

mono-, di-, or trimethylation

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81
Q

what 4 amino acids are histone tails particularly rich in

A

G (glycine), K (lysine), S (serine), R (arginine)

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82
Q

what happens when dna is methylated

A

inactivation

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83
Q

what happens when histone proteins are methylated

A

activation

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84
Q

what is genomic imprinting

A

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

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85
Q

who is always silenced in dwarf genes

A

the mother

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86
Q

what are glucocorticoids (GCs)

A

steroid hormones widely used for treatment of inflammation, autoimmune diseases, and cancer

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87
Q

what does histone acetylation influence

A

chromatin structure and transcription through recruitment proteins

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88
Q

what is a histone code

A

different patterns of histone modifications are ‘read” by various proteins to produce an effect on gene expression

89
Q

what is a bromodomain

A

an approximately 110 amino acid protein domain that recognizes acetylated lysine residues, such as those on the N-terminal tails of histones

90
Q

what is type 1 topoisomerase activity

A

catalyze changes in DNA topology via transient single-stranded breaks in DNA

91
Q

what is type 2 topoisomerase

A

catalyze changes in DNA topology via transient double-stranded breaks in DNA. ex, Gyrase

92
Q

what is SSB activity

A

single-stranded DNA binding protein

93
Q

what is the SSB activity complex for DNA replication of eukaryotes called

A

replication protein A (RPA)

94
Q

what is a primosome

A

a complex where DnaG is bonded to DNA helicase

95
Q

how is primase activated

A

by the helicase where it then synthesizes a short RNA primer

96
Q

what do polymerase detect

A

whether or not a mistake was made in DNA replication

97
Q

what happens when polymerase detects a mistake

A

a different type of domain is invoked where the polymerase can go in reverse

98
Q

how is proofreading in exonuclease activity is read

A

3’ - 5’

99
Q

can a ligase produce phosphates

A

no

100
Q

what is a klenow fragment

A

– 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
Q

how many nucleotides in distributive synthesis

A

ten nucleotides

102
Q

how many nucleotides in processive synthesis

A

thousands nucleotides

103
Q

what are internal RNA primers removed by

A

exonuclease

104
Q

what is a telomere

A

tandem repetitive sequence at the ends of linear chromosomes in humans

105
Q

what is telomerase

A

reverse transcriptase. RNA dependant DNA polymerase

106
Q

what does telomerase do

A

carry its own template and copies that instead of other templates.

107
Q

what is a template

A

template is something that codes for a specific pattern

108
Q

what does a reverse transcriptase carry

A

its own RNA sequence with it and copies that when it extends the end of the 3’ hydroxy.

109
Q

what subunit of Core POL III has polymerase activity

A

α subunit (encoded by the dnaE gene)

110
Q

what Core POL III subunit has 3’-5’ exonuclease activity

A

ε subunit (dnaQ)

111
Q

what does the θ subunit of Core POL III do

A

stimulates the ε subunit’s proofreading and maintains the heterodimer structure

112
Q

how many subunits does 3 B clamps have and what are the function(s)

A

2 subunits - sliding clamp(s)

113
Q

what is Pol α responsible for

A

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
Q

what are the 4 subunits in pol α

A

catalytic subunit POLA1
regulatory subunit POLA2
small primase subunit PRIM1
large primase subunit PRIM2

115
Q

what happens once primase has created the RNA primer

A

pol α starts replication elongating the primer with ~20 nucleotides

116
Q

eukaryotes do not have what type of clamp and what is it replaced with

A

do not have beta clamps, have PCNA instead

117
Q

what are mutations

A

changes in the genetic material (sequence) that can be irreversibly passed from cell to cell and/ or from parent to offspring

118
Q

what are mutagens

A

a physical or chemical agent that permanently changes genetic material, usually DNA, in an organism

119
Q

what are the two types of mutations

A

point (gene level) mutations and large scale (chromosomal level) mutations

120
Q

what is a point mutation

A

small-scale mutation that causes nucleotic substitutions, insertions, or deletions in DNA or RNA sequence

121
Q

what does the term frameshift mutation indicate

A

the addition or deletion of nucleotides (that change the reading frame)

122
Q

what is a transition

A

a pyrimidine to a pyrimidine or a purine to a purine

123
Q

what is a transversion

A

a switch in base pairs or pyrimidine to pyrimidine/ purine to purine

124
Q

what is a mutation

A

two strands separate and the incorrect pairing is fixed in the second generation. this second generation is the mutation

125
Q

what is a lesion

A

a mismatch in base pairing that causes a mutation (ex. A - G)

126
Q

what are the 3 stop codons

A

UAA, UAG, UGA

127
Q

what are the three types of point mutations

A

silent, missense, nonsense

128
Q

what is a frameshift

A

change of reading frames

129
Q

what is the start codon that allows us to figure out what three bases give us a codon

A

AUG

130
Q

what do insertions of 3 do

A

they do not change the reading frame

131
Q

what is a missense

A

a change in amino acids

132
Q

what is a nonsense

A

a base substitution mutation that changes the codon for the amino acid into a stop codon

133
Q

what do you call the mutations that convert a codon for an amino acid into a stop codon?

A

nonsense

134
Q

what are the three types of single chromosome mutation

A

deletion, duplication, inversion

135
Q

which one of our chromosomes has more telomeres than it should and has telomeric sequences in the middle where a centromere has atrophied

A

chromosome 2

136
Q

what are the 4 damage repair pathways

A

mismatch repair
base excision repair
nucleotide excision repair
recombination repair

137
Q

what is a molecular lesion

A

damage to the structure of a biological molecule such as DNA, RNA or protein

138
Q

what is a mutagen

A

chemical or physical agent capable of inducing changes in DNA called lesions and ultimately mutations

139
Q

what is a mutation

A

changes in the genetic material (sequence) that can be irreversibly passed from cell to cell and-or from parent to offspring

140
Q

what can mutagens be

A

physical, chemical, or biological

141
Q

what does methylation of cytosine give

A

uracil and damage to the base

142
Q

what is deprivation

A

if you hydrolyze the base out, there is nothing there anymore

143
Q

what is ROS

A

reactive oxygen species

144
Q

what is alkylation

A

addition of CnH2n+1

145
Q

what is an adduct

A

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
Q

what does cross linking do

A

links 2 bases together

147
Q

what is difference between genotoxic and cytotoxic

A

cytotoxic is used to kill cells and genotoxic is used to kill genomes

148
Q

what initiates melanin production

A

fragment of DNA with the crosslink

149
Q

what does a tan mean

A

tan means your system is repairing the damaged crosslinked region

150
Q

what does CH3 mark

A

the parental strand in bacteria

151
Q

what is the function of MutS

A

binds mismatch

152
Q

what is the function of MutL

A

links MutH and MutS

153
Q

what is the function of MutH

A

binds 7-meGACT

154
Q

what is the function of DNA ligase

A

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
Q

what does AP endonuclease do

A

enzyme that breaks phosphodiester bonds in DNA to repair damage and is found in both prokaryotic and eukaryotic organisms:

156
Q

function of UrvA

A

processes and recognizes DNA lesions

157
Q

function of UvrB

A

interacts with both the UvrA and UvrC proteins in addition to binding, bending, and incising DNA.

158
Q

functions of UvrC

A

cleaving the nucleotides either side of the DNA damage

159
Q

function of UvrD

A

functions within the TCR by using its inherent ATPase activity for backtracking the stalled RNAP without displacing it altogether

160
Q

what is a consensus sequence

A

a nucleotide or amino acid sequence consisting of the residues that most commonly occur at each position in a set of similar sequences

161
Q

what happens during the initiation phase of transcription

A

RNAP/ σ recognizes the promoter and starts the transcription

162
Q

what happens during the elongation phase of transcription

A

the RNA strand is continuously growing (50-70rNTPs /s)

163
Q

what do RNAP core enzymes do

A

carries out all steps of transcription except promoter-specific initiation that requires an accessory σ factor

164
Q

what happens during the termination phase of transcription

A

the rNAP stops synthesis and the nascent RNA is separated from the DNA template

165
Q

what is the ρ factor (Rho factor)

A

a hexameric helicase involved in the termination of transcription of some genes

166
Q

what are the 5 RNA polymerases in eukaryotes and what do they do

A

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
Q

how much of each type of RNA are contained in a cell?

A
  • about 75% rRNa
  • about 15% tRNA
  • less than 10% mRNA
168
Q

what does tRNA code for

A

methionine and its start codon

169
Q

can you only base pair with one thing at a single time

A

no, possible to base pair with two things at once

170
Q

what is the wobble hypothesis

A

codon variation for a particular amino acid is greatest in the third position

171
Q

what did crick and brenner propose about a single tRNA molecule

A

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
Q

what does the term wobble hypothesis indicate

A

that a certain degree of flexibility or “wobbling” is allowed at this position in the ribosome

173
Q

how many tRNAs recognize how many codons

A

~40 tRNAs recognize 61 codons

174
Q

in order for translation to happen what do we need

A

polypeptides, tRNA with amino acid, ribosomes, and aminoacyl-RNA-synthetase

175
Q

what does aminoacyl-RNA-synthetase do

A

catalyzes attachment of amino acids to tRNA

176
Q

what is called the second genetic code

A

the ability of aminoacyl-tRNA synthetase to recognize appropriate tRNA

177
Q

what is a ribosome

A

the site where translation takes place

178
Q

what are ribosomes a mixture of

A

RNA and proteins on the end

179
Q

in E. coli, how much of its dry weight is ribosomes

A

25% (around 15,000)

180
Q

what is a polyribosome (polysome)

A

a complex of an mRNA molecule and is translated by multiple ribosomes to form polypeptide chains during translation.

181
Q

when does translation of mRNA begin

A

on ribosomes that are free in the cytosol

182
Q

where does a lot of synthesis happen

A

in the rough endoplasmic reticulum

183
Q

what are the three sites on a ribosome and what do they do

A
  • 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
Q

what is the transcription factor II D (TFIID)

A

a general transcription factor that participates in the RNA polymerase II preinitiation complex

185
Q

what does the TFID complex do before the start of transcription

A

binds to the TATA box in the core promoter of the gene

186
Q

what is TFIID composed of

A

TBP and several subunits called TATA-binding proteins associated factors (TBP-associated factors (TAFs))

187
Q

what is TATA-binding proteins (TBP)

A

is a general transcription factor that binds specifically to a DNA sequence called the TATA box

188
Q

what is BRE

A

TFIIB recognition element

189
Q

what percent of human promoters have TATA boxes

A

10-20%

190
Q

what occurs concurrently

A

transcription and translation

191
Q

where does transcription happen

A

in the cytoplasm

192
Q

what is heterogeneous nuclear RNA (hnRNA)

A

primary transcript - what comes out of the transcript machinery

193
Q

what happens due to heterogenous nuclear RNA (hnRNA)

A

puts on a 5’ cap, removes introns and splices together exons, then puts on poly-A this

194
Q

where does transcription happen in eukaryotes

A

nucleus

195
Q

what does 5’ capping (Pol II) do

A

cap blocks the 5’ end of mRNA and can be methylated at several positions

196
Q

what does 7-methylguanylate residue do

A

attaches to the first nucleotide of the pre-mRNA by a 5’-5’ linkage

197
Q

what are the 4 functions of 7-methylguanylate residue

A
  • enable transport of mRNAs out of the nucleus
  • protect mRNA from degradation
  • enhance efficiency of splicing mRNAs
  • enhance translatability of mRNAs
198
Q

what do most eukaryotic mRNAs have

A

chain of AMP residues about 250 nucleotides long at their 3’ ends

199
Q

what is polyadenylation

A

the process of adding poly (A) to RNA

200
Q

when is poly (A) is added and by what

A

added post-transcriptionally by polyadenylate (poly (A)) polymerase

201
Q

what is the polyA signal and what does it do

A

5’-AAUAAA-3’
signal to remove part of the transcript

202
Q

what is the function of poly(A)

A

protects from degradation and is involved in the translation of mRNA

203
Q

the ends of nuclear introns are defined by what

A

the GU-AG rule

204
Q

introns often begin and end with what

A

begin with GU and end with AG (GU 5’, AG 3’)

205
Q

what is a lariat

A

a form that an intron is removed in

206
Q

what is a splicosome

A

a large complex molecular machine found primarily within the cell nucleus of eukaryotic cells

207
Q

what are spliceosomes composed of

A

5 small nuclear RNAs (snRNAs) and a range of associated protein factors

208
Q

what creates a snRNP

A

an RNA-protein complex where snRNAs and protein factors are combined

209
Q

what does snRNP so

A

identify splice site, branch site and 3’ splice site. the 3’ gets cut and lariat is made

210
Q

what does DNA polymerase need to work and why

A

Mg - extremely important and can change the fidelity

211
Q

what will DNA polymerase never get

A

base pairing or phosphodiester bonds

212
Q

what can DNA polymerase never do

A

initiate a new strand

213
Q

what is the easiest genome to replicate

A

a circular genome found in mitochondria

214
Q

what is an origin of replication

A

a bubble formed due to circular DNA duplex having no beginning or end

215
Q

what happens in DNA replication in a circular genome

A

both strands are replicated and at the end, ligase joins the newly synthesized strands

216
Q

what is an Okazaki fragment

A

a short segment of DNA that is synthesized discontinuously during DNA replication on the lagging strand:

217
Q

what does helicase do

A

melts DNA and opens up DNA duplex

218
Q

what does topoisomerases do

A

untying knots and unwinding DNA

219
Q

what is helicase activity

A

will load leading or lagging strands and will use ATP hydrolysis to break up H bonds

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