second half Flashcards
Why is DNA replication important?
It ensures that an exact copy of the species’ genetic information is passed from cell to cell.
How many hydrogen bonds are between the base pairs?
A-T has 2
C-G has 3
How many base pairs are there per turn?
10 base pairs per turn
What is the distance between stacked bases?
0.34 nm
T or F
DNA strands run parallel.
F
DNA strands run anti-parallel
What is the most common form of DNA?
Right-handed double helix
A linear double stranded DNA is 10,000 base pairs long.
How many complete turns of the of the double helix are there?
1000 turns
A linear double stranded DNA is 10,000 base pairs long.
What is the length of this molecule in micrometres?
3.4 micrometres
A linear double stranded DNA is 10,000 base pairs long.
How many phosphorus atoms are there, assuming one phosphorus atom per nucleotide?
20,000 phosphorus atoms
10,000 bp x 2 strands
In double stranded DNA, is G-C rich or A-T rich more stable? Why?
G-C is more stable because there are 3 H-bonds
What type of DNA replication did Watson-Crick propose?
Semi-conservative model of replication
What are the 3 types of replication?
- conservative
- dispersive
- semi-conservative
Describe the Meselson-Stahl experiment.
- technique called cesium chloride equilibrium-density gradient centrifugation
- original DNA was a single band of heavy
- after 1st replication DNA was a single band of intermediate
- after 2nd replication, one band of intermediate and one band of light
- after additional replications, the results of 2nd replication were repeated
- concluded that DNA replication is semi-conservative
Where does the phosphate group bind to in the nucleotide?
The phosphate group is always bound to the 5’-carbon of the sugar
What are phosphodiester bonds?
Phosphodiester bonds connect the 3’-carbon of one nucleotide to the 5’-phosphate of another nucleotide
Hairpins are formed in DNA as the result of?
Sequences on the same strand that are inverted and complementary
Describe are the 3 modes of DNA replication.
- Theta replication - occurs in most circular DNA, is bi-directional, produces two circular DNA molecules.
- Rolling circle replication - specialized form of replication that occurs in the F factor and some viruses, is uni-directional, produces multiple circular DNA molecules.
- Linear chromosome replication - occurs in the linear chromosomes of eukaryotic cells, is bi-directional, produces two linear DNA molecules.
What 5 things does DNA replication require?
- magnesium
- DNA dependent DNA polymerase
- 4 dNTPs
- template DNA
- RNA primer
T or F
A newly synthesized DNA strand is complementary and parallel to the parent strand.
F
The new strand is complementary and anti-parallel to the parent strand.
DNA synthesis is continuous on the ___ strand and discontinuous on the ___ strand.
Continuous on the leading strand and discontinuous on the lagging strand.
The short DNA segments produced by discontinuous DNA synthesis are called?
Okazaki fragments
Describe the activities of DNA Polymerase I in prokaryotes.
- aids in removal of RNA primers
- has 5’ to 3’ polymerase activity
- has 5’ to 3’ exonuclease activity
- proofreading: has 3’ to 5’ exonuclease activity
- short track synthesis
Describe the activities of DNA Polymerase III in prokaryotes.
- main replicative polymerase
- has 5’ to 3’ polymerase activity
- proofreading: has 3’ to 5’ exonuclease activity
- highly processive
T or F
Eukaryotic chromosome replication begins in the G1 phase.
F.
Actual replication begins in the S phase, but in the G1 phase the replication origins are prepared
What is the difference between exons and introns?
Exons are protein coding segments while introns are intervening non-coding segments.
Are transcription and translation coupled in eukayotic gene expression?
No, only in prokaryotes.
What is the difference between exons and introns?
These are found in eukaryotes: exons are protein coding segments while introns are intervening non-coding segments.
RNA synthesis is similar to DNA synthesis except for what 3 things?
- the precursors are rNTPs
- only one strand of DNA is used as a template
- RNA chains can be initiated without a primer
What are the 3 steps of transcription in prokaryotes?
- Initiation
- Elongation
- Termination
Describe the process of transcription in prokaryotes.
I - RNA polymerase binds, unwinds and joins first 2 nucelotides
E - complementary nucleotides continue to be added
E - localized DNA unwinding ahead of RNA polymerase creates a transcription bubble
E - transcription bubble moves with RNA polymerase and the unwound DNA rewinds behind it
T - transcription stops when RNA polymerase reaches the terminator region
T - the newly synthesized RNA and the RNA polymerase are released
What does the sigma factor do in prokaryotic transcription?
It controls the binding of RNA polymerase to the promoter.
What are the 2 important sequence promoters in prokaryotic transmission, and why?
The -35 sequence (5’-TTGACA-3’) is where the sigma factor binds.
The -10 sequence (5’-TATAAT-3’) is prone to unwinding.
Describe the process of transcription in E. coli.
I - promoter recognition requires the RNA polymerase holoenzyme.
I - sigma factor binds to the -35 element which positions RNA polymerase at the promote.r
I - transcription begins about 5 to 9 base pairs after the -10 sequence, at the first purine after at least two pyrimidines.
E - sigma factor is released and RNA polymerase begins to move along the template strand from 3’ to 5’.
E - localized DNA unwinding ahead of the RNA polymerase creates a transcription bubble.
E - positive supercoils formed in the double-stranded DNA ahead of RNA are removed by topoisomerases.
T - rho-independent is common in bacteria
T - weak H-bonding at U-A allows mRNA release from the DNA when RNA polymerase pauses at terminator.
T or F.
In prokaryotes the coding region of a gene is not interrupted so the sequence of the gene is co-linear with amino acid sequence of the protein.
T
What is the Shine-Dalgarno sequence?
The Shine-Dalgarno sequence is only found in prokaryotes and is involved in the initiation of translation.
What are the 3 main processing steps in eukaryotic nuclear pre-mRNA?
- Addition of 7-methyl guanosine cap
- Addition of PolyA tail
- Removal of introns
Describe how each type of intron is removed.
- rRNA introns are removed by reaction of the RNA molecule itself
- pre-mRNA introns are removed by spliceosomes
- tRNA introns are removed by endonucleolytic cleavage and ligation reactions
What are the 3 ways of RNA editing?
- changing the structure of individual bases
- modification of RNA by endogenous guide RNAs
- inserting or deleting uridine monophosphate residues
What are the classes of RNA?
- messenger RNAs
- transfer RNAs
- ribosomal RNAs
- small nuclear RNAs
- micro RNAs
- long non-coding RNAs
T or F
Transcription, translation and mRNA degradation happen simultaneously in prokaryotes.
T.
In eukaryotes, transcription occurs in the ___.
Nucleus
In eukaryotes, translation occurs in the ___.
Cytoplasm
What is the “One gene-One colinear polypeptide” theory?
The sequence of base pair triplets in the coding region of a gene specifies a colinear sequence of amino acids in its polypeptide product.
Amino acids are joined by ___.
Peptide bonds
Amino acids have a 3 groups; what are they?
- free amino group
- free hydroxyl group
- side (R) group
How are amino acids joined together?
The carboxyl group of one amino acid is covalently attached to the amino group of the next via peptide bond.
Describe the 4 levels of organization in proteins.
- Primary structure is the linear arrangement of amino acids.
- Secondary structure is determined by the spatial organization of amino acids.
- Tertiary structure is determined by the overall folding of the complete polypeptide.
- Quaternary structure is when more than one polypeptide interacts to make a functional protein.
T or F
The genetic code is degenerate. Why?
T.
Some amino acids are specified by more than one codon.
Of the 64 possible nucleotide triplets, ___ specify amino acids.
61 triplets specify amino acids.
What is the Wobble Hypothesis?
Crick’s Wobble Hypothesis explains that the base pairing at the 3rd base of a codon is flexible, which is why a single tRNA can respond to two or more codons.
What are ribosomes?
- composed of proteins and several different RNA molecules
- have a large subunit and a small subunit
- is an “RNA machine” with key roles in protein synthesis, including the formation of peptide bonds
What are the sites in the ribosome for translation?
A - aminoacyl site
P - peptidyl site
E - exit site
What is the Kozak sequence?
The Kozak sequence is found in eukaryotes and is used in translation to influence the efficiency of which AUG codon is used to start translation
In translation, which release factors recognize which stop codons?
- release factor 1 (RF-1): UAA, UAG
- release factor 2 (RF-2): UAA, UGA
Define the term “mutation”.
A heritable change in the sequence of an organism’s genetic information that may alter the phenotype of the organism, that occurs when DNA damage is not corrected.
___ is the source of all genetic variation.
Mutation
Describe the 2 categories of gene mutations.
- somatic mutations occur in somatic cells and will occur only in the descendants of that cell, not the progeny of the organism.
- germinal mutations occur in germ line cells and will be transmitted through gametes to the organism’s progeny.
What are the 3 types of point mutations?
- base substitutions
- frameshift mutations
- tautomeric shifts
What is a frameshift mutation?
Insertions or deletions of one or two base pairs that alters the reading frame of the gene downstream from the mutation site.
Describe the 2 types of base substitutions.
- a transition replaces a pyrimidine with a pyrimidine or a purine with a purine
- a transversion replaces a pyrimidine with a purine or a purine with a pyrimidine
Define the term “tautomeric shift”.
The movement of H atoms from one position in a nitrogen base to another position in the same base.
List the normal and tautomeric (rare) forms of each nitrogen base.
Adenine
normal = amino | rare = imino
Cytosine
normal = amino | rare = imino
Thymine
normal = keto | rare = enol
Guanine
normal = keto | rare = enol
What happens when the nitrogen bases are in their rare forms?
The bases can form A-C or G-T pairs.
Describe expanding nucleotide repeat mutations.
- expansion of triplet repeats
- cause of numerous human diseases
- mechanism of expansion involves DNA replication
- a dynamic mutation because the repeat copy number is in flux with each round of replication
Define the 2 types of phenotype-effect mutations.
- forward mutation is a genetic alteration that changes the wild type to a mutant
- reverse mutation changes the mutated site back to normal.
Define the 3 types of gene-effect mutations.
- missense mutation is a base substitution that results in an amino acid change in the protein
- nonsense mutation is a base substitution that changes a sense/normal codon to a stop codon
- silent mutation is a base substitution at the 3rd codon position that changes the codon but results in the same amino acid
Describe the 5 results of gene-effect mutations.
- a neutral mutation is a missense where the amino acid is changed to one of a similar chemical type
- a loss of function mutation is the result of mutations that cause a partial or full loss of protein function
- a gain of function mutation is the result of mutations that cause the cell to produce a gene or protein whose function is not normally present
- a conditional mutation is expressed only under certain circumstances
- a lethal mutation causes premature cell death
Huntington’s disease is a result of what?
Expanding nucleotide repeat mutation - repeated sequence of the CAG triplet.
Define “suppressor mutation”.
A suppressor mutation is a second site mutation that hides the effect of the first mutation.
Differentiate between intragenic suppression and intergenic suppression.
Intragenic suppression is when the suppressor mutation is on the same gene as the first mutation, whereas intergenic suppression is when the suppressor mutation is present on a different gene.
What are the 2 ways that DNA can be damaged?
- internal factors produce spontaneous mutations
2. external factors produce induced mutations
T or F
Most DNA damage is caused by external factors producing induced mutations.
F.
Most DNA damage is caused by spontaneous mutations brought on by internal factors.
What do spontaneous mutations result from?
- DNA replication errors
- DNA replication pausing
- Endogenous chemical reactions
What are the 3 types of DNA replication errors?
- tautomeric shifts
- wobble induced base mispairing
- strand slippage during replication
DNA replication pausing can be generated by ___ or ___.
- endogenous reactive oxygen species
- enzymes such as topoisomerases
What are the 4 types of endogenous chemical reactions that can cause spontaneous mutations, and what type of mutation do they result in?
- Depurination - transition or transversion
- Deanimation - transition
- Oxidation - transversion
- Alkylation - transition
Induced DNA mutations results from 2 types of mutagens, ___ and ___.
- chemical agents
- radiation
What are the 2 categories of chemical agent mutagens? Give examples.
- Chemicals that are mutagenic to both replicating and nonreplicating DNA
- alkylating agents
- nitrous acid
- hydroxylamine - Chemicals that are mutagenic to only replicating DNA
- base analogs
- acridine dyes
Chemical agent mutagens:
describe alkylating agents
- affects both replicating and nonreplicating DNA
- reacts with DNA bases adding methyl or ethyl groups
- directly or indirectly induces transitions, transversions, frameshifts and chromosomal aberrations
Chemical agent mutagens:
describe nitrous acid
- affects both replicating and nonreplicating DNA
- deanimating agent, removes amino group
- affects bases A,C,G
- causes transition mutations
Chemical agent mutagens:
describe hydroxylamine
- affects both replicating and nonreplicating DNA
- hydroxylates the amino group of C causing it to pair with A
- leads to a transition mutation
Chemical agent mutagens:
describe base analogs
- affects replicating DNA
- two common ones are 5-bromouracil and 2-aminopurine
- incorporated into DNA during replication
- when rare tautomers arise, will cause transition mutations
Chemical agent mutagens:
describe acridine dyes
- affects replicating DNA
- common ones are proflavin, ethium bromide, acridine orange
- intercalation of a dye causes frameshift mutations
Describe the 2 types of radiation induced mutations.
- Ultraviolet light induces mutations through excitation.
- X-rays induce mutations through ionization.
Describe mutagenesis by UV radiation.
UV light causes cross-linking of adjacent thymine bases which then forms thymine dimers, which block DNA replication and can cause DNA breaks.
List the 5 DNA repair mechanisms.
- Direct reversal
- Excision repair
- Mismatch repair
- Recombination
- Translesion synthesis DNA polymerase
What are the 3 mechanisms of direct repair of DNA damage?
- light dependent repair uses photolyase to repair thymine dimers (only prokaryotes)
- enzymatic removal of alkyl groups from DNA bases
- ligation of single-stranded nicks in DNA
Describe excision repair of DNA damage.
- DNA repair endonuclease recognizes, binds to, and excises the damaged base/bases
- DNA polymerase fills in the gap using the undamaged strand as a template
- DNA ligase seals the break/nick
Name the 2 kinds of excision repair.
- base excision repair (BER)
- nucleotide excision repair (NER)
The mutation of human nucleotide excision repair (NER) genes causes ___.
Xeroderma pigmentosum
Describe the process of mismatch repair (MMR).
- the MMR system uses hemi-methylated GATC sequence to identify a mismatched pair
- MMR compares old and new strands based on the methylation status of A in 5’-GATC-3’
- exonuclease removes a portion of the strand that includes the incorrect base
- DNA polymerase fills in the gap
- DNA ligase seals the nick
How many types of recombination DNA repair mechanisms are there?
2
- homologous recombination (HR)
- nonhomologous end joining (NHEJ)
Differentiate between the types of recombination DNA repair mechanisms.
Homologous recombination (HR)
- occurs during or after DNA replication
- a chromatid can be repaired using its sister chromatid
- usually occurs in the S or G2 phase
Nonhomologous end joining (NHEJ)
- uses entirely different set of proteins
- available throughout the rest of the cell cycle
T or F
Translesion synthesis (TLS) DNA polymerases are error prone repair mechanisms.
T.
What is the SOS response in E. coli?
If DNA is heavily damaged, the SOS response activates a host of DNA recombination, DNA repair and DNA replication proteins.
Define “transposable elements”.
Transposable elements are segments of DNA capable of moving from one location on a chromosome to another, or even to a different chromosome.
What are the 3 categories of transposable elements?
- cut and paste transposons
- replicative transposons
- retrotransposons
Where are each of the transposons found?
cut and paste transposons - prokaryotes and eukaryotes
replicative transposons - prokaryotes
retrotransposons - eukaryotes
How do bacterial transposons move?
Bacterial transposons move within and between chromosomes and plasmids.
What are the 2 types of cut and paste transposons in bacteria?
- insertion sequence (IS)
- composite transposons
___ are the simplest bacterial transposons.
Insertion sequences (IS)
Name the 3 parts of the general structure of a bacterial cut and paste transposon.
- gene that encodes transposase
- terminal inverted repeats
- target site duplication
Describe composite transposons in bacteria.
- created when two IS elements insert near each other
- a DNA sequence is captured
- IS element excision mobilizes the captured DNA
Describe the Ac/Ds transposon system in corn/maize.
- kernel colour is affected by the dominant C allele so kernels are clear
- the dissociation factor (Ds) is located at a site on chromosome 9
- the activator factor (Ac) stimulates chromosome breakage at the site of Ds
- if the Ds transposon is near C, it can lead to the loss of C
- this results in pigmented kernels
Give an example of a retrovirus.
Human Immunodeficiency Virus
Differentiate between a retrovirus and a retroviral-like element.
A retrovirus is infectious and a retroviral-like element is non-infectious.
General structure of retrovirus and retroviral-like element?
- genes that encode reverse transcriptase which copies RNA into DNA
- genes that encode integrase
- terminal inverted repeats at both ends of the element
- target site duplication which is repeated sequences at both ends resulting from staggered cleavage of DNA at the site of insertion
General structure of retrotransposon/retroposon?
- genes that encode reverse transcriptase and endonuclease activities
- 5’ and 3’ untranslated regions (UTR)
- polyA tail
- target site duplication which is repeated sequences at both ends resulting from staggered cleavage of DNA at the site of insertion
What are the 2 major categories of transposable elements in humans?
- long interspersed nuclear elements (LINEs)
- short interspersed nuclear elements (SINEs)
Structure of long interspersed nuclear elements (LINEs), specifically L1 elements?
- about 6 kb long
- internal promoter
- two open reading frames that encode a nucleic binding protein and a protein with endonuclease and reverse transcriptase activities
The human genome contains ___ complete L1 elements and ___ truncated L1 elements.
- 3000 to 5000
- more than 500,000
T or F
SINEs (short interspersed nuclear elements) are the most abundant class of transposable elements in the human genome.
F.
LINEs are the most abundant, SINEs are the second most.
T or F
The reverse transcriptase required for SINE transposition is provided by LINE elements.
T.
3 reasons why transposable elements are significant in scientific theory are?
- transposons are mutagens
- transposons can mobilize foreign genes
- transposons can generate changes in genome organization
Genetic regulation in bacteria is primarily focused on ___.
adapting the bacterium to its environment.
Define “constitutively expressed genes”.
Certain gene products are essential components of almost all living cells, so the genes that specify these products are continuously expressed in most cells. These genes are constitutive.
Define “inducible and repressible genes”.
Some gene products are only needed under certain conditions, and regulatory mechanisms allow the synthesis of these products when they’re needed. The genes are are inducible and repressible.
T or F
Enzymes involved in a catabolic process are often inducible.
T.
T or F
Enzymes involved in an anabolic process are often inducible.
F.
Enzymes involved in an anabolic process are often repressible.
Explain the repression of genes for tryptophan.
- genes are expressed in the absence of tryptophan
- when tryptophan is available those genes are repressed
- repression occurs at the level of transcription of the tryptophan biosynthetic genes
Define the term “operon”.
An operon is a single transcriptional unit that includes a series of structural genes, a promoter and an operator.
An example of a negative inducible operon in bacteria is?
The lac operon
An example of a negative repressible operon in bacteria is?
The trp operon
In positive control of bacterial gene expression, the regulatory protein is called an ___.
activator
The lac operon of E. coli is a ___-inducible but ___-regulated operon.
negatively-inducible
positively-regulated
The lac operon genes of E. coli are only transcribed when?
Lactose is present and glucose is absent.
Explain the analysis of the E. coli lac operon I.PO.Z.Y.A.
I - regulatory repressor gene
P - closely linked promoter
O - regulatory operator element
Z, Y, A - structural genes
E. coli lac operon
What happens when the lac operator is bound by the repressor?
RNA polymerase cannot access the promoter, so there is no lac operon transcription.
E. coli lac operon
Explain how the lac operon has both off and on characteristics.
Off
- in the absence of inducer allolactose
- repressor bind to the operator
- RNA polymerase cannot transcribe the Z,Y,A genes
On
- in the presence of inducer allolactose
- repressor binds inducer so becomes inactive
- operon is induced and Z,Y,A genes are transcribed
E. coli lac operon
___ is the wildtype gene
___ is the mutant gene
+ is the wildtype
- is the mutant
E. coli lac operon
The F’ factor lac genotype is presented on the ___ of the diagonal and the chromosomal lac genotype is presented on the ___.
The F’ factor lac genotype is presented on the left of the diagonal and the chromosomal lac genotype is presented on the right.
E. coli lac operon
What is the phenotype?
F’ I+ P+ Oc Z+ / I+ P+ O+ Z- Y- A-
constitutive expression of lac Z from F’ factor
E. coli lac operon
What is the phenotype?
F’ I- P+ O+ Z- Y- / I+ P+ Oc Z+ Y+ A+
constitutive expression of lac Z,Y,A from chromosome
E. coli lac operon
What is the phenotype?
F’ I- P+ O+ Z- Y- / I- P+ O+ Z+ Y+ A+
constitutive expression of lac Z, Y, A from chromosome
E. coli lac operon
Is the lac operon always induced in the presence of allolactose? Why?
- no
- not if glucose is present
- glucose is preferred over lactose as carbon source
- glucose prevents lac operon induction, known as negative regulation (in this case catabolite repression)
How does glucose regulate the E. coli lac operon?
- through cyclic AMP (cAMP) levels
- when glucose is high, cAMP is low and vice versa
- when cAMP levels are high, cAMP binds to the catabolite activator protein (CAP)
- the cAMP/CAP interaction promotes binding of RNA polymerase
1927
H. Muller
- discovered induced DNA mutations
- used X-rays to study X-linked mutations in Drosophila
- provided the first clue that phenotypic damage can result from X-rays
1930s
J. Beadle
E. Tatum
- one gene encoded one discrete polypeptide
1936 - 1941
B. McClintock
- studied chromosome breakage in corn/maize
- discovered cut-and-paste Ds and Ac transposable elements
- notion that DNA could be mobile
- 1983 Nobel Prize
1947
R. Franklin
- X-ray diffraction images of DNA
1953
J. Watson
F. Crick
M. Wilkins
- the double helix structure of DNA.
- 1962 Nobel Prize.
1956
F. Crick
- tRNAs were adaptors between mRNA codons and amino acids
1958
M. Meselson
F. Stahl
- proved semi-conservative replication with an experiment.
- cesium chloride equilibrium-density gradient centrifugation
- separated double-stranded DNA based on density
1960s
C. Yanofsky
- sequence of nucleotide triplets in the trpA gene of E. coli corresponded to the sequence of amino acids
1961
F. Jacob
J. Monod
- proposed the operon model to explain lactose utilization in E. coli
- 1965 Nobel Prize
1961
M. Nirenberg
G. Khorana
- homopolymers produced homopolypeptides while random copolymers produced polypeptides with different amino acids
- 1968 Nobel Prize
1961
F. Crick
- confirmed that the genetic code is a triplet code
1964
R. Holley
- nucleotide sequence of a yeast tRNA
- 1968 Nobel Prize
1964
M. Nirenberg
P. Leder
- short mRNAs stimulated the binding of ribosomes and the corresponding amino acid bound tRNA
- identified the amino acids specified by mixed codons
1970
D. Baltimore
H. Temin
S. Mizutani
- discovered reverse transcriptase which catalyzes reverse flow of genetic information from RNA to DNA
- 1975 Nobel Prize for Baltimore and Temin
1990s
R. Kornberg
- molecular structure/function of RNA polymerase II
- 2006 Nobel Prize
1990s
T. Lindahl
P. Modrich
A. Sancar
- various works on DNA repair
- 2015 Nobel Prize
2000
V. Ramakrishnan
T.A. Steitz
A. E. Yonath
- discovery of ribosome structure
- detailed analysis of how ribosomes work during protein synthesis
- 2009 Nobel Prize
What 3 factors affect mutation rates?
- the frequency of DNA changes
- how often DNA changes are repaired
- detection of the mutation
Base analogs are mutagenic because?
They are similar in structure to normal bases
Which of the following transposons possesses terminal inverted repeats?
a. insertion sequence
b. composite transposon
c. non-composite transposon
d. all of the above
d. all of the above
What is the difference between the template strand and the non-template strand?
The template strand is the DNA strand that is copied into an RNA molecule, whereas the non-template strand is not copied.
Which of the following is not a function of the promoter?
a. serves a sequence to which transcription apparatus binds
b. determines the first nucleotide that is transcribed into RNA
c. determines which DNA strand is template
d. signals where transcription ends
d. signals where transcription ends
Transciption happens in the direction of ___ and each new nucleotide is added to the ___ end.
- 5’ to 3’
- 3’-OH
What binds to the -10 consensus sequence found in most bacterial promoters?
a. the holoenzyme
b. the sigma factor
c. the core enzyme
d. mRNA
a. the holoenzyme
What characteristics are most commonly found in rho-independent terminators?
Inverted repeats followed by a string of adenine nucleotides.
The short lengths of DNA produced by discontinuous replication on the lagging strand of DNA of a replication fork are called ___ fragments.
Okazaki
During replication in E. coli, the enzyme called ___ synthesizes short stretches of nucleotides to get replication started.
primase
What is the enzyme that aids in filling in gaps at the ends of linear chromosomes following removal of primers?
Telomerase
At which location(s) on the leading strand of a replication fork are primers synthesized?
Only at the 5’ end of the newly synthesized strand
Primase synthesizes a single primer on the leading strand and synthesis occurs continuously in the ___ direction of movement of the replication fork.
5’ to 3’
The shortening of telomeres may contribute to the process of ___.
aging
Which activity of DNA polymerase I in E. coli allows it to remove the primers laid down by DNA primase?
5’ to 3’ exonuclease
DNA polymerase reads the template strand ___ and synthesizes the new strand ___.
- 3’ to 5’
- 5’ to 3’
Which activity of DNA polymerases in E. coli allows them to remove a nucleotide that has been inserted incorrectly?
3’ to 5’ exonuclease
The position of the start site of a bacterial transcription unit is determined by ___.
the location of the consensus sequences
Which of the following RNA can inhibit translation of mRNA in the cytoplasm?
a. rRNA
b. tRNA
c. miRNA
d. mRNA
c. miRNA
The molecule that connects the coding sequence of nucleotides in RNA to the amino acid sequence of a polypeptide is ___.
tRNA
An RNA molecule has the following percentages of bases: A = 30%, U = 23%, C = 20%, and G = 27%. What is the percentage of A in the template strand of DNA that encodes this RNA, assuming that the template strand contains no introns?
23%
Typically, in order for RNA to form secondary structures such as hairpin loop or stem loop, an RNA strand must contain ___.
short stretches of bases that will pair up
The ___ on a gene is the DNA sequence that the transcription apparatus recognizes and binds to initiate transcription.
promoter
Once transcription has been initiated, RNA polymerase adds nucleotides to the 3’ end of the growing RNA molecule until it transcribes a ___.
terminator
Which biological process does RNA NOT play a vital role in?
Stable, long-term genetic information storage
If you are performing an in vitro transcription experiment in the bacterium E. coli and you keep transcribing random mRNAs of varying lengths, what might be your issue?
The sigma factor is not binding to the core enzyme
What is the Shine-Dalgarno sequence?
5’-UAAGGAGGU-3’
Describe theta replication.
- is bidirectional
- double stranded DNA unwinds at replication origin
- forms single stranded templates
- a replication bubble forms with replication forks
- the forks proceed around the circle
- eventually 2 circular DNA molecules are produced
Describe rolling circle replication.
- is unidirectional
- replication is initiated by a break in nucleotide strands
- DNA synthesis begins at the 3’ end
- the inner strand is used as a template
- cleavage releases a single stranded linear DNA and a double stranded circle
- the linear DNA may circularize and later be a template
- produces multiple circular DNA molecules
Describe linear chromosome replication.
- is bidirectional
- each chromosome contains multiple origins
- at each origin DNA unwinds and produces a replication bubble
- DNA synthesis takes place on both strands at each end of the bubble
- eventually the forks of adjacent bubbles run into each other and the segments of DNA fuse
- produces two identical linear DNA molecules
