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