Replication, Transciption, Translation (Exam 1) Flashcards
In DNA replication, is the whole genome duplicated, or just part of it?
whole genome
How is DNA shape different between prokaryotes and eukaryotes?
Prokaryotes have circular DNA, whereas eukaryotes have linear DNA
How is the starting point of DNA replication in prokaryotes compared to eukaryotes?
Origin of replication in prokaryotes is only 1, whereas in eukaryotes there’s multiple
Prokaryotes and eukaryotes have similar mechanisms of replication. How are they the same?
-semi-conservative replication (1 old and 1 new strand in daughter cell)
-bi-directional replication (the fork advances in both directions)
How is DNA replication initiated? What 3 enzymes play a role in initiation?
origin(s) of replication are in TA rich regions
note: prokaryotes have only one origin, eukaryotes have multiple
3 enzymes
-DNA helicases separates strands of a DNA double helix by breaking up hydrogen bonds at the replication fork
-topoisomerases unwind DNA (relaxes and unwinds DNA from its super-coiled nature)
-SSBP binds to single strands and holds DNA open during replication (prevents it from re-annealing)
What happens during elongation of DNA replication?
What does DNA polymerase 1 do?
replaces RNA primer with complementary DNA during DNA replication
What enzyme in DNA replication joins okazaki fragments (of the lagging strand)?
DNA ligase
What creates an RNA primer?
primase creates a short RNA sequence primer during DNA replication for DNA polymerase 3 to begin synthesis
What strand in DNA replication is being synthesized in fragments and is not continuous?
okazaki fragments (of the lagging strand)
What strand in DNA replication has continuous replication and is in the same direction as the replication fork?
leading strand
What does DNA polymerase 3 do?
reads old strand to copy bases and put down complementary new bases
DNA polymerases are the major enzyme/workhorse of DNA replication. Why?
they create DNA polymer!
Also, they both have proofreading 3’-> 5’ ability to check for mutations/errors (this is known as exonuclease activity as well, which cuts from the end of the sequence)
What enzyme during DNA replication reads from 3’->5’ and adds nucleotides in 5’->3’ direction?
DNA polymerase
Which DNA polymerase replaces the RNA primer with DNA?
1
What are the 2 strands called in transcription?
template and coding strand
note: the template strand is always from 3’->5’ because it can be read and synthesized continuously! Its the easiest
What helps a specific gene be found at the beginning of transcription/helps it to initiate transcription?
promoter! It helps promote gene expression
each gene has its own promoter, info is fragmented
it will appear with a “+1”
What are exons? What are introns?
exon= sequence that will eventually be expressed in proteins
intron= will be removed/not expressed in protein
note- this happens in eukaryotic transcription
Where does transcription occur?
nucleus
What does RNA polymerase do?
opens up dsDNA and transcribes DNA-> RNA
What are the other names for post transcription modification?
test q
RNA processing or RNA maturation
Is eukaryotic transcription monocistronic or polycistronic?
monocistronic (1 promoter for each gene in eukaryotes)
What 3 major steps happen during post transcription modification?
1) splicing (introns removed)
2) capping (add 7’ Me- Guanosine cap)
3) poly-A tail
this is needed to protect RNA so it won’t degenerate when it leaves nucleus (mRNA is only one leaving once its mature)
Are transcription and translation coupled in eukaryotes?
no! only coupled in prokaryotes
What are the differences between DNA and RNA synthesis?
DNA replicates, RNA transcribes
Primer is DNA exclusive
Polymerase differs between DNA and RNA
Subunits differ (ATCG vs AUCG)
RNA has no proofreading ability since it is short
The complementary mRNA strand that would be synthesized from the DNA base sequence of CTGAC would be….
3’ GACUG 5’
T/F: The synthesis of mRNA is called translation
false
T/F: synthesis of a new strand of mRNA is in the 5’ -> 3’ direction
true
What are the 3 types of RNA found in eukaryotes?
mRNA, rRNA, tRNA
protein is linked together by what bonds?
peptide bonds
What are ribosomes made of?
ribosome protein and rRNA
ribosomes are the major workhorse proteins in translation
What are the subunits of a prokaryotic ribosome?
large subunit= 50S
small subunit= 30S
together= 70S
What are the subunits of a eukaryotic ribosome?
large subunit= 60S
small subunit= 40S
together= 80S
Which ribosome subunit has peptidyl transferase activity? What is this?
large subunit of eukaryotic ribosome (60S) and large subunit of prokaryotes (50S) has peptidyl transferase activity
this enzyme forms peptide bonds between amino acids
Which ribosome subunit recognizes shine delgarno sequences of mRNA (mRNA cap)?
small subunit of prokaryotic ribosome (30S)
Which ribosome subunit recoginizes the 7-Me-cap of mRNA?
small subunit of eukaryotic ribosome (40S)
What are the 3 things needed for translation?
-mRNA
-ribosome
-tRNA
What shape is tRNA?
clover leaf structure
Which RNA picks up amino acids?
tRNA
Which RNA recognizes codon on mRNA?
tRNA
If the codon is AUG, what is the anticodon?
5’ CAU 3’
A codon is made up of how many nucleotides?
3
How many codons are there in the codon table? How many code for amino acids?
64 codons, 61 code for amino acids (stop codons are the ones that dont)
What does the start codon AUG code for?
methionine
note: ATG would also code for this
What are the 3 stop codons?
-UAG
-UGA
-UAA
How does translation begin?
when mRNA and tRNA bind and the starting codon is AUG
What are the 3 sites within a ribosome?
A= attachment site
P= peptidyl binding site
E= free tRNA/exit site
Ribosome synthesizes protein from what terminal to what terminal?
N terminal to C terminal
N is free amino group in polypeptide
C is free carboxyl group
What is the end product of translation?
protein
What is post translational modification modifying?
protein
Where does post translational modification occur?
ER and golgi
What happens during post translational modification?
-oxidation reaction to help protein fold
-protein will be cleaved
-1 active protein is made (and in the case of insulin there will also be C-peptide)
during post translational modification, there can be folding, cutting, and other processes such as glycation (addition of a sugar molecule to a protein)
Is insulin a protein or lipid hormone?
protein hormone
Where is insulin secreted?
pancreatic B cells in the islets (alpha cells in this islets will secrete glucagon)
Does insulin increase or decrease blood sugar?
decrease
Does glucagon increase or decrease blood sugar?
increase
What does insulin have that helps it to fold during post-translational modification?
3 disulfide bonds (1 disulfide bond looks like this: -S-S-, which comes from thiol -SH + -SH)
What is a marker for endogenous insulin?
c-peptide
What are the 2 sources of insulin?
1) endogenous (from pancreas)
2) exogenous (from insulin injection)
Genes are DNA. What are the causes of damage to DNA?
-spontaneous aging
-deamination (removal of amino group in amino acids)
-oxidation (damages cell membrane/DNA with oxygen, note that antioxidants can decrease oxidation)
-UV light (makes a thymine thymine dimer on DNA)
-X-ray and gamma rays cause DNA fragmentation (damages the backbone)
-nitrites accelerate deamination of bases
What does it mean if a mutation is a “selective force”?
its advantageous
What does an excision endonuclease do?
enzyme that cuts out the damaged region out of the bubble, usually the T-T dimer and its in the middle of the chain
T-T dimers form in DNA when there is overexposure to UV light
and then DNA polymerase and ligase will rebuild new strand what was cut out and glue it
Can mutations occur in both DNA and RNA?
Yes, but DNA is permanent whereas RNA is not
What are the 3 types of point/substitution mutations?
1) silent (usually affects 3rd position of the codon)
2) nonsense (early stop codon, will be relatively short protein and non-functional)
3) missense (a nucleotide change results in a different AA, reduces the function)
What is frameshift mutation?
deletion or insertion of a number of nucleotides not divisible by 3, resulting in misreading of all nucleotides downstream
usually results in a truncated non-functional protein
What is xeroderma pigmentosum?
its an excision endonuclease deficiency (T-T dimers will build up and not get cleaved like they’re supposed to)
will result in hyperpigmentation of the skin, the sun is very dangerous to these people
What is denaturation in DNA?
breaking of the intra chain of H bonds in DNA creates single stranded nucleic acids
Tertiary and secondary structures of nucleic acids can be “melted” by moist heat and…
high pH
DNA/RNA with a high content of G/C base pairs will require more harsh denaturation conditions, which means…
higher melting temperatures
(DNA with a higher percentage of A/T and RNA with A/U will melt under less harsh conditions A/T and A/U base pairs have just 2 H bonds between them)
Denatured DNA/RNA will ____________ when returned to normal conditions. If this is done in the presence of foreign DNA or RNA then hybrid duplex strands will result
renature
Formation of hybrid duplex can have 3 different doubles stranded molecules. What are they?
-DNA/DNA
-RNA/DNA
-RNA/RNA
note: hybrid duplexes form where 2 different nucleic acid molecules have regions of complementarity
the more complementarity- the more stable the hybrid
the more mismatches- the more unstable and easier to denature
