Section 7: Molecular Genetics Flashcards
Describe the structure of DNA
Double helix with major and minor grooves
This carries the hereditary information of the cell
DNA
What is the DNA backbone made of?
5’ to 3’ phosphodiester bonds form a phosphate backbone
What are the nitrogen bases in DNA?
In RNA?
ATGC in DNA
AUGC in RNA
DNA replication begins at special sites in the middle of the DNA molecule (not the end) called
DNA strands separate to form __________ that expand in both directions
Thousands of them happen to speed up relication of 3 billion BP molecule in eukaryotic cells. How many origins of replication do prokaryotes have?
Origins of replication
Replication bubbles
One
In DNA replication, when is the second chromatid containing a copy of DNA assembled?
Interphase (S phase?)
During interphase, DNA is unzipped and each strand serves as a template for complementary replication
This is term means one strand of the two is old, the other is new, occurs in DNA replication of all known cells
Semi Conservative Replication
What is the enzyme that unwinds DNA?
It forms a Y shaped replication fork
Helicase
Single stranded binding proteins attach to each strand of uncoiled DNA to keep them separate
What break and join the double helix, allowing the prevention of knots?
(if you unwind a twist, the ends will get extra tight and knot up)
Topoisomerases
In what direction does DNA polymerase move?
Is the new strand parallel or antiparallel?
3’–>5’
Antiparallel (5’—->3’)
On this strand, the DNA polymerase works continuously as more DNA unzips
In this strand (the 5’–>3’ strand), the DNA polymerase has to go back to the replication fork and work away from it
What are the fragments that it produces called?
What connects these fragments?
Leading Strand
Lagging Strand
Okazaki Fragments
DNA ligase
In DNA replication, this is an enzyme that creates a small strip of RNA primer off which DNA polymerase can work since it can only add to an existing strand
Primase
What does DNA replication require at the start?
RNA primer
Every okazaki fragment has an RNA primer, these RNA strips are later replaced by…
DNA Polymerase 1
Other than replacing BPs from RNA primers, what else does DNA pol 1 do?
This polymerase is pure replication
DNA repair
DNA polymerase 3
DNA poly 1 and 3 have 3’–>5’ _____, it breaks phosphodiester backbone on a single strand of DNA and removes a nucleotide. It can only remove from 3’ end (in this case_ of the chain
Exonuclease
Which can also do proofreading, DNA poly 1 3, or both?
Which also has a 5’–>3’ exonuclease to take off the primer
both
Pol 1
in sum:
DNA Pol ______ mainly replicates the DNA 5’ to 3’ but can also proofread via 3’ to 5’ exonuclease.
DNA Pol ______ primarily breaks down RNA primer via 5’ to 3’ exonuclease and replaces it with DNA (laid down between Okazaki fragments mainly) via 5’ to 3’ polymerase while proofreading as it goes, can proofread
via 3’ to 5’ exonuclease as well
DNA polymerase 3
DNA polymerase 1
In prokaryotes, what happens to the good strand if there is an error in replication, so it doesn’t repair the wrong strand?
It is methylated
In all cases of repair, what must come seal the backbone afterward?
Ligase
Energy for elongation is provided by two additional ________ attached to each new nucleotide. Breaking the bonds
holding the two extra _________ provides chemical energy for the process (same w/ transcription!). Human rate 50n/s
Phosphates (both blanks)
A region of repetitive nucleotide sequences at each end of a chromatid, which protects the end of the chromosome from deterioration or from fusion with neighbouring chromosomes.
telomere
What two problems can occur in the replication of a telomere?
Not enough template strand where primase can attach
The last primase is removed
Do prokaryotes have telomeres?
No, circular DNA
enzyme that attaches to the end of template strand and extends the template strand by adding short sequence
of DNA over and over (not important code), allowing elongation of lagging strand to continue
For reference: https://www.youtube.com/watch?v=AJNoTmWsE0s
Telomerase
Telomerase carries an
RNA template: binds to flanking _____ end of telomere that compliments part of its RNA template, synthesizes to fill in over
the rest of its template
binds to 3’ end
For reference: http://upload.wikimedia.org/wikipedia/commons
/3/3b/Working_principle_of_telomerase.png
In protein synthesis, one-gene-one-polypeptide hypothesis defines a _____ as the DNA segment that codes for a particular polypeptide.
Also, genetic code is universal for nearly all organisms and most AAs have more than one codon specifying them. This concept is called
gene
redundancy/degeneracy
This type of RNA is a Single stranded template. Since there are 64 possible ways (4x4x4) ways that four nucleotides can be arranged
in triplet combinations, there are 64 possible codons. 3 of them are stop codons. Therefore, only 61 codes for amino acids
mRNA
This type of RNA has a C-C-A-3’ that attaches to an AA, and the other portion is the anticodon which base pairs with the codon in mRNA
tRNA
What part of tRNA base pairs with the codon of mRNA?
What fragment of tRNA attaches to an AA?
anticodon
C-C-A-3’
This is the term for the concept that the exact bp of the 3rd nucleotide in the anticodon and the 3rd nucleotide in the codon is often not required, allowing 45 different tRNA’s base-pair with 61 codons that code for amino acid. There is space for the 5’ anticodon on tRNA to move or…
Wobble
This type of RNA transports an AA to its mRNA codon
tRNA
Together w/ proteins, this type of RNA forms ribosomes
How many binding sites do ribosomes have? What are they?
rRNA
3, one for mRNA, tRNA that carries a growing polypeptide chain (Psite) and one for 2nd tRNA that delivers the next aa (A site)
The nucleolus is an assemblage of DNA being actively transcribed into..
rRNA
What are the termination sequences on mRNA?
UAA, UGA, UAG
Where is the ribosome assembled?
Where is it exported?
The nucleolus
Cytoplasm (large and small subunits separately)
The is the creation of RNA molecules from a DNA template
Prokaryotes are MONOCISTRONIC/POLYCISTRONIC
Eukaryotes are MONOCISTRONIC/POLYCISTRONIC
Transcription
Prokaryotes POLYCISTRONIC (each mRNA can create multiple polypeptide chains)
Eukaryotes MONOCISTRONIC (each mRNA creates a single polypeptide chain)
In this phase of transcription, the RNA polymerase attaches to a promoter region on DNA and unzips the DNA into two strands
The promoter region often contains what sequence?
Initiation
TATA (TATA box)
The most common sequence of nucleotides at the promoter region is called the _____ sequence
Variations from it cause what?
Consensus
less tight RNA polymerase binding and a lower transcription rate
In this phase of transcription, RNA polymerase unzips DNA and assembles RNA nucleotides using one strand of DNA as template.
Elongation
only ONE strand is transcribed!
This phase of transcription occurs when RNA pol reaches a special sequence, often AAAAAAA in eukaryotes
Termination
In what direction of the DNA strand is transcription occurring?
3’ to 5’ (synthesized RNA is 5’ to 3’)
In mRNA processing, before leaving the nucleus, pre-mRNA undergoes several modifications
First this sequence is added to the 5’ end of the mRNA. It’s a guanine with three phosphate groups, also called ___, providing stability at the point of attachment for ribosomes
5’ cap (-P-P-P-G-5’)
GTP
In mRNA processing, before leaving the nucleus, pre-mRNA undergoes several modifications
After the 5’ cap is added, this sequence is attached to the 3’ end of the mRNA. It provides stability and control of movement across the nuclear envelope
How many AAs is it?
A poly-A tail (AAA…AAA-3’)
200
What does the A poly A tail facilitate in prokaryotes?
Degradation
After the A poly A tail is attached to the 3’ end of the mRNA, this occurs to remove nucleotide segments from mRNA, deleting introns and splicing exons
RNA splicing
During DNA splicing in mRNA processing, before the mRNA moves into the cytoplasm, what delete the introns and splice the exons?
Do prokaryotes have introns?
Small nuclear ribonucleoproteins (snRNPs) and splicosome
No
After RNA splicing in mRNA processing, this occurs, which allows different mRNA to be generated from the same RNA transcript by selectively removing differences of an RNA transcript into different combination, coding for a different product
Alternative Splicing
EUKARYOTES/PROKARYOTES generally have ready to go mRNA upon transcription
Only in EUKARYOTES/PROKARYOTES do you need mRNA processing
Prokaryotes have ready to go mRNA, translation can occur immediately
eukaryotes require proessing,
In which can multiple RNA polyermases transcribe the same template simultaneously, prokaryotes, eukaryotes, or both?
Both
This process is the assembly of AAs based on reading of new RNA
What is the energy source?
Translation
GTP
This is located in the cytoplasm for translation, the amino acid attaches to it at the 3’ end requiring 1 ATP
Aminoacyl-tRNA
In this phase of translation, the small ribosome unit attaches to the 5’ end of mRNA, the tRNA-methionine attaches to the start sequence of mRNA and the large ribosomal unit attaches to form a complete complex
What is the start sequence of mRNA
Initiation
AUG
During the initiation of translation, the small ribosomal subunit attaches to what end of mRNA?
The large ribosomal subunit binds…
For reference: http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter
15/translation_initiation.html
5’
The small subunit
During this step of translation, the 2nd tRNA binds to the A site for peptide bond formation. This 1st tRNA is released without methionine. The 2nd tRNA moves to the p site and the next tRNA comes into A site to repeat process
Elongation
The movement of tRNA from the A site to the P site during elongation during translation is referred to as
Translocation