DNA And RNA Replication- Exam III Flashcards
DNA is ____ stranded and RNA is ____ stranded.
Double; single
If a 2’ hydroxyl group is present on the pentose sugar, the molecule is:
Ribose
If the 2’ hydroxyl group is absent on the pentose sugar (only a hydrogen in that position)
Deoxyribose
High energy ____ molecules are attached to the 5’ carbon of the pentose in both DNA and RNA
Phosphate
What are the purines?
A and G (pure as gold)
What are the pyramidines?
CUT (Cut the py)
Describe the structure of the purines
Double ring structure
Describe the structure of the pyrimidines
Single ring structure
What is the difference between uracil and thymine?
Uracil in RNA
Thymine in DNA
The steps of the staircase when referring to the double helix DNA molecules are:
The bases
What is chargaff’s rule?
A base pairs with T
G base pairs with T
How many bonds form between adenine and thymine? How many bonds form between cytosine and Guanine?
2 on A and T
3 on G and C
What base pairs are more stable and why?
G and C because they have an extra hydrogen bond
What control the expression of prokaryotic transcription?
Promotors & operons
In prokaryotic organisms the DNA is organized into a ___ or ____ fashion.
Linear or contiguous
In prokaryotic gene transcription, the RNA copy made is:
Ready for use in translation
As DNA transcription proceeds in a prokaryotic organism, the RNA transcript is described as:
Colinear
When we refer to the RNA copy as being colinear, what we mean is:
Identical copy of the DNA transcript
In eukaryotic organisms the DNA is broke up into ____ that will give rise to the protein sequence.
Coding regions or exons
Regions that do not get coded and separate exons
Introns
Regions at the 5’ and 3’ ends that do not encode proteins:
Untranslated regions (UTRs)
In eukaryotic organisms, one strand of the DNA is first copied in linear fashion and then then the introns are removed by a process called:
Splicing
In prokaryotic organisms, the RNA copy that gets made from the DNA is ready for ________. However, in eukaryotic organism, everything from the DNA gets copied into the RNA but ______ and ______ must take place to give rise to the mature mRNA which is transported out of the nucleus for use as the template for protein synthesis.
Protein synthesis; splicing and subsequent modification
In eukaryotic organisms, primary transcripts are often spliced in multiple combinations of exons. This process is called:
Alternative splicing
Alternative splicing gives rise to the possibility of ______ from the same transcript.
Numerous different proteins
The region of DNA that will encode a protein that includes all the regulatory elements to control its expression
Gene
In order to fit inside the cell or nucleus, linear DNA must be:
Condensed
in prokaryotic organisms, the DNA is condensed by a set of _____ and _____ in back and forth loops
Polyamines and proteins
In eukaryotes, DNA is first condensed into _____.
Nucleosome
Each nucleosome involves around _____ BP of DNA and a set of _____
200BP and a set of core histone proteins
Chromatin exists in two forms:
Euchromatin, and heterochormatin
Slightly more relaxed, transcriptionally active form of DNA
Euchromatin
Highly condensed and generally not transcriptionally active form of chromatin
Heterochromatin
Chromatin can be further condensed into ___ and _____ ultimately into _________ by function specific sets of proteins.
Solenoids; supersolenoids; chromosomes
DNA is broken up into fragments called:
Chromsomes
In humans we have 22 chromosomes called _____ and each exist as a _____.
Autosomes ; pair
The gametes contain _____ copy of a chromosomes
1
What is the number of protein coding genes in the human genome?
20,000-25,000
The average gene is about ______ BP long, and contains about ____ exons and a coding sequence of about ______ BP.
27,000
9
1340
On average each gene gives rise to about ____ isoforms or splice variants.
8
Human genome contains about _____ BP
~3.2 billion
It only takes a single BP change to cause:
Disease
Allie and Annie have difference of about ______ BP
1-2 million
Annie and Jordan have a difference of about _____ BP
6 million
Becuase the antiparallel orientation of the strands, and the fact that the strands are complementary, each strand can:
act as as template for synthesis of new DNA Strand
When is DNA replicated?
S phase of cell cycle
Central dogma of genetic information flow
DNA to RNA (transcription)
RNA to protein (translation)
The first and foremost principle of DNA replication is that it is all driven by:
Base pairing
You have a strand of DNA that serves as a template, and the nucleotide bases that make up that strand will dictate:
What base gets incorporated at that position in the strand being made
The molecule that catalyzes the stepwise addition of deoxyribonucelotide-triphosphate addition to the 3’ OH end of a polynucleotide chain
DNA polymerase
The reason the stepwise addition of a deoxyribonucelotide-triphosphate to the 3’ hydroxyl end of a polynucleotide chain is important is because that addition of the next base is driven by:
the favorable free energy that is released from the hydrolysis of the triphosphate molecule to a mono phosphate phosphodiester bond.
DNA synthesis on the strand that is being made, always proceeds:
5’—> 3’
For DNA synthesis to occur, you need a region of double stranded DNA and a:
Free 3’ hydroxyl group
DNA polymerase synthesizes the new strand in what direction?
5’ - 3’
DNA polymerase requires a _______ and a strand to build off of with a ______.
Template strand; free 3’ OH group
DNA polymerase contains _____ polymerase activity and a ______ exonuclease activity
5’-3’ polymerase activity
3’-5’ exonuclease activity
The free 3’ hydroxyl group of the deoxyribose will form a _____ bond with the next deoxyribose nucleoside triphosphate
Phosphodiester bond
The high fidelity of DNA replication requires:
Proofreading mechanism
The High fidelity refers to:
A pairing to T and C to G correctly without error
DNA polymerase are a _____ enzyme that remove their own polymerization errors
Self-correcting enzyme
DNA polymerase have a 3’-5’ ______ activity during DNA synthesis
Exonuclease activity
If the incorrect base gets put in, it will create a ____ that gets removed by the 3’-5’ exonuclease activity which will leave a _____ to basepair with the correct base.
Bulge, free 3’ hydroxyl group
DNA synthesis starts at ____ regions known as origins of replication.
AT rich
It’s important that the origins of replication are AT rich because:
They have weaker bonds making them easier to separate
Origins of replication form:
Replication forks
Daughter strand that is synthesized continuously, toward the replication fork
Leading strand
Daughter strand that is synthesized discontinuously, away from the replication fork
Lagging strand
DNA synthesis begins following DNA ____ and RNA _____ at replication origins.
Unwinding and RNA primer Synthesis
The RNA primers that come into the newly opened up area of double stranded DNA provide:
A double stranded template w free 3’ hydroxyl group
What strand do Okazaki fragments get made on:
Lagging strand
begins with synthesis ion a short RNA primer by a special nucleotide-polymerizing enzyme
The lagging strand of DNA synthesis
The enzyme that creates the short RNA primers made up on the lagging strand using DNA as a template
DNA primase
Unlike DNA polymerase, the DNA primase __________ by joining two nucleoside triphosphates together
Can start a new polynucleotide chain
The primase synthesizes a short polynucleotide in the 5’ to 3’ direction and then stops, making the 3’ end of the primer available for the ________ to produce the Okazaki fragment.
DNA polymerase
What is responsible for moving the RNA primers (about 10 nucleotides in length)
5’ to 3’ exonuclease activity of DNA polymerase
What joins the Okazaki fragments together?
DNA ligase
Explain the energy of the lagging strand
Energetically costly
THe DNA ligase uses _____ for energy
ATP hydrolysis
Only changes accumulated in the _____ can be inherited.
Gametes
A protein that uses the hydrolysis of ATP to change the shape of the protein and move rapidly along the DNA strand and if encountering a region of double stranded helix, it will pry the helix apart
DNA helicase
Single Strand DNA binding protein bind to the exposed strand of DNA and aid the helicase by:
Stabilizing the unwound helix (to avoid them from repairing together)
Single strand DNA binding proteins can also be referred to as:
Helix-destabilizing proteins
There are some anchoring proteins that are responsible for holding the DNA polymerase to the replication fork and allow it to move along as the DNA unwinds.
DNA sliding clamp/ sliding ring
DNA ligase works
Distally from all the other molecules
Premature aging disease with respect to DNA replication
Werner syndrome
Individuals with Werner’s syndrome cells either:
Divide more slowly or stop dividing at all
Werner syndrome is caused by a mutation in the:
DNA Helicase
