Microbial Genetic Diversity And Mutaton i Flashcards
What is DNA? What is it referred to as?
A polymer of nucleotides.
A strand
What do nucleotides consist of? 3 major parts.
- A 5-carbon sugar called deoxyribose
- A phosphate group (PO4) attached to the 5’
- One of four types of nitrogen-containing base attached to the 1’ carbon
What are the different functions of the 3 major parts of nucleotides?
Phosphate and sugar: covalently bonded forming backbone
Bases encode genetic info and all strands to associate together without covalently bonding (hydrogen bonds).
Nucleic acids are formed when nucleotides are covalently bonded together by dehydration synthesis reactions.
What happens when the phosphate group that is attached to the 5’ carbon of one nucleotide?
It becomes chemically bonded to the 3’ hydroxyl group on the previous nucleotide.
What is important to note about the nucleotides being asymmetrical? What is it actually called?
Means that each end of the chain is chemically different. One end is a free 5’ phosphate (the 5’ end) and the other has a 3’ hydroxyl group (3’ end).
Directionality
Why can nucleotides only be added to the 3’ end of DNA? That is why DNA is replicated and RNa is transcribed from the 5’ to 3’ end.
The chemistry of the reactions that build a DNA strand require it.
What are the 5 possible bases? Which ones are used to build DNA?
Purines: A and G
Pyrimidines: C, T and U (RNA only)
Explain double stranded DNA (dsDNA).
The back bones face toward the outside of the molecule and bases face inward toward each other.
Strands are held together by hydrogen bonds.
What is the non-covalent interaction between bases on opposite strands called?
A base pair
What is the length of DNA usually measured in?
The number of bases.
What are the base pairing rules for DNA? What do they allow us to determine?
A pairs with T
G pairs with C
Complimentarity
What is complimentarity?
The base sequence of one DNA strand can always be determined from the base sequence of the opposite strand
What must true for the double stranded structure to form? (2 things)
- The strands of DNA must be oriented in opposite directions (anti-parallel)
- The strands must be twisted into a double helix
What are the spaces between the 2 backbones of the DNA double helix?
- The minor groove (smaller)
- The major groove (larger) which binds transcription regulators.
These alternate as we move along the strand
How do bacteria primarily reproduce and using which process?
Asexually
Binary fission
What happens in the second stage of binary fission?
The bacterial chromosome is copied by DNA replication. Each cell produced by binary fission inherits one copy of parental chromosome. (Genetically identical; clones)
Even though cells produced by binary fission are considered genetically identical or clones, bacteria has a variety of mechanisms to ______________________. Many of these begin with or involve _______________.
Increase genetic diversity
DNA replication processes.
How many chromosomes do bacteria and archaea typically have? Where are they located?
One and in the nucleoid.
Explain bacterial chromosomes.
Circular (no ends) and much longer than the cell if stretched out.
Densely packed (super coiling)
What is the first stage of DNA replication? Where does it occur?
Initiation
Replication origin (oriC)
What must the oriC of the DNA be for initiation?
Un-supercoiled and the strands separated
What protein is the initiation of DNA replication accomplished by?
DnaA that binds to several spots on the replication origin
What happens once DnaA binds?
It will hydrolyze ATP to unwind the DNA. It then can separate the strands once the unwinding reaches the DNA-unwinding element (DUE) sequences.
What is the stage after initiation in DNA replication?
Elongation.
What happens during elongation in DNA replication?
Structure called the replisome will move in one direction along each DNA strand and will use enzymes to unwind and separate the strands. As it does this, it reads each sequence and makes a copy. This is done by the base pairing (complimentarity) rules.
What is produced during elongation of DNA replication?
dsDNA molecules, each with one original strand of the parent cell and one newly strand from the replisome.
What is it called when one half of the parental DNA “saved”?
Semi-conservative
Replication from the origin is ________________. A replisome forms on both sides of the ________. Each replisome copies outward in _______________ directions.
Bi-directional
OriC
Opposite
What is the replication fork?
The region where the replisome is copying in both directions until the replisomes reach the terminator sequence.
What happens at the terminator sequence of DNA replication?
The replisomes disassemble and replication is complete.
What does the replisome consist of? Name 4.
12 different proteins that work together to copy DNA.
1. Helicase
2. DNA polymerase
3. Clamp proteins
4. Clamp loader (not a protein)
What does helicase do?
Unwinds and separates the DNA strands
What does DNA polymerase do?
Copies each strand of the DNA
What are the function of clamp proteins?
To keep the DNA polymerase attached to the DNA
What does the clamp loader do?
- Attaches the clamp proteins to DNA polymerase
- Holds the structure of the replisome together by binding to each others replisome protein
What is the core of the replisome?
DNA polymerase
How many different DNA polymerases do bacteria have, each with specialized functions? Which one is used in the replisome?
5
DNA polymerase 3
What is the primary function of DNA polymerase?
The synthesis of DNA polymers
Explain what happens during the synthesis of DNA
DNA polymerase coordinates a nucleophilic attack from the 3’ hydroxyl group to the DNA strand against the nucleotide triphosphate being added. This reaction removes 2 phosphates and forms a covalent bond that adds the nucleotide to the strand.
This is why DNA nucleotides can only be added from the 5’ end to the 3’ end.
What is one major problem that the replisome has to solve? Explain how it fixes them.
Both stands of DNA replicated in the replication fork so only one strand of DNA has a free 3’ hydroxyl group.
Fixes 2 things:
1. One strand of the DNA is replicated in the 5’ to 3’ direction called continuous synthesis.
2. the other strand is synthesized in small pieces in the 5’ to 3’ direction called discontinuous synthesis.
3. The lagging strand is looped around (trombone loop) so that it enters the DNA polymerase from the back of the replisome instead of the front. It essentially takes the backward strand and flips it around by copying from the 5’ to 3’ direction while moving forward.
Why is it called continuous synthesis? What is the strand called?
Because the complete strand of DNA is made without stopping. This process is fast so this is the leading strand.
Why is it called discontinuous synthesis? What is the strand called?
Because the DNA synthesis starts and stops. It is slow so this is called the lagging strand.
What does the trombone loop need to be protected from? What protein is the loop bound by?
Protected from the breakdown by the cell and has anti-viral protection.
Single stranded binding protein (SSB)
continuous synthesis on the lying strand only needs to start elongation __________. The polymerase on the leading strand always has access to a ______________________ for synthesis.
Once
3’ hydroxyl
What are the small chunks of discontinuous synthesis called?
Okazaki fragments
What does each Okazaki fragment start with?
A small piece of RNA called a primer that provides the free 3’ hydroxyl needed by DNA polymerase 3.
What synthesizes the primer of Okazaki fragments and what is it attached to?
An RNA polymerase enzyme called primase which is attached to the lagging strand by the clamp loader.
Explain the synthesis on the lagging strand. (4 steps)
- Primase makes a series of RNA primers.
- DNA polymerase 3 synthesizes the DNA that replicates the DNA between the primers (Okazaki fragments)
- A different kind of DNA polymerase called DNA polymerase 1.
- Okazaki fragments are eventually connected together into a continuous DNA strand by an enzyme called DNA ligase.
What does DNA polymerase 1 do? (2 things)
- Destroys the RNA primers
- Synthesizes new DNA to replace RNA primers.
What are DNA nicks? How are they sealed?
A nick is a discontinuity in a dsDNA molecule where there is no phosphodiester bon between adjacent nucleotides of one strand.
Sealed when DNA ligase uses ATP to form a covalent bond between 2 fragments.
The complete replisome includes: (5 things)
- One DNA polymerase 3 for each strand
- A set of clamp proteins for the DNA polymerase on each strand.
- DNA helicase that (a) unwinds the supercoiling of the DNA and (b) separates the strands by breaking between the base pairs
- Single stranded binding proteins to protect the trombone loop
- the clamp loader that forms the basic structure of the replisome and attaches clamp proteins.
