Microbial Genetic Diversity And Mutaton i

Question 2

What is DNA? What is it referred to as?

Answer 2

A polymer of nucleotides.

A strand

Question 3

What do nucleotides consist of? 3 major parts.

Answer 3

1. A 5-carbon sugar called deoxyribose
2. A phosphate group (PO4) attached to the 5’
3. One of four types of nitrogen-containing base attached to the 1’ carbon

Question 4

What are the different functions of the 3 major parts of nucleotides?

Answer 4

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.

Question 5

What happens when the phosphate group that is attached to the 5’ carbon of one nucleotide?

Answer 5

It becomes chemically bonded to the 3’ hydroxyl group on the previous nucleotide.

Question 6

What is important to note about the nucleotides being asymmetrical? What is it actually called?

Answer 6

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

Question 7

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.

Answer 7

The chemistry of the reactions that build a DNA strand require it.

Question 8

What are the 5 possible bases? Which ones are used to build DNA?

Answer 8

Purines: A and G
Pyrimidines: C, T and U (RNA only)

Question 10

Explain double stranded DNA (dsDNA).

Answer 10

The back bones face toward the outside of the molecule and bases face inward toward each other.
Strands are held together by hydrogen bonds.

Question 11

What is the non-covalent interaction between bases on opposite strands called?

Answer 11

A base pair

Question 12

What is the length of DNA usually measured in?

Answer 12

The number of bases.

Question 13

What are the base pairing rules for DNA? What do they allow us to determine?

Answer 13

A pairs with T
G pairs with C
Complimentarity

Question 14

What is complimentarity?

Answer 14

The base sequence of one DNA strand can always be determined from the base sequence of the opposite strand

Question 15

What must true for the double stranded structure to form? (2 things)

Answer 15

1. The strands of DNA must be oriented in opposite directions (anti-parallel)
2. The strands must be twisted into a double helix

Question 16

What are the spaces between the 2 backbones of the DNA double helix?

Answer 16

1. The minor groove (smaller)
2. The major groove (larger) which binds transcription regulators.
   These alternate as we move along the strand

Question 17

How do bacteria primarily reproduce and using which process?

Answer 17

Asexually
Binary fission

Question 18

What happens in the second stage of binary fission?

Answer 18

The bacterial chromosome is copied by DNA replication. Each cell produced by binary fission inherits one copy of parental chromosome. (Genetically identical; clones)

Question 19

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 _______________.

Answer 19

Increase genetic diversity
DNA replication processes.

Question 20

How many chromosomes do bacteria and archaea typically have? Where are they located?

Answer 20

One and in the nucleoid.

Question 21

Explain bacterial chromosomes.

Answer 21

Circular (no ends) and much longer than the cell if stretched out.
Densely packed (super coiling)

Question 23

What is the first stage of DNA replication? Where does it occur?

Answer 23

Initiation
Replication origin (oriC)

Question 24

What must the oriC of the DNA be for initiation?

Answer 24

Un-supercoiled and the strands separated

Question 25

What protein is the initiation of DNA replication accomplished by?

Answer 25

DnaA that binds to several spots on the replication origin

Question 26

What happens once DnaA binds?

Answer 26

It will hydrolyze ATP to unwind the DNA. It then can separate the strands once the unwinding reaches the DNA-unwinding element (DUE) sequences.

Question 27

What is the stage after initiation in DNA replication?

Answer 27

Elongation.

Question 28

What happens during elongation in DNA replication?

Answer 28

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.

Question 29

What is produced during elongation of DNA replication?

Answer 29

dsDNA molecules, each with one original strand of the parent cell and one newly strand from the replisome.

Question 30

What is it called when one half of the parental DNA “saved”?

Answer 30

Semi-conservative

Question 32

Replication from the origin is ________________. A replisome forms on both sides of the ________. Each replisome copies outward in _______________ directions.

Answer 32

Bi-directional OriC Opposite

Question 33

What is the replication fork?

Answer 33

The region where the replisome is copying in both directions until the replisomes reach the terminator sequence.

Question 34

What happens at the terminator sequence of DNA replication?

Answer 34

The replisomes disassemble and replication is complete.

Question 35

What does the replisome consist of? Name 4.

Answer 35

12 different proteins that work together to copy DNA. 1. Helicase 2. DNA polymerase 3. Clamp proteins 4. Clamp loader (not a protein)

Question 36

What does helicase do?

Answer 36

Unwinds and separates the DNA strands

Question 37

What does DNA polymerase do?

Answer 37

Copies each strand of the DNA

Question 38

What are the function of clamp proteins?

Answer 38

To keep the DNA polymerase attached to the DNA

Question 39

What does the clamp loader do?

Answer 39

1. Attaches the clamp proteins to DNA polymerase 2. Holds the structure of the replisome together by binding to each others replisome protein

Question 40

What is the core of the replisome?

Answer 40

DNA polymerase

Question 41

How many different DNA polymerases do bacteria have, each with specialized functions? Which one is used in the replisome?

Answer 41

5 DNA polymerase 3

Question 42

What is the primary function of DNA polymerase?

Answer 42

The synthesis of DNA polymers

Question 43

Explain what happens during the synthesis of DNA

Answer 43

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.

Question 44

What is one major problem that the replisome has to solve? Explain how it fixes them.

Answer 44

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.

Question 45

Why is it called continuous synthesis? What is the strand called?

Answer 45

Because the complete strand of DNA is made without stopping. This process is fast so this is the leading strand.

Question 46

Why is it called discontinuous synthesis? What is the strand called?

Answer 46

Because the DNA synthesis starts and stops. It is slow so this is called the lagging strand.

Question 48

What does the trombone loop need to be protected from? What protein is the loop bound by?

Answer 48

Protected from the breakdown by the cell and has anti-viral protection. Single stranded binding protein (SSB)

Question 49

continuous synthesis on the lying strand only needs to start elongation __________. The polymerase on the leading strand always has access to a ______________________ for synthesis.

Answer 49

Once 3’ hydroxyl

Question 50

What are the small chunks of discontinuous synthesis called?

Answer 50

Okazaki fragments

Question 51

What does each Okazaki fragment start with?

Answer 51

A small piece of RNA called a primer that provides the free 3’ hydroxyl needed by DNA polymerase 3.

Question 52

What synthesizes the primer of Okazaki fragments and what is it attached to?

Answer 52

An RNA polymerase enzyme called primase which is attached to the lagging strand by the clamp loader.

Question 53

Explain the synthesis on the lagging strand. (4 steps)

Answer 53

1. Primase makes a series of RNA primers. 2. DNA polymerase 3 synthesizes the DNA that replicates the DNA between the primers (Okazaki fragments) 3. A different kind of DNA polymerase called DNA polymerase 1. 4. Okazaki fragments are eventually connected together into a continuous DNA strand by an enzyme called DNA ligase.

Question 54

What does DNA polymerase 1 do? (2 things)

Answer 54

1. Destroys the RNA primers 2. Synthesizes new DNA to replace RNA primers.

Question 55

What are DNA nicks? How are they sealed?

Answer 55

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.

Question 56

The complete replisome includes: (5 things)

Answer 56

1. One DNA polymerase 3 for each strand 2. A set of clamp proteins for the DNA polymerase on each strand. 3. DNA helicase that (a) unwinds the supercoiling of the DNA and (b) separates the strands by breaking between the base pairs 4. Single stranded binding proteins to protect the trombone loop 5. the clamp loader that forms the basic structure of the replisome and attaches clamp proteins.