Genomes

Question 1

Cell expands _______ at the same time that it replicates DNA

Answer 1

Cytoplasm

Question 2

The ______ grows from each side of the cell, separating the 2 ______ ______

Answer 2

The septum grows from each side, separating the 2 daughter cells

Question 3

What does a replication bubble consists of and what do they do?

Answer 3

A replication bubble consists of 2 replication forks that move in two different directions around the chromosome

Question 4

To replicate DNA the double helix must _______. Exposing bases (__,__,__,__) that can pair with another base on the growing (____) strand.

Answer 4

The double helix must unwind. Exposing bases A, T, G, C. That can pair with anotherbase on the growing (new) strand.

Question 5

What does Helicase do?

Answer 5

Helicase breaks the hydrogen bonds between nitrogenous bases, opening the DNA helix

Question 6

What does single stranded binding proteins do? (SSBP)

Answer 6

Bind to the newly exposed single stranded DNA and blocks formation of hydrogen bonds and nitrogenous bases

Question 7

What is the purpose of topoisomerase II (DNA gyrase)?

Answer 7

Relieves the supercoiling of the chromosome by breaking and resealing the DNA

Question 8

New DNA is synthesized by ___ ______ __ using old DNA as a template. New DNA is synthesized in what direction? (2 part question)

Answer 8

DNA polymerase Ill
5’—> 3’

Question 9

DNA polymerase Ill cannot synthesize ____ __ ___

Answer 9

DNA de novo

Question 10

What is every new strand Of DNA initiated with?

Answer 10

RNA primer

Question 11

____ builds the short RNA primer

Answer 11

Primase

Question 12

What helps hold DNA polymerase Ill onto chromosome during replication?

Answer 12

A protein sliding clamp

Question 13

What end does DNA strands elongate at?

Answer 13

3’ end

Question 14

The leading strand is synthesized….

Answer 14

Continuously

Question 15

The lagging strand is synthesized…..

Answer 15

Discontinously in Okazaki fragments

Question 16

To connect the small Okazaki fragments of the lagging strand into one continuous strand of DNA
DNA polymerase I does what?
DNA ligase does what?

Answer 16

DNA polymerase 1 removes RNA primer and fills the resulting gap with DNA (exonuclease activity)
DNA ligase seals the gaps between adjacent fragments of DNA

Question 17

At the end of replication there are 2 concatenated double stranded circular chromosomes. What does topoisomerase IV do?

Answer 17

Topoisomerase IV cuts the circular chromosome reseals the DNA after the two circular chromosomes separate

Question 18

Newly synthesized DNA is ______ methyl groups are added to _______ (C) bases.

Answer 18

Methylated
Cytosine (c) bases

Question 19

What enzyme can correct mistakes? (Exonuclease proofreading)
What do uncorrected mistakes result in?

Answer 19

DNA polymerase l. They detect/correct mismatches. Uncorrected mistakes result in mutations

Question 20

Bacteria can also exchange DNA between microbes outside of the normal replication & cell division.
1. It is usually mediated by ________ _______
2. ____, _____ scale changes
3. What does it gain or lose ?
4. Can it occur between different species?

Answer 20

1. Horizontal transfer
2. Rapid, large-scale changes
   3.it gains or loses entire genes or cluster of genes
3. Yes it can occur between different species

Question 21

(2 part question)
Describe vertical transfer
Describe horizontal gene transfer (what is it also known as)

Answer 21

Vertical genome transfer: transmission of entire genome from parent to offspring (DNA replication then cell division)

Horizontal gene transfer:(aka lateral gene transfer) the acquisition of a piece of DNA from another cell, not through traditional reproduction

Question 22

What are the three mechanisms of horizontal gene transfer?

Answer 22

• Transformation
• transduction
• conjugation

Question 23

Describe transformation:

Answer 23

The uptake and expression of exogenous free DNA from the environment

Question 24

What is transduction?

Answer 24

The transfer of DNA from one cell to another by a bacteriophage

Question 25

What is the function of a DNA phage?

Answer 25

It injects its DNA into a live bacterial cell. It takes over the cell to produce more virus particles. The new phage DNA takes over the cell to produce more virus particles.New phage particles are then released into the environment, often by lysing the host cell.

Question 26

What is generalized transduction?

Answer 26

The process of when a phage carries a fragment of host DNA from one cell to another

Question 27

Generalized transduction involves the _____ life cycle of the phage and can move any gene

Answer 27

Lytic life cycle

Question 28

Specialized transduction _________ cycle Moves only get genes connected to site of prophage insertion

Answer 28

Lysogenic cycle

Question 29

What are the 5 steps of generalized transduction?

Answer 29

1. Phage infects the donor bacterial cell 2. Phage DNA/proteins are made, and the bacterial chromosome is broken into pieces 3. Occasionally during assembly, pieces of bacterial DNAare packaged into capsid. Then donor cell lyses/releases phage particles contain DNA 4. Phage carrying bacterial DNA infects a new host cell, the recipient cell. 5. Recombination can occur, producing a recombinant cell with a genotype different from both recipient cells

Question 30

What are the 6 steps of specialized transduction?

Answer 30

1. Prophage exists in galactose - using host (containing gaf genes) 2. Phage genome excises, camping with it the adjacent gaf gene from the host 3. Phage mature, cell lyses releasing phage carrying gaf gene 4. Phage infects a cell that cannot utilize galactose (lacking gaf gene) 5. Along with prophase, bacterial gaf gene becomes integrated into the new hosts DNA 6. Lysogenic cell can now metabolize glucose

Question 31

What is conjugation ("bacterial sex’')? What does it require? What does conjugation occur between?

Answer 31

transfer of DNA between bacteria through direct contact. Requires cell-to-cell contact (initiated by a sex pills that protrudes from donor cell) and special transfer plasmid. Conjugation can occur between unrelated species of bacteria

Question 32

F factor can remain as a _____ in the cell or it can ______ into the _____

Answer 32

Plasmid Integrate into the chromosome

Question 33

When F factor integrates (by _________) into the chromosome of an F+ cell, what happens to the cell?

Answer 33

(By recombination) the cell becomes a high frequency of recombination (Hfr) cell.

Question 34

Where does conjugation mostly occur in?

Answer 34

Gram (-) negative species

Question 35

What does conjugation require? Where is it generally seen? True or false: Other types of conjugation have been identified in Gram positive bacteria

Answer 35

Conjugation requires membrane to membrane contact • Generally seen in organisms with an outer membrane or lipid layer – Gram negative – Mycobacterium True

Question 36

Agrobacterium tumefaciens What is the new name? What wind of species and what does it cause? What plasmid does it contain, how is it transferred? What is it used in a lab for?

Answer 36

New name: Rhizobium radiobacter • Bacterial species that causes crown gall disease (tumors) • Contains a tumor-inducing plasmid (Ti) that can be transferred via conjugation to plant cells • Used in lab for inserting foreign genes into plants

Question 37

This happens when a new piece of DNA has entered the cell: If the new DNA is a self-replicating plasmid, what happens? If the foreign DNA is not capable of autonomous replication, then it is either what Two things?

Answer 37

• If the new DNA is a self-replicating plasmid, the plasmid will coexist in the cell separate from the host chromosome. • If the foreign DNA is not capable of autonomous replication, then it is either – degraded by restriction endonucleases or – incorporated into the chromosome through recombination

Question 38

Foreign DNA can be degraded by _____ ______ the bacterial chromosome is protected by _______

Answer 38

-Restriction endonucleases -Methylation

Question 39

What is recombination?

Answer 39

an enzyme- mediated process in which two DNA molecules exchange portions by breaking and reforming their sugar phosphate backbones.

Question 40

(Consequences of horizontal transfer) - bacteria can gain:

Answer 40

- New metabolic capabilities - antibiotic resistance - acquired pathogenicity or increased virulence (e.g. Toxic genes)

Question 41

E. coli O157:H7 • Contains ______ genes not found in E. coli K-12 • Includes _______ factors, _______ pathways, prophages acquired through horizontal transfer • Toxin gene from ________ ________; causes ______ _______

Answer 41

-1,387 genes -virulence factors, metabolic pathways -toxin gene from Shigella Flexneri -causes bloody diarrhea

Question 42

Corynebacterium diphtheriae •Symptoms? •Transmission? •Treatment? •Gram (+) or (-) ? •Shape? •Arrangement? •Produces what? •Toxin is encoded by a ________ that has integrated into the _______ _______

Answer 42

– Symptoms: sore throat, fever, swollen glands in neck, “pseudomembrane” – thick grey layer of dead tissue that can cover throat and make it hard to breathe – Transmission by direct contact, or through air – Treatment: antitoxin (binds to toxin) and antibiotics (kill bacteria) -gram positive -Pleomorphic Rod -no specific arrangement - produces diphtheria toxin -bacteriophage that has integrated into the bacterial chromosome