Genomes Flashcards
Cell expands _______ at the same time that it replicates DNA
Cytoplasm
The ______ grows from each side of the cell, separating the 2 ______ ______
The septum grows from each side, separating the 2 daughter cells
What does a replication bubble consists of and what do they do?
A replication bubble consists of 2 replication forks that move in two different directions around the chromosome
To replicate DNA the double helix must _______. Exposing bases (__,__,__,__) that can pair with another base on the growing (____) strand.
The double helix must unwind. Exposing bases A, T, G, C. That can pair with anotherbase on the growing (new) strand.
What does Helicase do?
Helicase breaks the hydrogen bonds between nitrogenous bases, opening the DNA helix
What does single stranded binding proteins do? (SSBP)
Bind to the newly exposed single stranded DNA and blocks formation of hydrogen bonds and nitrogenous bases
What is the purpose of topoisomerase II (DNA gyrase)?
Relieves the supercoiling of the chromosome by breaking and resealing the DNA
New DNA is synthesized by ___ ______ __ using old DNA as a template. New DNA is synthesized in what direction? (2 part question)
DNA polymerase Ill
5’—> 3’
DNA polymerase Ill cannot synthesize ____ __ ___
DNA de novo
What is every new strand Of DNA initiated with?
RNA primer
____ builds the short RNA primer
Primase
What helps hold DNA polymerase Ill onto chromosome during replication?
A protein sliding clamp
What end does DNA strands elongate at?
3’ end
The leading strand is synthesized….
Continuously
The lagging strand is synthesized…..
Discontinously in Okazaki fragments
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?
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
At the end of replication there are 2 concatenated double stranded circular chromosomes. What does topoisomerase IV do?
Topoisomerase IV cuts the circular chromosome reseals the DNA after the two circular chromosomes separate
Newly synthesized DNA is ______ methyl groups are added to _______ (C) bases.
Methylated
Cytosine (c) bases
What enzyme can correct mistakes? (Exonuclease proofreading)
What do uncorrected mistakes result in?
DNA polymerase l. They detect/correct mismatches. Uncorrected mistakes result in mutations
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?
- Horizontal transfer
- Rapid, large-scale changes
3.it gains or loses entire genes or cluster of genes - Yes it can occur between different species
(2 part question)
Describe vertical transfer
Describe horizontal gene transfer (what is it also known as)
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
What are the three mechanisms of horizontal gene transfer?
- Transformation
- transduction
- conjugation
Describe transformation:
The uptake and expression of exogenous free DNA from the environment
What is transduction?
The transfer of DNA from one cell to another by a bacteriophage
What is the function of a DNA phage?
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.
What is generalized transduction?
The process of when a phage carries a fragment of host DNA from one cell to another
Generalized transduction involves the _____ life cycle of the phage and can move any gene
Lytic life cycle
Specialized transduction
_________ cycle
Moves only get genes connected to site of prophage insertion
Lysogenic cycle
What are the 5 steps of generalized transduction?
- Phage infects the donor bacterial cell
- Phage DNA/proteins are made, and the bacterial chromosome is broken into pieces
- Occasionally during assembly, pieces of bacterial DNAare packaged into capsid. Then donor cell lyses/releases phage particles contain DNA
- Phage carrying bacterial DNA infects a new host cell, the recipient cell.
- Recombination can occur, producing a recombinant cell with a genotype different from both recipient cells
What are the 6 steps of specialized transduction?
- Prophage exists in galactose - using host (containing gaf genes)
- Phage genome excises, camping with it the adjacent gaf gene from the host
- Phage mature, cell lyses releasing phage carrying gaf gene
- Phage infects a cell that cannot utilize galactose (lacking gaf gene)
- Along with prophase, bacterial gaf gene becomes integrated into the new hosts DNA
- Lysogenic cell can now metabolize glucose
What is conjugation (“bacterial sex’’)? What does it require? What does conjugation occur between?
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
F factor can remain as a _____ in the cell or it can ______ into the _____
Plasmid
Integrate into the chromosome
When F factor integrates (by _________) into the chromosome of an F+ cell, what happens to the cell?
(By recombination)
the cell becomes a
high frequency of recombination (Hfr) cell.
Where does conjugation mostly occur in?
Gram (-) negative species
What does conjugation require?
Where is it generally seen?
True or false: Other types of conjugation have been identified in Gram positive bacteria
Conjugation requires membrane to membrane contact
• Generally seen in organisms with an outer membrane or lipid layer
– Gram negative
– Mycobacterium
True
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?
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
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?
• 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
Foreign DNA can be degraded by _____ ______
the bacterial chromosome is protected by _______
-Restriction endonucleases
-Methylation
What is recombination?
an enzyme- mediated process in which two DNA molecules exchange portions by breaking and reforming their sugar phosphate backbones.
(Consequences of horizontal transfer)
- bacteria can gain:
- New metabolic capabilities
- antibiotic resistance
- acquired pathogenicity or increased virulence (e.g. Toxic genes)
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 ______ _______
-1,387 genes
-virulence factors, metabolic pathways
-toxin gene from Shigella Flexneri
-causes bloody diarrhea
Corynebacterium diphtheriae
•Symptoms?
•Transmission?
•Treatment?
•Gram (+) or (-) ?
•Shape?
•Arrangement?
•Produces what?
•Toxin is encoded by a ________ that has integrated into the _______ _______
– 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
