Exam 2: Week 9

Wild-Type Strain

isolated from nature

Genomes of Cells

double stranded DNA

Viral Genomes

double or single stranded DNA or RNA

Mutant

a cell or virus derived from wild type that carries a nucleotide sequence (genotype) change

phenotype (observable) may be altered

genotype is designated by three lowercase letters followed by capital, all italicized ex: his C

phenotype designated by capital letter and two lowercase letters then +/- ex: His+

Mutation

a permanent change in the base sequence of DNA

change in DNA may cause a change in product encoded by the gene

may be neutral, beneficial, or harmful

Mutagens

agents that cause mutations

Spontaneous Mutations

occur in the absence of a mutagen

Silent (Neutral) Mutation

doesn’t affect the activity of the product

degeneracy of genetic code

may affect a non-vital location of resulting protein

Base Substitution (Point Mutation)

change in one base of DNA

mRNA will carry the incorrect base in that position

incorrect amino acid may be incorporated into resulting protein

Missense Mutation

base substitution results in the change of an amino acid

Nonsense Mutation

base substitution results in a nonsense (stop) codon

Frameshift Mutation

insertion or deleting of one or more nucleotide pairs

shifts the translational reading frame

causes changes in many amino acids downstream from site of original mutation

Chemical Mutagens

chemicals that directly or indirectly cause mutations

ex: nitrous acid: causes adenine to bind with cytosine instead of thymine

ex: frameshift mutagens: chemicals that cause small deletions or insertions resulting in frameshifts

Nucleoside Analog

structurally similar to normal nitrogenous bases, but incorporate into DNA in place of a normal base and cause mistakes in base pairings

Radiation

ionizing radiation (x and gamma rays) causing formation of ions that oxidize nucleotides and break the deoxyribose phosphate backone

ex: UV radiation cause thymine dimers which prevent proper replication and transcription of DNA

Photolyases

light repair enzymes

use light to separate thymine dimers

Nucleotide Excision Repair

enzymes cut out incorrect bases and fill in correct bases

SOS (Save Our Ship) Repair

coordinated cellular responses can introduce mutations to save the cell

mutations are heritable, if damage can be corrected before cell division, no mutation occurs

in bacteria, stalled replication or major DNA damage activates this, bacteria allows DNA repair to occur without template resulting in errors and mutations

How does a Bacterium decide which Proteins to Make at which Time?

some proteins like RNA polymerase are required for growth

most proteins are needed only under a limited set of conditions

to complete successfully with others, microbes cannot waste energy making unneeded proteins

Constitutive Genes

expressed at a fixed rate, do not appear to be regulated and are always on

Repression

inhibits gene expression and decreases enzymes synthesis

mediated by repressors, proteins that block transcription

default position is on

Induction

turns on gene expression

initiated by an inducer

default position is off

Promoter

segment of DNA where RNA polymerase initiates transcription of structural genes

involved in gene expression

Operator

segment of DNA that controls transcription of structural genes

involved in gene expression

Operon

set of operator and promoter sites and structural genes they control

involved in gene expression

Inducible Operon

structural genes are not transcribed unless an inducer is present

ex: lac operon of E. coli

three enzymes encoded by lac operon are needed to metabolize lactose, structural genes for these enzymes are adjacent on the chromosome and their transcription is regulated together

control region includes:

1. promoter: transcription begins

2. operator: stop or go signal

Operon Model of Gene Expression

in absence of lactose: repressor binds to operator preventing transcription

in presence of lactose: allolactose (inducer) binds to repressor, repressor cant bind to operator and transcription occurs

repressor turns off transcription, ex: arginine becomes corepressor when plentiful and binds/activates arginine repressor to bind to operator stopping synthesis

Positive Control

regulator protein facilitates transcription

Catabolite Repression

inhibits cells from using carbon sources other than glucose

Cyclic AMP (cAMP)

builds up in cells when glucose isn’t available

an example of an alarmone, a chemical that promotes a cell’s response to environmental or nutritional stress

binds to catabolic activator protein (CAP) that binds to lac promoter, initiating transcription and allowing cell to use lactose

Transcriptional Control

sensing conditions within the cell

ex: corynebacterium diphtheriae

• outside a human host, it encounters sufficient iron for growth, it doesn’t need to produce toxin

• in human throat, iron is sequestered in host cells and toxin will kill these cells and release iron that the bacteria can use

repressor proteins stop gene expression

Post-Transcriptional Control

regulatory mechanisms that stop protein synthesis after transcription has occurred

Riboswitch

a part of an mRNA molecule that binds to a substrate and changes the mRNA structure

translation is initiated or stopped

post transcriptional control

MicroRNA’s (miRNA’s)

base pair with mRNA to make it double stranded

double stranded RNA is enzymatically destroyed, preventing production of a protein

post transcriptional control

Changes in Genetic Material

result in genetic variations which can impact microbial function

survival and reproduction of a microbe with a new genotype may be favored by natural or man-made environments

Natural Selection

the survival of new genotypes

Genetic Recombination

exchange of genes between two DNA molecules to form new combination of genes

contributed to genetic diversity

Vertical Gene Transfer

transfer of genes from an organism to its offspring

Horizontal Gene Transfer

transfer of genes between cells of the same generation

all horizontal transfer mechanisms involve a donor cell that gives some of its DNA to a recipient cell

part of donor DNA is incorporated into recipient DNA

recipient is now a recombinant

Plasmids and Transpoons

genetic elements that exist outside a chromosome

Mobile Genetic Elements

move from one chromosome to another or from one cell to another

Plasmids

self replicating circular pieces of DNA

1-5% the size of a bacterial chromosome

found primarily in bacteria

code for proteins that enhance the pathogenicity of a bacterium, toxin production

Conjugative Plasmid

carries genes for sex pili and transfer of the plasmid

Dissimilation Plasmids

encode enzymes for the catabolism of unusual compounds

Resistance Factors (R Factors)

encode antibiotic resistance, sometimes to multiple different antibodies

some can be transferred horizontally

Transpoons

segments of DNA that can move from one region of DNA to another

contain insertion sequences (IS)

complex ones carry other genes, ex: antibiotic resistance, entertoxin production

Insertion Sequences

code for transposase that cuts and reseals DNA

may inactivate genes if they insert within genes

Transformation in Bacteria

genes transferred from one bacterium to another as naked DNA

Conjugation

plasmids transferred from one bacterium to another through cell to cell contact

gram negative bacteria: attachment and transfer by sex pili

gram positive bacteria: a sticky substance holds participating cells together

cells must be opposite mating types, donor has conjugative plasmid and recipient lacks one

Conjugation in Bacteria

donor cells carry the plasmid (F factor) and are called F+ cells

the recipient (F-) cell will become F+ when it has received the plasmid

involves HFR cells

HFR Cells

contain the F factor integrated into the chromosome

may transfer chromosomal genes as well as part of the F factor

recipient doesn’t become F+ because it doesn’t receive entire F factor

Transduction in Bacteria

DNA is transferred from a donor cell to a recipient via a bacteriophage (virus that infects bacteria)

Generalized Transduction

random bacterial DNA is packaged inside a phage and transferred to a recipient cell

in bacteria

Specialized Transduction

specific bacterial genes are packaged inside a phage and transferred to a recipient cell

in bacteria

Genes and Evolution

mutations and recombination create cell diversity

diversity is the raw material for evolution

natural selection acts on populations or organisms to ensure the survial of organisms fit for a particular environment