Microbio Ch. 8.1-8.4: Structure/Function of Genetic Material, Bacterial Gene Expression, Changes in Genetic material, Genetic Transfer and Recombination

Genetics

The study of genes, how they carry information, are expressed, and replicated.

Genome

All the genetic information in a cell.

Chromosomes

Structures containing DNA that physically carry hereditary information.

Genes

Segments of DNA that encode functional products, usually proteins.

Genotype

The genetic makeup of an organism.

Phenotype

The physical expression of an organism's genes.

Short Tandem Repeats (STRs)

Repeating sequences of 2-5 base pairs of noncoding DNA.

DNA Backbone

Consists of deoxyribose-phosphate.

DNA Base Pairing Rules

Adenine pairs with thymine (A-T), and cytosine pairs with guanine (C-G).

Helicase

Enzyme that unwinds and separates double-stranded DNA.

Topoisomerase and Gyrase

Enzymes that relax the strands

DNA Polymerase

Enzyme that adds nucleotides and elongates DNA strands in the 5' to 3' direction.

Leading vs. Lagging Strands

Leading strand is synthesized continuously; lagging strand is synthesized discontinuously into Okazaki fragments.

DNA Ligase

enzyme that makes covalent bonds that joins Okazaki fragments and DNA strands.

RNA Structure

Single-stranded, contains ribose sugar, and uses uracil (U) instead of thymine (T).

Messenger RNA (mRNA)

Carries coded genetic information from DNA to ribosomes.

Transfer RNA (tRNA)

Transports amino acids during protein synthesis and features an anticodon.

Ribosomal RNA (rRNA)

An integral structural and functional part of ribosomes.

Transcription

Synthesis of a complementary RNA strand from a DNA template.

Codon

A group of three mRNA nucleotides that specifies a particular amino acid.

Start Codon

AUG, which initiates translation.

Stop Codons

Nonsense codons (UAA, UAG, UGA) that terminate translation.

Genetic Code Degeneracy

Each amino acid is coded by multiple codons.

What are exons?

regions of DNA that code for proteins

What are introns?

regions of DNA that do not code for proteins; removed after RNA transcription

Endonucleases

cut DNA backbone internally within a strand of DNA; facilitate repair and insertions

Exonucleases

cut DNA from an exposed end of DNA; facilitate repair

Primase

RNA polymerase that synthesizes RNA primers from DNA template

Photolyase

uses visible light energy to separate UV-induced pyrimidine dimers

RNA polymerase

copies RNA from DNA template

DNA replication fork sequence (step 1)

enzymes unwind the parental double helix

DNA replication fork sequence (step 2)

proteins stabilize the unwound parental DNA

DNA replication fork sequence (step 3)

leading strand is synthesized continuously from the primer by DNA polymerase

DNA replication fork sequence (step 4)

the lagging strand is synthesized discontinuously. primase synthesized a short RNA primer, which is then extended by DNA polymerase

DNA replication fork sequence (step 5)

DNA polymerase digests DNA primer and replaces it with DNA

DNA replication fork sequence (step 6)

DNA ligase joins the discontinuous fragments of the lagging strand

Most bacterial DNA replication is

bi-directional

replication is highly accurate due to

proofreading capability of DNA polymerase

3 phases of transcription

initiation, elongation, termination

initation in transcription

RNA polymerase binds to promoter sequence on DNA

elongation in transcription

5' --> 3' direction of growing RNA, adding nucleotides

termination of transcription

RNA polymerase reaches a terminator sequence (Stop codon) and detaches from the template

amino acids are joined by

peptide bonds

in bacteria, translation can begin before transcription is complete (t/f)

true, both take place in cytoplasm

Constitutive genes

Genes expressed at a fixed rate that are always turned on.

Inducible genes

Genes expressed only as needed; their default position is off.

Repressible genes

Genes expressed only as needed; their default position is on.

Operon

A segment of DNA consisting of operator and promoter sites and the structural genes they control.

Promoter

A segment of DNA where RNA polymerase initiates transcription of structural genes.

Operator

A segment of DNA that controls the transcription of structural genes.

lac operon

An inducible operon in E. coli where allolactose acts as the inducer.

Catabolite repression

A process that inhibits cells from using carbon sources other than glucose.

cAMP and CAP with glucose

When glucose is present, cAMP levels are low and CAP is inactive.

trp operon

A repressible operon where excess tryptophan acts as a corepressor.

Epigenetic control

Methylating nucleotides turns genes off without altering the underlying DNA sequence.

Riboswitch

A part of an mRNA molecule that binds to a substrate and changes mRNA structure to control translation.

Mutation

A permanent change in the base sequence of DNA.

Mutagens

Agents that cause mutations and increase mutation rates 10 to 1000 times.

Spontaneous mutations

Mutations occurring without mutagens, resulting from replication errors.

Silent mutation

A base substitution leading to a codon encoding the same amino acid, leaving the protein unchanged.

Nonsense mutation

A base substitution leading to a stop codon, resulting in a truncated, nonfunctional protein.

Missense mutation

A base substitution leading to a codon encoding a different amino acid.

Frameshift mutation

Insertion or deletion of nucleotides not in multiples of three, shifting the reading frame.

Nitrous acid

A deaminating chemical mutagen that removes amino groups from DNA bases.

Nucleoside analog

A chemical similar to normal bases that incorporates into DNA and causes pairing mistakes.

UV radiation

Causes pyrimidine dimers on the same DNA strand, preventing proper replication and transcription.

Photolyases

Light-repair enzymes that use light to separate thymine dimers.

Nucleotide excision repair

Enzymes cut out incorrect bases and fill in correct ones.

Auxotroph

A mutant organism with a nutritional requirement absent in the parent.

Prototroph

The wild-type organism that lacks special nutritional requirements.

Ames test

Exposes mutant bacteria to measure reversion rates and assess potential carcinogenicity.

Vertical gene transfer

Transfer of genes from an organism to its offspring.

Horizontal gene transfer

Transfer of genes between cells of the same generation.

Genetic recombination

Exchange of genes between two DNA molecules to form new gene combinations.

Transformation

Transfer of genes from one bacterium to another as naked DNA.

Griffith's experiment

Demonstrated transformation using smooth (S) and rough (R) strains of Streptococcus pneumoniae.

Plasmids

Extra-chromosomal, self-replicating, circular pieces of DNA carrying nonessential genes.

Conjugative plasmids

Plasmids that carry genes for sex pili and plasmid transfer.

Resistance (R) factors

Plasmids that encode antibiotic resistance.

Conjugation

Plasmids transferred between bacteria through cell-to-cell contact.

F+ cell

Donor cell that carries the F plasmid and makes the F pilus.

F- cell

Recipient cell that lacks the F factor before conjugation.

Hfr cell

Bacterial cell containing the F factor integrated into its chromosome.

Transduction

DNA transfer from a donor to a recipient cell via a bacteriophage.

Generalized transduction

Random bacterial DNA packaged inside a phage and transferred to a recipient.

Specialized transduction

Specific bacterial genes adjacent to the prophage packaged inside a phage.

Virulent phage

Phage capable of causing destruction and death of a host cell via the lytic cycle.

Temperate phage

Phage that ordinarily does not cause a disruptive infection, using the lysogenic cycle.

Prophage

Phage DNA incorporated into host cell DNA and remaining latent.

Phage conversion

Phenomenon where a host cell exhibits new properties encoded by a prophage.

Induction

Exposure to stimuli that leads to excision of a prophage and initiates the lytic cycle.

Transposons

Segments of DNA that can move from one region of DNA to another.

Transposition

The ability of a genetic sequence to move from one location to another.