Microbial Genetics: DNA Structure and Function

Genetics

Study of inheritance and inheritable traits as expressed in an organism's genetic material.

Genome

The entire genetic complement of an organism, including its genes and nucleotide sequences.

Gene

a particular section of dna that codes for proteins

Gene product

Protein.

Flow of genetic information

DNA → RNA → Protein (the central dogma of molecular biology)

Levels of Genetic Study

Organism level, Cell level, Chromosome level, Molecular level.

Prokaryote

A type of cell that lacks a nucleus and membrane-bound organelles. (haploid)

Eukaryote

A type of cell that has a nucleus and membrane-bound organelles.

haploid

one set of chromosomes

diploid

two sets of chromosomes

Chromosomes

Structures within cells that contain DNA and carry genetic information.

structure of chromosomes in prokaryotic cells

typically a circular molecule of DNA in the nucleoid

structure of chromosomes in eukaryotic cells

linear chromosomes within the nucleus

Nucleus

The membrane-bound organelle that contains the cell's genetic material.

Plasmids

Small molecules of DNA that replicate independently and carry information for cellular traits.

fertility factors

proteins that enable them to engage in conjugation with other bacteria more effectively

resistance factors

encode antibiotic resistance

bacteriocin factors

carry genes for proteinaceous toxins (which are proteins that kill or stop the growth of other bacteria)

virulence plasmids

carry genes that cause disease or to make the bacteria more harmful

cryptic plasmids

plasmids that do not encode any known accessory function.

Mitochondrion

An organelle that produces energy for the cell through respiration.

Viruses

Infectious agents that can only replicate inside the living cells of an organism.

gene therapy

a technique that places a gene into a cell to correct a hereditary disease or to improve the genome

Recombinate cell

a cell that contains DNA from two different sources, combined together using genetic engineering.

polymer

large compound formed from combinations of many monomers

Extra chromosomal DNA

DNA that is not part of the chromosomal DNA and can exist independently.

ether linkage

a type of chemical bond where an oxygen atom connects two carbon atoms.

antiparallel

two strands going in opposite directions, like the two sides of a zipper.

RNA

A nucleic acid involved in protein synthesis and gene expression.

-single stranded

DNA

The molecule that carries the genetic instructions for life.

purines

Bases with a double-ring structure. (A&G) -larger

pyrimidines

single-ring structure made of carbon and nitrogen atoms (C&T) -smaller

Chloroplast

An organelle found in plant cells that conducts photosynthesis.

nucleotide

a building block of DNA, consisting of a five-carbon sugar covalently bonded to a nitrogenous base and a phosphate group.

Double helix

The structure of DNA, consisting of two strands twisted around each other.

Base pair

A pair of complementary nitrogenous bases in DNA, held together by hydrogen bonds.

Chargaff's Rules

The principle that %G = %C and %A = %T in DNA.

rRNA

makes structure and catalyzes the formation of a peptide bond

tRNA

carries amino acids to the ribosome during protein synthesis.

mRNA

conveys genetic information from DNA to the ribosome.

DNA Replication

An anabolic polymerization process that requires monomers and energy to produce two identical copies of DNA. (semiconservative)

semiconservative

method of replication that implies that each new strand of DNA is half original and half new

monomer unit of DNA

triphosphate deoxyribonucleotides

5 prime

the end of the phosphate group

3 prime

a nucleotide with a free OH group on its sugar

DNA polymerase

An enzyme that synthesizes new DNA strands by adding nucleotides. (Replicates DNA only 5ʹ to 3ʹ)

Leading strand

The DNA strand that is synthesized continuously during replication. (follows parent strand)

Lagging strand

The DNA strand that is synthesized discontinuously in short segments during replication. "Okazaki fragments"

Bidirectional

A characteristic of bacterial DNA replication where replication occurs in both directions from the origin.

Topoisomerases

Enzymes that remove supercoils in the DNA molecule. (specifically dna gyrase)

Methylation

A process where DNA is modified with methyl groups, playing a role in genetic expression, initiation of DNA replication, protection against viral infection, and DNA repair.

histones

Globular proteins in eukaryotic cells that assist in DNA packaging/organizing into chromatin

dna replication steps

1) Helicase- unwinds the parental double helix

2) DNA topoisomerase - upstream of helices alleviating torsional strain

3) Single-strand binding proteins (SSBP) stabilize unwound DNA, aided by DNA gyrase.

4) Primase synthesizes a short RNA primer for DNA polymerase to bind to in the 5' to 3' direction to start replication on each strand.

5) DNA polymerase synthesizes the leading strand in 5' to 3' direction while the lagging strand is made discontinuously by primase making short pieces and then DNA polymerase extending these to make Okazaki fragments.

6) DNA ligase joins the Okazaki fragments together

supercoils

extra turns in the DNA beyond those generated by the shape of the base pairs (make hard to read dna)

replication

two strands being created based on complementary

Genotype

The set of genes in the genome.

Phenotype

The physical features and functional traits of the organism.

gene expression

process by which a gene produces its product and the product carries out its function (ex. protein)

Transcription

The process where information in DNA is copied as RNA nucleotide sequences.

Translation

The process where polypeptides are synthesized from RNA nucleotide sequences.

Central dogma of genetics

The framework describing the flow of genetic information from DNA to RNA to protein.

Reverse transcription

The process where RNA is converted back to DNA. "reverse of central dogma"

Exonuclease

an enzyme that removes nucleotides from the ends of a DNA or RNA strand.

Four types of RNA transcribed from DNA

RNA primers, mRNA, rRNA, tRNA (Occurs in nucleoid of prokaryotes)

Prokaryotic transcription

occurs in the nucleoid &, involves RNA primers, mRNA, rRNA, and tRNA.

3 steps of prokaryotic transcription

initiation, elongation, termination

Eukaryotic transcription

The process of transcription that occurs in the nucleus, mitochondria, and chloroplasts, involving three types of RNA polymerases and numerous transcription factors.

Capping in eukaryotic transcription

A processing step in mRNA transcription where a modified guanine nucleotide is added to the 5' end of the mRNA.

Polyadenylation in eukaryotic transcription

A processing step in mRNA transcription where a poly-A tail is added to the 3' end of the mRNA. (adds a lot of adenine nucleotides)

Splicing in eukaryotic transcription

The process of removing introns from pre-mRNA and joining exons together. (cutting/pasting)

Translation participants

include messenger RNA, transfer RNA, and ribosomes.

Degenerate genetic code

The property of the genetic code where multiple codons can code for the same amino acid.

Ribosome

A cellular structure composed of rRNA and protein that synthesizes polypeptides during translation.

Initiation of translation

The first stage of translation where the ribosome assembles around the start codon of the mRNA.

Elongation of translation

The stage of translation where amino acids are added one by one to the growing polypeptide chain.

Termination of translation

The stage of translation where release factors recognize stop codons, leading to the release of the polypeptide.

coding region

A section of DNA that contains the code for protein synthesis

noncoding regions

DNA segments that do not code for proteins.

exons

a section of mRNA that will translated into protein

intron

sequence of DNA that is not involved in coding for a protein (garbage)

capping & polyadenylated

make the mRNA more stable, help regulate gene expression, allow for nuclear export, and ensure translation by ribosomes happens correctly.

Splieceosmoes

allows for modularity and flexibility by enabling alternative splicing, which lets one gene code for multiple proteins (legos)

codon

three ribonucleotides of mRNA that code for a particular amino acid

start codon

AUG (proteins always start with Methionine)

stop codon

UAA, UAG, UGA (termination of a protein) -Multiple so that it can help with mutations and stuff

anticodon

group of three bases on a tRNA molecule that are complementary to an mRNA codon

additional protein factors

stages of translation require what

Polyribosome

A complex of multiple ribosomes translating a single mRNA strand simultaneously.

Promoter

A DNA sequence that signals the start of a gene and where RNA polymerase binds to initiate transcription.

Terminator

A DNA sequence that signals the end of a gene and where transcription stops.

RNA strand

The strand of ribonucleic acid that is synthesized during transcription.

Regulation of Genetic Expression

The process by which cells control the timing and amount of gene expression.

bacterial gene expression

bacteria express genes as response to environment, only express genes when products are needed

Operons

Groups of coordinately expressed and regulated genes in bacteria.

Structural gene

A gene that codes for a protein or RNA molecule.

(s) =group & same function

RNA polymerase

The enzyme responsible for synthesizing RNA from a DNA template.

Operator

A segment of DNA that a repressor binds to, blocking transcription.

Repressor

A protein that inhibits gene transcription by binding to the operator.

Inducible operons

Operons that must be activated by inducers to initiate transcription. (lactose operon)

Repressible operons

Operons that are continuously transcribed until deactivated by repressors. (arginine operon)