Chapter 9

Structure of a nucleotide: phosphate, deoxyribose sugar, nitrogenous base

DNA polymerase 3: synthesizes new daughter strand of DNA but the DNA molecule must be unwound first, can only add nucleotides onto existing chain, and can only add in the 5’ to 3’ direction

Replication fork: the place where the DNA helix is unwound and replication begins

Circular DNA will have ____ replication forks: two

Primer: the length of RNA that is inserted initially during replication

Leading strand: strand of new DNA that it synthesized in the 5’ to 3’ direction

Lagging strand: strand of new DNA that is sealed in the 3’ to 5’ direction

Okazaki fragments: short segments of DNA synthesized in the 5’ to 3’ direction which are sealed in the opposite direction

Transcription: DNA synthesized into RNA

Translation: RNA produces proteins

Participants in transcription and translation: mRNA, tRNA, rRNA, ribosomes, enzymes, raw materials

Central dogma: DNA makes RNA which makes proteins which creates the function

RNA: single stranded molecule that exists in helical form and can have secondary and tertiary levels of complexity

mRNA: transcript of a structural gene or genes of DNA

Codons: a series of triplet bases that hold the message of the transcribed mRNA

tRNA: contains sequences of bases that form hydrogen bonds with complementary sections of the same tRNA strand

Anticodon: found at the bottom of cloverleaf, designates the specificity of the tRNA that complements the mRNA codon

rRNA: long polynucleotide molecule that contributes to the structure of the ribosome, rRNA and protein create the subunits of the ribosome

Initiation of the transcription: it is initiated when RNA polymerase recognizes the promoter region, the template strand is copied by RNA polymerase

Elongation of transcription: proceeds in the 5’ to 3’ direction the mRNA is assembled

Termination of transcription: the polymerases recognize a code that signals the separation and release of the mRNA strand

Principle of translation: mRNA nucleotides are read in codons in groups of 3, the codon dictates the amino acids, this is universal for archaea, bacteria, and viruses

Start codon: AUG (f-Methionine)

Stop codon: UAA, UAG

Redundancy: certain amino acids are represented by multiple codons

Wobble: only the first two nucleotides are required to encode the correct amino acid, permit mutation without altering the message

Stages of translation: initiation, elongation, termination

Initiation of translation: the ribosome encounters the start codon and tRNA come with the compliment amino acid

Elongation of translation: tRNA 2 enters the A site and form peptide bonds between amino acids and this process continues by translocating to the next mRNA

Termination of translation: the ribosome reaches the stop codon (nonsense codon) and an enzyme breaks off the amino acid chain

Translocation: shifting the ribosome down the mRNA strand to read new codons

Posttranslational modifications: proteins begin to fold, cofactors may be added, tertiary and possible quaternary structures formed

Cotranslational only occurs in: bacteria and archaea

AUG is the stop code for: prokaryotes not eukaryotes

Eukaryotic proteins only code for one protein while bacterial mRNAs: often code form several genes

Introns: intervening sequences of bases that do not code for a protein

Exons: coding regions

Spliceosome: recognizes exon-intron junctions and enzymatically cuts through them and joins the exons

Operons: found only in bacteria and archaea, coordinated set of genes regulated a single unit

lac operon regulator: composed of the gene that codes for the repressor, a protein capable of repressing the operon

lac operon control locus: promoter and operator (on/off switch of transcription)

lac operon structural locus: made up of three genes each coding for a different enzyme needed to catabolize lactose

Allosteric: change in shape or activity of an enzyme

In absence of lactose for the lac enzyme the repressor: binds to the operator blocking the transcription of structural genes

Repressible operons are usually in on mode but will turn off when: a nutrient is no longer required

Excess nutrients can serve as a ____ to block the action of the operon: corepressor

Drugs that inhibit protein synthesis in bacteria: Rifamycin and Actinomycin D

Drugs that interfere with the ribosome of bacteria: Erythromycin, Spectinomycin, Chloramphenicol, Aminoglycosides

Recombination of DNA: one bacterium donates DNA to another bacterium

Plasmids: extrachromosomal DNA that can replicate on their own and move between cells, found in bacteria and fungi, not essential but can have advantageous traits

Recombinant organism: any organism that contains and expresses genes that originated in another organism

Horizontal gene transfer and types: any transfer of DNA that results in organisms acquiring new genes that did not come from parents, conjugation, transformation, transduction

Transformation horizontal gene transfer: bacterial cell accepts small fragments of soluble DNA from the surrounding environment

If a cell can accept genetic material through transformation then the cell is: competent

Generalized transduction horizontal gene transfer: random fragments of disintegrating host DNA are taken up by a phage during assembly

Specialized transduction horizontal gene transfer: a highly specific part of the host genome is incorporated into the virus

Transposons/ Transposable elements: ‘jumping genes’ that can shift from one part of the genome to another

General effects of transposable elements: scramble genetic language and can be beneficial or adverse depending on where, what genes relocated, and the type of cell

Effects of transposable elements on bacteria: changes in morphology, pigmentation and antigenic characteristics, replacement of damaged DNA, transferred drug resistance

Mutation: any change to the nucleotide sequence in the genome, in microbes very obvious

Wild type microbe: a microbe exhibits natural characteristic which is in the majority of the population

Mutant strain microbe: an organism with a mutation

Spontaneous mutation: a random change in the DNA from errors in replication

Induced mutation: result from exposure to mutagens

Examples of mutagens: nitrous acid, ethidium bromide, acridine dyes, nitrogen base analogs, radiation

Point mutations: small mutations that affect only a single base on a gene

Lethal mutations: lead to cell dysfunction or death

Neutral mutations: produce neither adverse nor helpful changes

Missense mutation: any change in the code that leads to different amino acids

Nonsense mutation: changes normal codon into stop codon

Silent mutation: alters a base but does not change the amino acid produced

Back mutation: a mutated gene reverts to original form

Frameshift mutation: one or more bases inserted into or deleted from newly synthesized DNA strand, this alters the reading frame of the mRNA and nearly always results in a nonfunctional protein

Ames test: rapidly detects chemicals with carcinogenic potential, uses bacteria to mutate their DNA to monitor gene expression