Exam 3

central dogma

DNA → RNA → protein

DNA structure

double helix, backbone of deoxyribose phosphate, two strands of nucleotides, anti parallel

DNA gyrase

relaxes supercoiling

DNA ligase

makes covalent bonds to join DNA strands, okazaki fragments

DNA polymerase

adds nucleotides to growing strand in the 5’→3’ direction, initiated by RNA primer, lagging strand creates okazaki fragments, removed RNA primers

helicase

unwinds double strand

rRNA

ribosomal, integral part of ribosomes

tRNA

transfer, transports amino acids during protein synthesis

mRNA

messenger, carries coded info from DNA to ribosomes

transcription in prokaryotes

synthesis of complementary mRNA strand from DNA template

Transcription process

RNA polymerase binds to promoter sequence on DNA, proceeds in 5’→3’, only one of the two DNA strands is transcribed, stops when reaches terminator sequence

translation process

61 sense codons encode the 20 amino acids, starts with start codon AUG ends at nonsense codons, tRNA transports required amino acids, tRNA have anticodon that base pairs with the codon, amino acids joined by peptide bonds

translation

mRNA is decoded to build proteins, occurs in ribosomes

repression

inhibits one gene expression and decreases enzyme synthesis, mediated by repressors that block transcription, default on

induction

turns on gene expression, initiated by inducer, default off

promoter

segment of DNA where RNA polymerase initiates transcription of structural genes

operator

segment of DNA controlling transcription of structural genes

operon

set of operator and promoter sites and the structural genes they control

inducible/lac operon

structural genes not transcribed unless and inducer is present, in absence of lactose the repress or binds to the operator and prevents transcription, in presence of lactose allolactose (inducer) binds to the repress or and transcription occurs

inducer in lac operon

allolactose

trp operon

excess tryptophan is a corepressor that binds and activates repressor to bind to operator, stopping tryptophan synthesis

spontaneous mutations occur when

absence of a mutagen

mutagen

agents that cause mutations

base substitution mutation

change in one base

missense mutation

base substitution results in change in an amino acid

nonsense mutation

base substitution results in a nonsense/stop codon

frame shift mutation

insertion or deletion of one or more nucleotide pairs

chemical mutagens

mutated DNA by directly or indirectly altering structure or sequence

nitrous acid

chemical mutagen, causes adenine to bind to cytosine

nucleoside analog

chemical mutagen, incorporates into DNA in place of a normal base

photolyase

an enzyme in bacteria that separate thymine dimers and fix mutations

nucleotide excision repair

enzymes cut out incorrect bases and fill in correct ones

positive/direct selection

detects mutant cells bc they grow or appear different

negative/indirect selection

detects mutant cells that can’t grow or perform a certain function

auxotroph

mutant that has a nutritional requirement absent in the parent

genetic recombination

exchange of genes between two DNA molecules; creates genetic diversity

crossing over

two chromosomes break and rejoin, results in insertion of foreign DNA into chromosome

vertical gene transfer

organism to offspring

horizontal gene transfer

organism to organism of same generation

transformation in bacteria

DNA fragments from donor cell is taken p by recipient, donor DNA aligns with complementary bases, recombination occurs

plasmids

self replication circular pieces of DNA

conjugative/fertility plasmid

carried genes for sex pili

resistance plasmids (r factors)

encode antibiotic resistance

conjugation in bacteria

plasmids transferred from one bacterium to another via sex pili

transposons

segments of DNA that can move from one region of DNA to another, contain insertion sequences that code for transposase

transposase

cuts and reseals DNA

transduction in bacteria

DNA transferred from one bacterium to another by a virus

Viruses have DNA or RNA?

either, but not both

Viruses have no

ribosomes or ATP-generating mechanism

receptor sites for animal viruses

typically on plasma membrane

virion

fully developed viral particle

capsid

virus protein coat made of capsomeres

envelope

lipid, protein, and carbohydrate coating on some viruses

helical virus

hollow, cylindrical capsid; rabies and ebola

polyhedral virus

many sides; poliovirus

complex virus

complicated structure; bacteriophage

virus family name ends in

viridae

virus order name ends in

ales

virus genus name ends in

virus

baltimore classification system

based on virus nucleic acid and how mRNA is produced

bacteriophage plaque

clearings on a lawn of bacteria on surface of agar, each plaque corresponds to a single virus

PFU

plaque forming unit

lytic cycle

phage cause lysis and death of host cell

lysogenic cycle

phage DNA incorporated into host DNA, remains dormant as a prophage

steps of lytic cycle

attachment, penetration, biosynthesis, maturation, release

prophage

inserted phage DNA

animal virus steps

attachment, entry, uncoating, biosynthesis, maturation, release by budding

uncoating

separating the viral nucleic acid from its capsid by viral or host enzymes

how are enveloped viruses released from host cell

budding

how are non-enveloped viruses released from host cell

rupture

DNA virus biosynthesis

replicate DNA in host cell nucleus, synthesize capsid proteins in cytoplasm, capsid proteins migrate to nucleus for assembly

DNA virus examples

Adenoviridae, Poxviridae, Herpesviridae, Papoviridae, Hepadnaviridae

Coronaviridae

single stranded RNA, enveloped

Togaviridae

single stranded RNA, enveloped

Picornaviridae

single stranded RNA, non

Rhabdoviridae

single stranded RNA, mostly enveloped

Adenoviridae

double stranded DNA, non

Poxviridae

double stranded DNA, enveloped

Herpesviridae

double stranded DNA, enveloped

Papovaviridae

double stranded DNA, non

Hepadnaviridae

double stranded DNA, enveloped

Retroviridae

single stranded RNA, produce DNA intermediate

Reovirus

double stranded RNA, non

Rotavirus

double stranded RNA, non

reverse transcriptase

produces DNA from viral RNA genome

latent virus

remains in asymptomatic host cell for long period; Herpesvirus, Shingles

Persistent viral infection

occurs gradually over a long period and is generally fatal; papillomavirus, Hepatitis B

prions

scrapie protein accumulates in brain cells and forms plaques, misfolds other proteins and spreads

prion disease examples

mad cow disease

Pathogenicity

ability of an organism to cause disease

virulence

the degree at which a pathogenic organism can cause disease

Parenteral route

deposited directly into tissues when barriers are penetrated (injections, bites, etc.)

Skin entry points

hair follicles, sweat gland ducts

Mucous membranes entry route

respiratory tract, digestive canal, genital system

Adherence

adhesins/ligands on the pathogen bind to receptors on host cell

Ligands

glycocalyx, fimbriae, viral spikes

invasins

surface proteins produced by bacteria that rearrange actin filaments of the cytoskeleton to cause membrane ruffing which results in bacteria being engulfed

What pathogens use actin to move from one cell to the next?

Shigella and Listeria

Capsules

glycocalyx around the cell wall, impair phagocytosis of many photogenic organisms

Cell wall components

M protein in some Streptococcus that resist phagocytosis, mycolic acid resists digestion