microbiology (BIOL215) exam 2

NADH

often used to generate PMF for ATP synthesis

PMF

proton motive force, form of energy generates an an electron transport chain moves protons across a membrane to create a chemiosmotic gradient

precursor metabolites

metabolic intermediates that link catabolic and anabolic pathways because they can either be broken to generate ATP or used to make subunits of macromolecules

organotroph v lithotroph

organo = source of electrons is ORGANIC molecules
litho = source of electrons is INORGANIC molecules

TCA cycle

provides energy
need: acetyl-CoA
output: ATP, NADH, FADH2

helicase

unwinds/separates the DNA helix at the replication fork

primase

synthesizes small fragments of RNA to serve as primers for DNA synthesis

how does transcription start

RNA polymerase binds to a promoter

role of sigma factor

recognizes promoter, synthesis of factor controls transcription of set of genes

slight risk mutations

single base changes to the promoter, RBS, or regulatory regions, and substitutions to amino acids (missense)

catabolism

breakdown of components such as glucose, can release energy

anabolism

metabolic processes that synthesize and assemble the subunits of macromolecules, using the energy of ATP

ATP

energy currency of cells. hydrolysis of the bonds between P groups can be to power reactions

heterotroph v autotroph

hetero = source of carbon is ORGANIC
auto = source of carbon is INORGANIC

chemotroph v phototroph

chemo = energy source REDOX reactions
photo = energy source LIGHT

glycolysis

provides cell with energy in form of ATP
need: glucose and 2 ATP
output: pyruvate, NADH and ATP

ETC

provides energy
need: NADH and FADH2
output: ATP

general structure of DNA?

2 polynucleotide strands connected by hydrogen bonds
antiparallel arrangement(5' to 3')
A+T / G+C

how are nucleotides linked together

phosphodiester linkages

what is a plasmid?

genetic elements in addition to the chromosome, replicate independently

what kind of information is in a plasmid?

contain expendable/nonessential genes (expendable does not mean helpful)
- conjugative plasmids (allow conjugation)
- resistance plasmids (confer antibiotic resistance)

DNA polymerase

synthesizes DNA, uses existing strand as a template to make new. complementary strand

gyrase

temporarily breaks strands of DNA, relieving tension by unwinding strands

ligase

forms covalent bonds between adjacent fragments of DNA

how does translation start/end?

initiating tRNA base pairs with start codon and occupies the P-site.
translation ends when ribosome reaches top codon/ components disassemble, releasing newly formed polypeptide

what causes mutations?

mis-incorporation of bases by DNA poly., radiation (radicals damaging DNA, UV lights & thymine dimers), and chemical mutagens (base analogs, nucleotide/DNA altering chemicals)

silent mutation

change to DNA, no change in the protein
ACG/ACC (it will still code for the same protein)

missense mutation

change to DNA. change in protein
GAU/GCU (codes for Asp, codes for Ala)

nonsense mutation

change to DNA, change in protein
UCA/UGA (codes for Ser, but UGA is a stop codon) information is "lost"

insertion

insert a base, changes the protein

deletion

base is removed, change in protein

low risk mutations

have small changes to places where DNA is either not transcribed, or protein will have no change when translated

high risk mutations

ex: nonsense
since it puts a stop codon n a gene, all remaining information that should have been translated is now lost

insertion/deletion mutations

often change phenotypes, can change reading frame, changes protein structure, and can result in loss of whole genes

tRNA

interprets the genetic code' carries a specific amino acid dictated by its anticodon

single stranded binding proteins

bind to single stranded DNA to prevent reannealing and stabilize the DNA template during replication

operator

short DNA sequence located between promoter and genes it controls in operon. acts as a binding site, and can either inhibit or enhance transcription

numbering rules

upstream are assigned at negative numbers, downstream are assigned positive numbers, transcription start site is +1

rho independent termination

structure of strand, a loop, essentially "knocks off" RNA polymerase, ending transcription

rho dependent termination

rho attaches to rut site, essentially chases rna polymerase to stop codon, termination is complete

induction - gene expression

activation of gene expression in response to external stimuli

repression - gene expression

inhibition of gene expression

negative control

repressors that inhibit transcription by blocking RNA polymerase

positive control

activators that stimulate transcription by enhancing RNA polymerase activity

lac operon

absence of lactose results in LacI repressing, preventing RNA from transcribing lac genes. Lactose is inducer, allowing for transcription