Microbio exam 3

genome

genome

the total of all genes in an organism whether they are found on a single chromosome or distributed among multiple replicons

genes

the units of heredity (most are located on chromosomes)

transformation

the internalization of free DNA from the environment into bacterial cells

what kind of chromosomes do most archaea and bacteria have?

circular

enhancer

a noncoding DNA regulatory region in eukaryotes that can lead to activation of transcription when bound by an appropriate transcription factor. It location on the chromosome can be far removed from the regulated gene.

promoter

a noncoding DNA regulatory region immediately upstream of a structural gene that is needed for transcription initiation

nucleobase

(also called a nitrogenous base) forms a nucleotide of nucleic acids (U, A, C, G, T)

phosphodiester bond

the phosphoryl bond that includes ester links with two adjacent nucleotides in a nucleic acid

antiparallel

oriented such that the two strands are in opposite directions (5’-to- 3’ and 3’-to-5’)

purines

nitrogenous bases with fused rings ( adenine and guanine)

pyrimidines

single-ring nitrogenous bases (cytosine, thymine, and uracil)

denature

to lose secondary or tertiary structure in a protein or nucleic acid because of high temperature or chemical treatment

nucleoid

the looped coils of a bacterial chromosome

topoisomerases

the enzymes that change DNA supercoiling

quinolone antibiotic

antibiotic that inhibits DNA synthesis by targeting bacterial topoisomerases such as DNA gyrase

positive supercoils

tightening of the coil

negative supercoils

unwinding of the coil

what kind of supercoils do most bacteria, eukaryotes, and archaea possess?

negatively supercoiled DNA

how do bacteria replicate their DNA quickly and minimize errors?

replication efficiency

semiconservative replication

each daughter cell receives one parental strand and one newly synthesized strand; allows for each daughter duplex to be checked for accuracy against its parental strand

replications fork

parental strands are seperated while extending the new growing strands

DNA replication

1.) initiation: the melting (unwinding) of the helix and the loading of DNA polymerase enzyme complex

2.) elongation: the sequential addition of deoxyribonucleotides to a growing DNA chain, followed by proofreading

3.)termination: the DNA duplex is completely duplicated,the negative supercoils are restores, and key sequences of new DNA are methylated

replication from a single origin

replication in bacteria begins at a single defined DNA sequence called the origin

catenane

a pair of linked rings of DNA that occurs as a by-product of replication of circular chromosomes

homologous recombination

the exchange of strands between two molecules of DNA; exchange occurs within extensive regions of identical or nearly identical sequence

plasmids

extrachromosomal elements found in bacteria, archaea, and eukaryotic microbes; usually circular and negatively supercoiled; much smaller than chromosomes and encode only a few genes

secondary chromosome

carries at least one essential gene; smaller than primary chromosome

telomeres

ends of eukaryotic chromosomes

transcription

the copying of DNA to RNA

RNA polymerase (DNA-dependent RNA polymerase)

an enzyme complex that carries out transcription, making RNA copies of a DNA template

DNA template strand

specifies the base sequence of the new complementary strand of RNA

RNA polymerase consists of:

core polymerase and a sigma factor (holoenzyme)

core polymerase

contains the proteins required to elongate an RNA chain

sigma factor

a protein needed only for initiation of RNA synthesis, not for its elongation

A bacterial core RNA polymerase is a complex of four different subunits:

2 alpha, 1 beta, 1 beta-prime

beta-prime subunit

houses the Mg 2+ which contains the catalytic site for RNA

alpha subunit

assembles the beta and beta-prime subunits into a functional complex. It also communicates through physical “touch” with various regulatory proteins that can bind DNA

sigma factor proteins

used to guide RNA polymerase to the beginning of each gene whose expression is needed under certain conditions.

1. binds to RNA polymerase through the beta and beta-prime subunits

2. the bound sigma factor recruits the core enzyme to the promoters, marking the beginning of a gene

consensus sequence

consists of the most likely base (or bases) at each position of the predicted promoter. some positions in a consensus sequence are highly conserves, meaning that the same base if found in that position in every promoter

sequences identified and bound by E.coli sigma -70

located at -10 and -35 bp upstream of the transcription start site

open reading frame (ORF)

protein-coding region

polygenic

containing both operon genes

monocistronic

(referring to RNA products of transcription) RNA encodes the product of a single gene. This gene has its own promoter and transcription terminator

polycistronic

(referring to RNA products of transcription) RNA encodes the products of one or more adjacent genes in one contiguous RNA molecule

operon

the combination of the regulatory regions and all the genes that are cotranscribed in the polycistronic message

3 stages of transcription

1. Initiation

2. Elongation

3. Termination

initiation

the RNA polymerase binds to the promoter, melts open the DNA helix, and catalyzes placement of the first RNA nucleotide

elongation

the sequential addition of ribonucleotides to the 3’ OH end of a growing RNA chain

termination

whereby sequences trigger release of the polymerase and the completed RNA molecule

Rho factor

binds to an exposed region of RNA after the ORF at C-rich sequences that lack obvious secondary structure; used for termination in some genes

rifamycin B

selectively target bacterial RNA polymerase and bind to the polymerase’s beta subunit near the Mg2+ active site, this blocking the RNA exit channel

rifampicin (rifampin)

used for treating tuberculosis, leprosy, and bacterial meningitis

actinomycin D

its phenoxazone ring is a planar structure that inserts, or intercalates, between GC pairs within DNA

messenger RNA (mRNA)

the class of RNA molecules that encode proteins; doomed to a short existence due to their degradation by intracellular RNases

ribosomal RNA (rRNA)

forms the scaffolding on which ribosomes are built; forms the catalytic center of the ribosome; has unusual bases

transfer RNA (tRNA)

ferry amino acids to the ribosome; has unusual bases

small RNA (sRNA)

do not encode proteins but used to regulate the stability or translation of specific mRNAs into proteins; contain untranslated leader sequences that precede the actual coding region

tmRNA

has properties of both tRNA and mRNA

catalytic RNA

also called ribozymes; associated with proteins; the enzymatic (catalytic) activity resides in the RNA portion of the complex rather than in the protein

RNA stability

measured in terms of half-life

half-life

the length of time the cell needs to degrade half the molecules of a given RNA species

codons

triplets of nucleotides

stop codons

trigger a series of events that dismantle ribosomes from mRNA and release a completed protein

anticodons

RNA sequences that match and bind to specific codons on the mRNA being translated

aminoacyl-tRNA synthetases

enzymes that match and attach the correct amino acid to the correct tRNA

ribosomes

catalyze the linkage of amino acids during translation using mRNA as the code and charged tRNAs as the source of amino acids

start codons

mark where translation starts and set the correct reading frame

ribosome-binding site (Shine- Dalgarno sequence)

purine-rich sequence located four to eight bases upstream of the start codon

aminoacyl-tRNA acceptor site (A site)

(first position) where the incoming aminoacyl-tRNA enters the complex and its anticodon binds the codon of the mRNA

peptidyl-tRNA site (P site)

(second position) binds the tRNA that is attached to the growing polypeptide

exit site (E site)

(third position) where the tRNA will be jettisoned from the ribosome after giving up its amino acid to the polypeptide chain

initiation factors for E.coli

IF1, IF2, IF3

polysome

multiribosome structure that is the result of an mRNA molecule with multiple ribosomes moving along its length at once

most ribosomes are located at the poles of what cells?

rod-shaped cells

translation terminates when:

a stop codon is reached. A release factor enters the A site and triggers peptide bond formation, thus freeing the completed protein from tRNA in the P site

glycoproteins

involved in important microbial processes such as biofilm formation, virulence, and colonization of the human gut

mass spectrometry

experimentally determines the exact mass of an unknown protein or peptide fragment.

chaperones

helper proteins that aid in the folding of other proteins

heat-shock proteins (HSPs)

more resistant to heat denaturation than the average protein

mutation

any permanent, heritable alteration in a DNA sequence, whether harmful, beneficial, or neutral

point mutation

a change in a single nucleotide

transition

replacing a purine with a different purine or a pyrimidine with a different pyrimidine

transversion

swapping a purine for a pyrimidine

insertions/ deletions

the addition or subtraction of one or more nucleotides, making the sequence either longer of shorter than it was originally

inversion

when a fragment of DNA is flipped in orientation relative to the flanking DNA on either side

duplication

produces a second copy of a sequence fragment on the DNA molecule, usually adjacent to the original copy

transposition

the movement of a sequence fragment from one location to another

reversion

restores a mutated sequence to its original sequence

silent mutations

mutations that do not change the amino acid sequence of a translated open reading frame (ORF)

missense mutation

changes the amino acid sequence of the protein

loss-of-function mutation

the decrease or elimination of the activity of a protein by a missense change

gain-of-function mutation

when a protein gains a new activity, such as an expanded substrate specificity or a completely different substrate specificity.

knockout mutation

a mutation that eliminates function

nonsense mutation

a point mutation that changes an amino acid codon into a translation termination codon (ex. UCA to UAA)

truncated proteins

the result of a nonsense mutation; truncations can completely knock out the function of proteins, especially in cases where the mutation occurred early in the ORF; degraded by cellular proteases

frameshift mutation

when the number of bases inserted or deleted is not a multiple of three and the reading frame of translation changes; cause the ribosome to encounter a premature stop codon

genotype

the genome sequence of an organism

phenotype

the observable characteristics of an organism

mutagens

chemical agents or forms of electromagnetic radiation that can damage DNA

tautomeric shifts

the change in the bonding properties of amino (-NH2) and keto (C-O) groups; if occurring during DNA replication, number of mutation events will increase