microm 410 midterm 2 glossary

8/2/2019 Microm 410 Midterm 2 Glossary

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operon with a lot of genes encoding

different things.

P Site Peptidyl site

Where the polypeptide chain isRho-dependent terminator Protein-depend00>requires protein

Rho to bind tightly to the C-richrut site on the RNA

Translocates53 on RNA Collision of Rho with a paused

RNA pol causes termination

ribosome site of protein synthesis assemble as 2 subunits, each with

distinct set of proteins and rRNAs

rRNA forms the skeleton of ribosome(ribosomal proteins assemble here),catalyze peptide bond formation

(23S) stable (lasts for hours)

serves a structural role as a scaffold forribosomal proteins and functional roles in

protein synthesis.

Shine Dalgarno Sequence The sequence on mRNA that the 30s

initiation complex identifies to define the

start site.

Binds to the 3 end of the 16s ribosomalRNA, which becomes a part of the 30S

subunit

Variety of purine (A,G) sequences, often 5-

10 bases to the 5 side of the start codon.

Can have multiple RBS

Sigma Factor 28 Recognizes a different -35 (upstream)sequence and -10 sequence and used for

motility and chemotaxis

Sigma Factor 54 Recognizes different sequences used for

nitrogen regulation.

Sigma Factor 70 Recognizes a difference -35 (upstream)

sequence and -10 sequence used for normalgrowth

Termination stage Two terminators (intrinsic or Rho-

dependent sequences) makes the courepause, RNA_DNA duplex falls apart, RNA

pol leaves DNA

tRNAs adaptors between ribosome and


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message, bringing correct amino

acid to translation complex

Stable (lasts for hours) Flattened structure looks like 4

single-stranded regions with a 3

end +3 loops All tRNAs are transcribed with

normal RNA bases, but then many

bases are modified and the tRNAfolds into a very stable structure

Each different tRNA coded by adifferent gene, despite conserved

elements

Ranges in length from around 73-93nucleotides

All with the same 3 sequence(CCA) where the amino acidattaches

Anticodon loop will base pair withmRNA

Universal genetic code Most codons are interpreted in sameway in different organisms

Wobble base pairing Allows amino acids to have severalcodons recognized by 1 tRNA

Have irregular base pairing at theend because it is more flexible

EX. Alanine is encoded by 4possible codons all of the formGCX.

Transport secretion and mutations

Antiporter 1 molecule transfer energizes another one


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ATP-dependent transporters

Conformational changes in the proteins thatresult in solute passage are energized by

ATP hydrolysis

Atp-hydrolyzing protein: 2 ATP for 1

molecule of solute

Membrane spannign transporter: formchannel

Periplasmic binding protein: highsubstrate affinity.

ATP-hydrolyzing protein 2 ATP for 1 molecule of solute in ATP-

dependent transporter

Base analogs Incorporate into DNA isntead of normalbases, but base pair incorrectly. Reparied

bby mismatch report.

Exs.

5-bromouracil: replaces T, but pairs with

C

2-aminopurine: replaces A but pairs with

C.

DnaK/DnaJ Prevent protein from folding too quickly

Group translocation: chemical modification of the transportedsubstance driven by phosphoenolpyruvate

(active transport)no accumulation ofsolutes because the solute is modified

Hsp Heat shock protein

Attempt for cell to refold denaturedproteins.

Intercalating dyes Physically insert themselves and pushDNA base pairs apart.

Single base pair insertions/deletions


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Frameshift mutations

Lesions often fixed by mismatch repair

systems

Exs. Acridines or ethidium bromide.

Ionizing radiation Lead to formation of free radicals, leadingto both ss and ds breaks in DNA

Ds breaks=most damaging and only

reparable by recombination and/or error-prone repair

ssDNA=opposing strand can repair by

being a template.

Lex A responses Three things UvrA, UmuCD, lexA

LexA protein Repressor of expressor of SOS regulation

that is inactivated by the activation of the

RecA protein

Membrane spanning transporter Forms the channel for transport in ATP-dependent transporter

Missense mutation Reduced/no activity

Molecular chaperones Interact with newly synthesized or with

misfolded polypeptides to help acquirenormal, final structures

Can also help polypeptide attain structure,

but are NOT PART of the final protein

structure.

Chaperones often hydrolyze ATP during

proper protein folding. Chaperones canalso prevent folding or aggregation before

localization of proteins beyond cytoplasm.

Non-ionizing radiation (ultraviolet light) Absorbed by the bases on nucleic acids, the

bases can be affected. Examples include

pyrimidine dimers, which can causemisreading by DNA pol.

Effect: production of pyrimidine dimers

and where 2 adjacent pyrimidine dimers on

same DNA become covalently bonded.

Nonsense mutation Single base substitution change

Periplasmic binding protein A carrier with high substrate affinity inATP-dependent transporter.

Photo-reactivation systems Repear damage in DNA by UV light

cleaves pyrimidine dimers generated by

UV radiation, all organisms exceptmammals have this.

Light energizes a photolyase (enzyme that

absorbs E from light) which removes


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lesion.

Reactive chemicals Deaminate various bases, causing faultybping during replication. Repair with

specific DNA glycosylases

Exs. Nitrous acid or hydroxylamine

RecA protein: Senses DNA damage and activated tobecome protease that cleaves receptorprotein

Sec apparatus Step 1: SecA + SS-precursor, SecBchaperone associates.

Step 2: Complex to membrane due to

SecA-SecEYG; secA cleaves ATP andthreads precursor into SecEYG pore like a

sewing machine.

Step 3: repeat ATP-driven SecA cycle

feeding 20-30 aa segments through Sec;PMF driven SecEYG cycle. SS-cleavageby Lep occurs early.

SUMMARY:

Essential: SecA, SecEY, Lep

Helpful: SecB, SecG, SecDF

secondary protein structure Spontaneous formation.H-bonding between oxygen and nitrogen

atoms. Include alpha helices and B strands.

Signal Sequences (SS) Used in both proks and euks to direct

precursor proteins for secretion.SS are cleaved from precursor during

localization processmature potion is thenin cellular destination.

One of the first molecules to besynthesized so translation can occurearly on

Wide variety of amino acidsequences can be used

N-terminal domain: 15-25 aa First: Region of 3-8 residues with1-3 amino acid Next: hydrophobic core (7-15

hydrophobic amino acids)

Last: sometimes a more polar region where

cleavage by specific peptidase occurs.

Silent mutation Change in genotype no change inphenotype


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Simple transport driven by the energy in the proton motive

force.

SOS response to DNA damage System of three things

RecA activated by DNA damageLexA

inactivatedSOS response no longer

repressedSymporter Simultaneous movement inwards using 1

protein

Tat secretion Alternative appartus used in export offolded bacterial prtoeins: TatABC

Tat substrates with distinct N-terminus

targeting signal (Twin Arg Tag): 25-40amino acids with a motif in the basic

region.

Tat signal-containing folded protein binds

TatBCTatATatA Membrane transporter that is dependent on

PMF that relies on TAT secretion from

TATBC

TatBC Involved in TAT secretion that recognizes

arginine residues on proteins

tertiary/quaternary protein folding Can occur spontaneously but is frequently

aided by molecular chaperones

(chaperonins)protein-folding factors.

The ABC System : periplasmic binding proteins are involved

and energy comes from ATP.

Transport proteins Are there because passive diffusionis not very effective Generally are specific for particular

solute

Usually consume energy in someform during the transport process

Usually transport the solute without any

chemical modification of that solute.

Umu CD Error prone DNA repair.

Uniporter One molecule movement

UvrA Error free DNA repair


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Regulation

microm 410 midterm 2 glossary

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