Micro Exam 3

DNA --> RNA --> protein

major dogma

constant production

regulate transcription

degrade RNA

regulate translation

regulate enzyme activity

degrade protein

major modes of regulation

constant poduction

constitutive proteins are needed at the same level at all times

regulate transcription and enzyme activity

two most important modes of regulation

regulation of transcription

post-translational regulation

two major levels of regulation in the cell

regulation of transcription

major; regulates amount of a protein; slower (minutes)

regulation of translation

similar to regulation of transcription but is minor

post-translational regulation

regulate activity of preexisiting proteins; very fast (seconds)

DNA binding proteins

atoms involved in protein-DNA interaction

requires regulatory sequences that are many times adjacent to the promoter

transcription

DNA binding proteins are central to regulation of

helix-turn-helix motif

one of the most common DBP

two per monomer

nonpolar forces between helices stabilize motif

regulation helix

first helix in the helix-turn-helix motif that forms H bonds with bases in the major groove

major groove

main site of protein binding on the DNA

stabilizing helix

second helix in the helix-turn-helix motif

zinc finger

leucine zipper

other common DBP

inverted repeats

frequently are binding sites for homodimeric regulatory proteins

small molecules

influence the binding of regulatory proteins to DNA through allosteric interactions, covalent modifications, etc.

zinc fingers

contain protein structure that binds a Zn ion

three can bind to DNA

leucine zippers

leucine residues are spaced every 7 amino acids and interact to form a homodimer

blocking or activation of transcription

DNA binding by a protein can lead to

operator

the piece of DNA that overlaps the promoter site and serves as the on-off switch

activator-binding site

nucleotide sequence that precedes an ineffective promoter

does not have to be adjacent to promoter

thought to change DNA conformation

operon

composed of binding sites, genes, and regulatory elements

promoter

can be strong or weak

can bind dominant or alternaive sigma factors

repressor

homodimeric DBP

negative control

regulatory mechanism that stops transcription

repression

induction

types of negative control

repression (arg operon)

repressor inactive (not bound to signal)

cannot bind to operator

transcription proceeds

repressor active (bound to signal)

binds to operator

blocks transcription

induction (lac operon)

repressor active (not bound to signal)

binds to operator

blocks transcription

repressor inactive (bound to signal)

cannot bind to operator

transcription

LacI

lac operon repressor

repression

preventing synthesis of an enzyme in response to a signal (bound --> active)

anabolic enzymes

enzymes not synthesized when not needed

induction

synthesis is prevented in absence of a signal (not bound --> active)

catabolic enzymes

enzymes synthesized only when needed

activation

form of positive control

activation (mal operon)

activator inactive (not bound to signal)

cannot bind to activator binding site

no transcription

activator active (bound to signal)

binds to activator binding site

transcription

MalT

mal operon activator

activator protein

helps RNAP recognize promoter

may cause change in DNA structure

may interact directly with RNAP

regulon

multiple operons controlled by same regulatory protein

positive and negative control

maltose regulon

has 4 maltose operons under control of same activator

global regulation

simultaneous regulations of many different genes

CRP

cAMP receptor protein

global regulatory element

functions as activator protein in lac operon, needed in active form for transcription

catabolite repression

not using the less energetic carbon source

glucose

inhibits activity and synthesis of cAMP by inhibiting adenylate cyclase

cAMP cannot bind to and activate CRP

no transcription

transcription proceeds

CRP and lactose in lac operon

no transcription

glucose present (no active CRP) and lactose absent (repression) in lac operon

low expression

glucose present (no active CRP) and lactose present (no repression) in lac operon

transcription proceeds

glucose absent (cAMP, active CRP) and lactose present (no repression) in lac operon

flagellar genes

controlled by catabolite repression

cAMP

key molecule in many metabolic control systems

derived from nucelic acid percursor

NrpR blocks TFB and TBP binding (no transcription)

NrpR binds alpha-ketoglutarate

NrpR released, TFB and TBP bind (transcription)

regulation of N metabolism in Archaea

Pyrococcus furiosus

uses a single regulatory protein to switch between fermentation and sulfur reduction

no sulfur --> active, activates transcription of hydrogenase which represses transcription

sulfur --> inactive (oxidized)

NrpR

example of archaeal repressor protein from Methanococcus moripaludis