module 5

why don’t bacteria express every gene in their genome

gene expression requires a lot of energy

why is selective gene expression efficient for bacteria

they express only genes needed for survival in their current envionment

why must bacteria adjust gene expression to their enviornment

because they live in a wide range of environments

define metabolism

what cells need to synthesize and break down for survival

what is anabolic reaction

uses energy and smaller molecules to build a larger molecule

what is a catabolic reaction

breaks a larger molecule into smaller molecules and releases energy

does an anabolic reaction use or release energy

uses energy

does a catabolic reaction use or release energy

release energy

what happens to molecules during anabolism

smaller molecules are combined into a larger molecule

what happens to molecules during catabolism

larger molecule is broken into smaller molecules

what are housekeeping genes

genes that are expressed constitutively or always on

what is constitutive expression

gene expression that is always on

what are examples of housekeeping genes

dna polymerase, rRNA, tRNA, glycolysis genes

what regulation is associated with catabolic pathways

induction

what regulation is associated with anabolic pathways

repression

what molecule induces the catabolic pathway shown

carbon source

what does induction do in the catabolic pathway

promotes expression of genes encoding catabolic enzymes

what molecule represses the anabolic pathway

the end product

what does repression do in the anabolic pathway

inhibits expression of genes encoding anabolic enzymes

in a catabolic pathway: when carbon source is present this means

induction of gene expression

what is an open

group of genes that encode proteins with a related cellular function

what can influence whether an operon is expressed

presence or absence of effector molecules

what are effector molecules

non-protein small molecules that bind to transcription factors

when effectors binds to transcription factors what happens

it changes TF shape and function

what is the regulatory region made of

promoter and operator

what is a promoter

the region that drives expression of the operon’s genes

what is the operator

part of the regulatory region where regulation occurs

what are structural genes

genes in an operon that encode proteins with related functions

how many promoters can drive multiple related genes in an operon

one

what type of mRNA is produced from an operon

Polycistronic

what are regulatory proteins

activators and repressors that regulate gene expression

where do regulatory proteins bind

the regulatory region where the promoter and operator are located

what are effector molecules

environmental cues that bind regulatory proteins

what is an example of an environmental cue

a carbon (energy) source

what is polycistronic mRNA

a single mRNA that encodes more than one distinct protein

how many proteins can one polycistronic mRNA encode

more than one

what protein does lacZ encode

B-galactosidase (B-gal)

what protein does lacY encode

permease

what protein does lacA encode

transacetylase

what does an effector molecule bind to

regulatory protein

what can a regulatory protein act as

activator or repressor

environmental cue —- effector—— regulatory protein —— ??

activator or repressor activity that regulates gene expression

in positive gene regulation, what does binding do?

binding promotes transcriptioni

in positive regulation what regulatory protein is used

an activator

what does an activator do to transcription

promotes transcription

what does binding in negative gene regulation do

binding prevents transcription

what regulatory protein is used in negative regulation

repressor

what does a repressor do in negative transcription

prevents transcription

how many binding sites do regulatory proteins have

two

what are the two binding sites on a regulatory protein

one for DNA and one for an effector binding

what happens when an effector binds to a regulatory protein

it changes the shape of the protein

in positive regulation, what happens when the effector binds to the protein

activator changes shape and is no longer bound to DNA

in negative regulation, what happens when an effector binds to a repressor

The repressor changes shape and is no longer bound to DNA

what are cis acting elements

DNA sequences that affect only genes in the same operon

what are examples of cis acting elements

promoter and operator

what are trans-acting factors

proteins that diffuse and affect genes anywhere in the cell

are regulatory proteins usually cis or trans-acting

trans-acting

where can genes encoding activators and repressors be located relating to the operon they regulate

anywhere in the genome; dont have to be near the operon

why can trans-acting factors regulate genes elsewhere in the cell

because proteins diffuse through the cytosol w

what are 2 examples of trans-acting proteins

activators and repressors

what is lacI

the regulator gene that encodes the lacI repressor

what protein is produced by lacI

the lacI repressor

what are the structural genes of the lac operon

lacZ, lacY, and lacA

what makes up the lac operon’s regulatory region

the pIac (promoter) and O (operator)

what type of regulation is the lac operon a classic example of

negative regulation

where is the lacI located relative to the lac operon

it is separate from the lac operon’s regulatory region and structural genes

do regulatory protein genes need to be next to the operon they regulate

no they do not

what does permease do relating to lactose

allows lactose to enter the cell

what enzyme acts on lactose inside of the cell

B-galactosidase

what sugar are produced when lactose is broken down

glucose and galactose

where do glucose and galactose go after lactose breakdown

glycolytic pathway

what lactose-derived molecule is the inducer in the lac operon

allolactose

what is the role of allolactose

induction of the lac operon

what happens to the lac operon when there is no lactose present

the lac operon is repressed and no transcription occurs

where does the lacI repressor bind when lactose is absent

operator

how does lacI prevent transcription when lactose is absent

lacI binds the operator, preventing RNA pol from associating

why is lacZYA not transcribed when lactose is absent

The repressor binds to the operator, which keeps the lac operon turned OFF

what happens to the lac operon when lactose is present

it is induced

how does lactose lead to induction of the lac operon

lactose enters cell and allolactose is produced which induces the operon

when allolactose binds to the lacI repressor what happens

lacI is released from operator

what happens after lacI leaves the operator

RNA pol. can transcribe the lacZYA

how does allolactose lead to lacZYA transcription

it binds lacI, causing it to leave the operator so transcription can occur

what is produced when lacZYA is transcribed

one polycistronic mRNA

what is the effector molecule for the lacI repressor

allolactose

what 2 binding sites does the lacI repressor have

the DNA binding site and the allolactose binding site

How does allolactose change the lacI repressor

it changes the lacI’s shape, which alters its ability to bind to the operator

is molecule binding permanent of reversible

reversible

why is molecule binding reversible

molecules bind and unbind dynamically

what is basal transcription

a low background level of transcription

why can basal transcription of the lac operon occur

lacI sometimes temporarily unbinds from the regulatory region

how do lacI and RNA pol interact with the lac regulatory region

dynamically; they unbind and bind

how much can induction of lacZYA transcription increase protein levels

1,000 fold

how do induced lacZYA protein levels compare with basal levels

they are 1000x higher

what happens to lacZYA protein levels after induction

they increase dramatically after a lag and reach about 1000x the basal level