BIOL 300 Final

4.1

4.1

Gene regulation can occur at any of the several stage. The focus of this section is :

Transcriptional regulation

EUK V. PROK IN GENE REGULATION

EUK:

MULTIPLE LEVELS

TRANSCRIPTIONAL REGULATION IS LONG TERM BUT SLOW, TAKES TIME

EUK MRNAS ARE STABLE

Mostly Activators

*DEFAULT STATE IS INHIBITED

PROK:

LIMITED NEED FOR REGULATION TO ACHIEVE ITS CELL TYPES, TISSUES AND STAGES

FOCUSES ON TRANSCRIPTION REGULATION

PROK MRNA IS UNSTABLE

Most repressors

*DEFAULT STATE IS ACTIVATED

GENES MAY BE REGULATED OR UNREGULATED. UNREGULATED IS ____

CONSTITUTVE AT BASAL LEVEL, MEANING THEY ARE ALWAYS ON AND EXPRESSED

GENES MAY BE REGULATED OR UNREGULATED. REGULATED IS ____

VARIES TO RESPOND TO ENVIRONMENTAL CONDITIONS, CELLS DON'T ALWAYS NEED TO BE EXPRESSED

IMPORTANCE OF GENE REGULATION HERE:

METABOLISM

RESPONSE TO ENVIRONMENTAL STRESS

CELL DIVISION

IN BACTERIA, GENE EXPRESSION IS REGULATED AT LEVEL OF INITIATION OF TRANSCRIPTION. WILL GENE EXPRESSION BE INCREASED OR DECREASED?

INC OR DEC

BIND TO REGULATORY SEQUENCES AND PROMOTE OR INHIBIT TRANSCRIPTION (not specific)

REGULATORY PROTEINS / REGULATORY TRANSCRIPTION FACTORS

BINDS TO DNA AND INHIBITS TRASNCRIPTION

NEGATIVE CONTROL

REPRESSOR

BINDS TO DNA AND INCREASES TRANSCRIPTION

POSITIVE CONTROL

ACTIVATOR

EFFECTOR MOLECULES ARE DIFFERENT THAN THESE IN THAT THEY

BIND TO REGULATORY PROTEINS ACTIVATORS OR REPRESSORS, NOT DIRECTLY TO DNA

CAUSES CONFORMATIONAL CHANGE, WHICH AFFECTS THEIR ABILITY TO BIND TO DNA

EFFECTOR MOLECULE #1

INC TRANSCRIPT

BIND ACTIVATOR OR REPRESSORS AND CAUSE AND PREVENT BINDING TO DNA

INDUCIBLE GENES

INDUCER

EFFECTOR MOLECULE #2

INIHIBIT TRANSCRIPT

BIND REPRESSORS AND ACTIVATORS AND CAUSE AND PREVENT BINDING DNA

REPRESSIBLE

INHIBITOR

NO INDUCER:

INDUCER:

REPRESSOR PROTEIN BLOCKS TRANSCRIPT

BINDS TO REPRESSOR, CAUSES CONFORMATIONAL CHANGE THAT PREVENTS REPRESSOR PROTEIN FROM BINDING TO DNA AND TRANSCRIPT PROCEEDS

NO INDUCER:

INDUCER:

ACTIVATOR PROTEIN CANNOT BIND AND NO TRANSCRIPT PROCEEDS

BINDS TO ACTIVATOR, CAUSES CC, ALLOWS BINDING AND TRANSCRIPTION PROCEEDS

NO COREPRESSOR:

COREPRESSOR:

REPRESSOR PROTEIN WILL NOT BIND AND TRANSCRIPTION PROCEEDS

COREPRESSOR BOUND TO REPRESSOR, CONF CHANGE ALLOWS REPRESSOR TO BIND AND TRANSCRIPT INHIBITED

NO EFFECTOR:

INHIBITOR:

ACTIVATOR PROTEIN WILL BIND AND TRANSCRIPTION PROCEEDS

BINDS TO ACTIVATOR, CAUSES CONFORMATIONL CHANGES THAT INHIBITS ACTIVATOR FROM BINDING TO DNA AND TRANSCRIPT INHIBITED

CLUSTER OF STRUCTURAL GENES UNDER SHARED PROMOTER AND TERMINATOR

ENSURES GENES ARE TRANSCRIBED TOGETHER

ENCODES POLYCISTRONIC MRNA

SEPARATE START AND STOP CODONS

*COMMON IN BACTERIA

OPERON

WHEN AN OPERON IS INDUCIBLE

TURNED ON BY SMALL MOLECULE

WHEN AN OPERON IS REPRESSIBLE:

ON BY DEFAULT, TURNED OFF BY SMALL MOLECULE

THE SIGNIFIGANCE OF ECOLI AND LAC OPERON SHOWS HOW BACTERIA CAN TURN GENES OFF AND ON TO ADAPT TO THEIR ENVIRONMENT. ITS A CONTROL SWITCH. GLUCOSE IS ________ LACTOSE FOR ENERGY

PREFERRED OVER LACTOSE. WHEN GLUCOSE IS ABSENT, BACTERIA SWITCH TO USING LACTOSE

THE LAC OPERON ENCODES PROTEINS INVOLVED IN UPTAKE AND METABOLISM OF A PARTICULAR SUGAR, LACTOSE. WHAT ARE ITS TWO TRANSCRIPTION UNITS

LAC OPERON

LACI GENE

WHAT ARE ITS DNA ELEMENTS

PROMOTER: BINDS RNA POLYMERASE

OPERATOR SITE: BINDS LAC REPRESSOR PROTEIN

CAP SITE BINDS CAP PROTEIN, WHICH RECOGNIZES DNA SEQUENCE (When lactose is present)

STRUCTURAL GENES:

ENCODES B GALACTOSIDASES

CLEAVES LACTOSE AND LACTOSE ANALOGS INTO GLUCOSE AND GLACTOSE

CONVERTS TO ALLOLACTOSE

LAC Z

STRUCTURAL GENES:

ENCODES LACTOSE PERMEASE

MEMBRANE PROTEIN REQUIRED FOR TRANSPORTING LACTOSE AND ANALOGS

LAC Y

STRUCTURAL GENES:

ENCODES GALACTOSIDE TRANSACETYLASE

LAC A

GENE THATS NOT APART OF THE LAC OPERON AND HAS ITS OWN I PROMOTER

EXPRESSED AT LOW LEVELS

*ENCODES LAC REPRESSOR

FUNCTIONS AS A TETRAMER

ONLY A SMALL AMOUNT OF PROTEIN IS NEEDED TO REPRESS THE LAC OPERON

LAC I

LAC OPERON DETAILS

CAN BE TRANSCRIPTIONALLY REGULATED

USED WHEN NEEDED, NORMALLY OFF

PRODUCTS ALLOW CELLS TO TAKE UP AND METABOLIZES B-GALACTOSIDE SUGARS LIKE LACTOSE

ACTIVATORS AND REPRESSORS HELP REGULATE

REGULATED BY INDUCIBLE, NEGATIVE, CONTROL MECHANISIM CALLED THE LAC REPRESSOR

ALLOLACTOSE IS AN INDUCER

WHAT IS THE INDUCER? EXPLAIN PROCEESS

ALLOLACTOSE

IF PRESENT, BINDS TO LAC REPRESSOR AND INACTIVATES

IF ABSENT, REPRESSOR PROTEIN REMAINS TIGHTLY BOUNDS TO OPERATOR SITE

IN THIS INSTANCE, THE LAC REPRESSOR REMAINS BOUND TO OPERATORT WITHOUT ANY LACTOSE GOING IN ENVIRONMENT

WHEN THERE IS NO LACTOSE, THERE IS NO

ALLOLACTOSE, SO LAC REPRESSOR IS BOUND***

WHEN ALLOLACTOSE IS PRESENTS, IT WILL

BIND TO REPRESSOR AND ALTERS CONFORMATION AND PREVENTS IT BINDING

TRANSCRIPTION PROCEEDSSSS

DESCRIBE THE SECOND WAY LAC OPERON IS TRANSCRIPTIONALLY REGULATED / REGULATED BY AN ACTIVATOR PROTEIN:

CATABOLITES REPRESSION

VIA CYCLIC AMP, CAMP, PRODUCED FROM ATP VIA ADENYLYL CYCLASE

CAMP BINDS TO CAP, ACTIVATING IT

CAMP CAP COMPLEX BINDS TO SITE NEAR LAC PROMOTER AND INCREASES TRANSCRIPTION *

WHEN GLUCOSE IS PRESENT, LAC OPERON IS ______

CELLS USES GLUCOSE _____

WHEN GLUCOSE LEVELS DROP, WHAT INCREASES?

REPRESSES

FIRST

CAMP LEVELS INCREASE

CAP IS A _____

GLUCOSE SENSOR

TRANSCRIPTION ACTIVATED OF LAC OPERON WHEN GLUCOSE IS LOW

WHAT HAPPENS WHEN CELLS ARE EXPOSED TO BOTH LACTOSE AND GLUCOSE

E COLI USES GLUCOSE FIRST, BECAUSE CATABOLITE REPRESSION PREVENTS THE USE OF LACTOSE

WHAT IS IT CALLED WHEN THE TWO SUGARS ARE USED BY BACTERIUM?

DIAUXIC GROWTH

ONLY LACTOSE:

ALLOLACTOSE AND CAMP LEVELS ARE HIGH

ALLOLACTOSE BINDS TO REPRESSOR

CAMP CAP

CAP INTERACTS WITH RNA POLY AND BINDS TO PROMOTER,

*TRANSCRIPTION PROCEEDS

NO LACTOSE OR GLUCOSE

CAMP LEVELS ARE HIGH AND CAP IS BOUND

GLUCOSE CAUSES CAMP LEVELS TO DECREASES

*TRANSCRIPTION IS INIHBITED

BOTH LACTOSE AND GLUCOSE

LACTOSE CAUSES REPRESSOR TO BE INACTIVE

*GLUCOSE CAUSES CAMP LEVELS TO BE LOW, CAMP IS RELEASED FROM CAP,

*SINCE CAP DOES NOT BIND, TRANSCRIPTION OCCURS BUT AT A LOW RATE

ONLY GLUCOSE:

ADENYLYL CYCLASE INHIBITED:

* DECREASE IN LEVELS OF CAMP CAUSES TRANSCRIPTION RATE OF LAC OPERON TO LOWER

3 OPERATOR SITES FOR LAC REPRESSOR

O1: NEXT TO PROMOTER

O2: DOWNSTREAM IN LACZ

O3: UPSTREAM OF PROMOTER

LAC REPRESSOR CAN BIND TO O1/O2 AND O1/O3, BUT NOT O2/O3 TF

TRUE

IF O2 AND O3 ARE MISSIN WITH O1,

REPRESSION IS NOT ACHIEVED

WHAT DOES THIS CREATE STRUCTURALLY?

A LOOP THAT BRINGS THE OPERATOR SITES TOGETHER , VIA REPRESSOR SITES

WHAT DOES A CAMP CAP COMPLEX CREATE STRUCTURALLY?

A BEND IN DNA STRUCTURE

SUMMARY OF FLUCOSE AND LACTOSE:

SLIDE 30 OF LECTURE 4.1

Which of the following is an INCORRECT function associated with a lambda gene?

cI induces the expression of its own.

both cro and cI represses immediate early gene

Q is the antiterminator for late genes.

N is the antierminator for delayed early genes.

cII binds to PRM (Promoter Right Maintenance)

cII binds to PRM (Promoter Right Maintenance)

A regulatory circuit in which an inactive repressor is produced and requires a corepressor to be activated is said to be:

positive repressible

negative repressible

constitutive

positive inducible

negative inducible

negative repressible

The binding of ______to lac repressor causes lac repressor to ______ to the operator site, thereby ______ transcription.

glucose; not bind; increasing

glucose; bind; inhibiting

allolactose; bind; inhibiting

allolactose; not bind; increasing

allolactose; not bind; increasing

What is the common feature of trp operon and a phage operon that use antiterminators?

Both involve an alternative terminator.

Both response to tRNA levels.

Both rely on coupled translation for the termination.

Both encode antiterminator protein.

Both involve an alternative terminator.

Mutated repressor that cannot bind to the inducer can lead to:

no change in the operon expression pattern

constitutive activation of the operon

constitutive repression of the operon

constitutive repression of the operon

Wrong function for cII?

inhibiting the translation of cro

promoting the expression of cI by generating a highly efficient 5'UTR

inhibiting the transcription of cro through PRE

promoting the transcription of cI from PRE

inhibiting the transcription of cro through PRE

When ribosome is halted at the trp codons,

2 and 3 anneal, attenuator doesn't form

1 and 2 anneal, attenuator forms

2 and 3 anneal, attenuator form

1 and 2 anneal, attenuator doesn't form

2 and 3 anneal, attenuator doesn't form

The next 5 questions are from the 4.2 quiz.

...

What is the function of the Lambda cro protein?

promotes the lytic pathway

RNAse inhibitor

promotes site-specific recombination

respressor of cI

activator cI

respressor of cI

What is the function of Lambda N protein?

ribonuclease

general activator

transcriptional activator

anti-terminator

promotes the lytic pathway

anti-terminator

Which of the following terms describes a bacteria cell that has a phage incorporated into its chromosome?

prophage

lysogen

lytic

bacteriophage

temperate

lysogen

On the context of the bacteriophage life cycle, induction refers to

packaging of phage DNA into the capsid

integration of phage DNA into the bacterial chromosomes

transcription of early phage genes by the host cell RNA polymerase

the transition from the lysogenic to the lytic state

the lysis of the host cell

the transition from the lysogenic to the lytic state

What is the function of Lambda cIII protein?

promotes induction

anti-terminator

transcriptional activator

protease inhibitor

promotes the lytic pathway

protease inhibitor

LAC OPERON RESPONSES

ONLY GLUCOSE, REPRESSOR BINDS: TS LOW

GLUCOSE AND LACTOSE, REPRESSOR DOESNT BIND: TS LOW

CAMP, CRP, AND REPRESSOR: TS LOW

CAMP, CRP, LACTOSE, AND NO REPRESSOR: TS HIGH

TRP OPERON FUNCTION

INVOLVED OF BIOSYNTHESIS OF AMINO ACID TRYPTOPHAN

TRP THAT ENCODE ENZYMES IN TRPTOPHAN BIOSYNTHESIS

E, D, C, B, A

TRP THAT ARE INVOLVED IN REGULATION OF TRP OPERON

R AND L

TRPR

ENCODES TRP REPRESSOR PROTEIN, NOT APRT OF TRP OPERON, HAS ITS OWN PROMOTER

TRPL

ENCODES A SHORT PEPTIDE CALLED THE LEADER PEPTIDE, PART OF TRP OPERON, ATTENUATION

WHEN TRYPTOPHAN LEVELS ARE LOW, _________ DOES NOT BIND TO THE TRP REPRESSOR PROTEIN. WHAT HAPPENS?

TRYPTOPHAN DOES NOT BIND

PREVENTS REPRESSOR PROTEINS FROM BINDING TO THE OPERATOR SITE

WITH THESE CONDITIONS, RNAP CAN TRANSCRIBE THE OPERON. THIS LEADS TO THE EXPRESSION OF

TRPA-E (WHOLE OPERON TRANSCRIBED)

WHEN TRYPTOPHAN LEVELS ARE HIGH, TRYPTOPHAN ACTS AS A ....., BINDING TO THE TRP REPRESSOR PROTEIN

COREPRESSOR

THIS COMPLEX THEN BINDS TO THE ______ AN D______

OPERATOR SITE, INHIBITS TRANSCRIPTION

ANOTHER MECHANISM OF REGULATION FOR TRP OPERON

ATTENUATION

WHEN THIS OCCURS, THE RNA IS TRANSCRIBED _______ AND THEN ______

TO THE ATTENUATOR SEQUENCE, TRANSCRIPTION TERMINATED

DETAILS ABOUT THE ATTENUATOR

SEGMENT OF DNA

AT THE TRP OPERON, TRANSCRIPTION TERMINATES SHORTLY PAST THE TRPL REGION

TRPTOPHAN PRODUCTION INHIBITED

DETAILS ABOUT ATTENUATION

SEGMENT OF TRP DOWNSTREAM FROM OPERATOR SITE PLAYS A ROLE IN ATTENUATION

SHORT PIECE OF MRNA THAT TERMINATES ATTENUATOR

FIRST GENE AFTER THE OPERON IS

TRPL

WHICH HAS AN ATTENUATOR AND ENCODES SHORT PEPTIDE: LEADER PEPTIDE

HOW MANY TRYPTOPHAN CODONS ARE WITHIN THE MRNA FROM THE TRPL GENE? WHAT DOES IT DO

TWO TRYPTOPHAN CODONS. A WAY FOR BACTERIA TO SENSE TRYPTOHAN LEVELS

MRNA FROM TRPL HAS ____ REGIONS THAT ARE COMPLEMENTARY TO EACHOTHER

FOUR

CAUSES MRNA TO FORM STEM LOOPS, 1-2, 2-3, 3-4

*3-4 IS UNIQUE, COMBINES WITH URICH ATTENUATOR, RHO DEPENDENT TERMINATION , RNAP PAUSES AND URICH DISSOCIITES

SCENARIO 1: TRANSCRIPTION IS NOT COUPLED WITH TRANSLATION

REGION 1 HYDROGEN BONDS TO REGION 2

REGION 3 HYDROGEN BONDS TO REGION 4

TRANSCRIPTION TERMINATION BECAUSE OF 3-4, AT U RICH ATTENUATOR, RNAP FALLS OFF

SCENARIO 2: TRANSLATION IS COUPLED WITH TRANSCRIPTION AND LEVELS OF TRYPTOPHAN ARE LOW

RIBOSOMES PAUSES AT THE TRP CODONS IN THE TRPL GENE BECAUSE INSUFFICIENT TRNA-TRP

PAUSE BLOCKS REGION 1 OF MRNA SO REGION 2 CAN HYDROGEN BOND WITH ONLY REGION 3

3-4 CAN'T FORM

TRANSCRIPTION TERMINATION DOES NOT OCCUR AND RNAP TRANSCRIBES REST OF OPERON

SCENARIO 3: TRANSLATION IS COUPLE WITH TRANSCRIPTION AND LEVELS OF TRPTOPHAN ARE HIGH

TRANSLATION OF TRPL GENE PROGRESSES TO STOP CODON, RIBOSOME PAUSES

BLOCKS REGION 3, ENABLES REGION 3 TO BOND WITH REGION 4

TERMINATES TRANSCRIPTION AT U RICH, RNAP DROPS, GENES IN TROP OPERON RE NOT TRANSCRIBED

THIS IS A GOOD THING SINCE THE CELL DOESNT NEED MORE TRPTOPHAN

REPRESSION VS ATTENUATION

-BOTH REGULATE AMOUNT OF TRYPTOHAN,

-BOTH REGULATED BY TRYPTOPHAN LEVELS

ATTENUATION IS MORE FINELY TUNED AND REGULATED BY AVAILABILITY OF CHARGED TRYPTOPHAN TRNA

TRYPTOPHAN HIGH

RIBOSOME MOVES QUICKLY, TERMINATOR HAIRPIN FORMS, TRANSCRIPTION OF TRP OPERON ENDS

TRPYTOHAN LOW

RIBOSOME MOVES SLOWLY, NON TERMINATOR HAIRPINS, AND TRANSCRIPTION OF TRP OPERON CONTINUES

INDUCIBLE VS REPRESSIBLE REGULATION

OPERONS IN CATABOLISM/BREAKDOWN ARE INDUCIBLE

OPERONS IN ANABOLISM/BIOSYNTEHSIS ARE REPRESSIBLE

4.2

4.2

KNOW 3 QUALITIES OF VIRUSES

NONLIVING IN NUCLEIC ACID GENOMES

CANNOT REPLICATE ON THEIR OWN

INFECT LIVING HOSTL CELLS TO PROLIFERATE

VARY WITH STRUCTURE AND ABILITY TO INFECT

VIRUS CONSISTS OF A

GENOME+PROTEIN COAT

NO CELL STRUCTURE

NO REPLICATION AND METABOLISM

VIRUS REGULATION

ABOUT HOW VIRUSES HOST CELL REGULATION SYSTEM

VIRUS TROPISMS:

ARE FOR ENTRY INTO CELL, REQUIRE INTERACTION OF VIRUS PROTEINS AND CELL SURFACE PROTEIN

THIS MAKES VIRUS TROPISM LIMITED TF

TRUE, ONLY INFECT WITH CERTAIN RECEPTORS, CERTAIN CELL TYPES AND CERTAIN SPECIES

HOW CAN VIRUSES EVOLVE

1. BETWEEN CLOSELY RELATED SPECIES, HOMOLOHS

2. VIRUSES MUTATE TO ADAPT TO NEW HOST

THREE WAYS VIRUSES DIFFER

1. HOST RANGE: CELL AND RANGE

2. STRUCTURE: NUCLEIC ACID GENOME DNA OR RNA, PROTEIN CAPSID, ENVELOPE

3. GENOME COMPOSITION: DNA OR RNA, SINGLE OR DOUBLE STRANDED, HOW MANY GENES IT CARRIES

NOW ONTO BACTERIOPHAGE, WHAT IS IT

-VIRUSES THAT INFECT BACTERIA

-DIFFERENT SPECIES HAVE THEIR OWN PHAGES

-SSDNA, DSDNA, SSRNA, DSRNA GENOMES

-MODEL FOR EUKARYOTIC VIRUSES IS SIMILAR

-USEFUL FOR DRUG RESISTANT BACTERIAL STRAINS

-CONTROL BACTERIAL POPULATIONS IN NATURES

VIRAL REPLICATION

ATTACHMENT: TO SURFACE

ENTRY: VIRAL GENOME ENTERS

SYNTHESIS OF VIRAL COMPONENTS: VIRAL PROTEINS AND DNA ARE MADE BY HOST CELL

VIRAL ASSEMBLY: VIRAL COMPONENTS ASSEMBLE INTO VIRUS PARTICLES

RELEASE: VIRUS RELEASED FROM HOST CELL

PHAGE LIFE CYCLE 1:

REPLICATE GENOME AND PROTEIN COAT WITHIN SAME HOST CELL

VIRUS ASSEMBLE INTO WHOLE VIRUS PARTICLES

NEWLY PRODUCED WHOLE VIRUS PARTICLES ARE RELEASED AS HOST CELL UNDERGOES LYSIS

LYTIC CYCLE

PHAGE LIFE CYCLE 2:

VIRUS GENOME IS INTEGRATED INTO HOST GENOME AS PROPHAGE

INTERGRATED VIRUS GENOME PROLIFERATES TOGETHER WITH THE HOST CELL GENOME

NO PRODUCTION OF VIRUS PROTEIN SHELLS OR WHOLE PARTICLES

CAN TRANSITION TO LYTIC

LYSOGENIC CYCLE

E. COLI CARRIES A BACTEROPHAGE CALLED _____. KNOW ITS DETAILS

LAMBDA

QUIESCENT, LAMBDA GENOME CAN BE ACTIVATED TO GENERATE FREE PHAGE PARTICLES

THROUGH TWO LIFE CYCLES

LYSOGENY: INTEGRATED WITHIN BACTERAIL HOST GENOME AND REPLICATES PASSIVELY ALONG W IT. VIRAL DNA IS INCOROPORATED AS A HOST CHROMOSOME

LYTIC PATHWAY: GENOME REPLICATES FREE FROM BACTERIAL GENOME (DIRECTS PRODUCTION OF PHAGE CAPSID PROTEINS, AND KILLS HOST TO RELEASE NEW PHAGE PARTICLE). NEW VIRUS PARTICLES ARE MADE

TWO TYPES OF PHAGES

1. VIRULENT

2. TEMPERATE

PHAGE THAT UNDERGOES LYTIC CYCLE

VIRULENT

PHAGE THAT CAN SWITCH BETWEEN BOTH CYCLES

TEMPERATE

WHAT CONDITIONS FAVORS LYSOGENIC

STARVATION