Chapter 16 Regulation Of Gene Expression

Front 1

Where does expression first begin on the DNA molecule?

Back 1

At the promoter. This is where RNA polymerase binds and begins transcription.

Front 2

There are two types of regulatory proteins. What are they?

Back 2

Repressor proteins and activator proteins. These proteins basically "decide" which genes get turned off or on

Front 3

What exaclty is negative regulation?

Back 3

When a given gene that is normally transcribed has a speacil repressor protein bind to the "repressor binding site" - this will STOP the transcription from continuing

Front 4

What exaclty is positive regulation?

Back 4

When a given gene that is normally NOT transcribed has a speacil activator protein bind to the "activator binding site" - this will STIMULATE transcription

Front 5

Viruses are cells. T or F?

Back 5

False: they are acellular particles (these particles are called virions)

Front 6

Generally, what is a virus made up of?

Back 6

Nucleic acid and a few proteins

Front 7

Viruses use ______ cells to carry out metabolic functions while they reproduce.

Back 7

host

Front 8

What is bacteriophage?

Back 8

Viruses that infect bacteria

Front 9

Bacteriophages undergo different types of cylces. Name these cycles

Back 9

Lytic cycle and lysogenic cycle

Front 10

Phage takes over their host cell by taking over synthesis. What do they inject into the host cell?

Back 10

Their DNA

Front 11

What does the word "lyse" mean?

Back 11

Burst (explode): This is what happens to the host cell in the lytic cycle

Front 12

There are two stages in the lytic cycle or a virus. What are they?

Back 12

Early stage and late stage

Front 13

Explain exactly what is happneing in the lytic stage.

Back 13

1. A virus infects a host cell and injects its DNA into it.
2. The host's own RNA polymerase binds to the virus' DNA at the promoter site.
3. The viral genes are transcribed
4. Three proteins are made: one shuts down the host's gene transcription, the second stimulates viral replication and the third assists in the "late stage" of the cycle
5. Viral enzymes digest (kill) the host's chromosomes which provide nucleotides for further synthesis.

Front 14

Explain exaclty what is happening in the late lytic stage.

Back 14

1. The third protein from the early cycle begins to stimulate viral gene transcription
2. These genes encode the capsid (virus head) and speacil enzymes that aid in "exploding" the cell
3. The host cell eventually explodes, releasing all of the new virons

Front 15

How long does the lytic cycle take (in minutes) from beginning to end?

Back 15

30 minutes

Front 16

This is a diagram of both the early and late stages of the lytic cycle.

Back 16

Study diagram

Front 17

It is possible for bacteriophage (virus) to carry bacterial genes from one host to another. T or F?

Back 17

True (this is a rare event!)

Front 18

Where does bacteriophage package their own DNA?

Back 18

In their capsid (the head)

Front 19

If a bacteriophage has some of it's hosts' DNA in its own capsid and then attempts to inject this DNA into a new host, what will happen? What is this called?

Back 19

1. The infection WILL NOT produce new viruses because virus replication is not possible if the virus is "shooting up" the bacteria with bacterial DNA. This DNA will recombine with the host's chromosome and the host will SURVIVE.
2. This is called tranduction (this scenario is RARE)

Front 20

Explain in detail the lysogenic cycle.

Back 20

1. Lysogeny postpones the lytic cyle for the sole purpose of replicating "silently" until the time is "just right" to perform the lytic cycle
2. The virus injects its DNA into the host
3. This DNA integrates itself into the host's chomosomes becoming a PROPHAGE
4. The host cell divides - the viral DNA is replicated

Front 21

Explain what takes place when (and why) a host cell transitions from the lysogenic cycle to the lytic cycle.

Back 21

1. If the lysogenic cycle cell is not growing well, it "cuts its loses" and enters the lytic cycle
2. If growing rapidly, the regulatory protein "cl" attaches to a special promoter that REPRESSES the lytic cycle (and will therefore remain in the lysogenic cycle)
3. However, if the cell is not growing rapidly, the protein "Cro" attaches to a different promoter which ACTIVATES the lytic cycle
4. This process is litteraly a "switch": if one promoter is activated, then the other is turned off.

Front 22

Eukaryotic cells are susceptible to three different types of viruses. What are they?

Back 22

1. DNA viruses
2. RNA viruses
3. Retroviruses

Front 23

Explain the characteristics of a eukaryotic DNA virus? Give an example.

Back 23

Some viruses contain single-stranded DNA. The "other" strand is made after infection takes place
Example: herpes

Front 24

Explain the characteristics of a eukaryotic RNA virus? Give an example.

Back 24

1. Some virus genomes are made up of a single stranded RNA
2. This strand is translated by the host and produces viral proteins
Example: influenza

Front 25

Explain characteristics of retroviruses? Give and example.

Back 25

1. The viruse's genome is RNA (instead of DNA)
2. This RNA encodes a protein that makes a complimentary strand of DNA
3. This DNA integrates with the host chromosome
4. The new viral DNA (through transcription) creates more viruses
Example: HIV

Front 26

HIV is an enveloped virus. What does this mean?

Back 26

It is enclosed within a phospholipid membrane which originated from the virus's last host cell

Front 27

What is a distinctive feature of the retrovirus (HIV) life cycle?

Back 27

Reverse transcriptase: basically this is the revers of the central dogma - RNA to DNA synthesis

Front 28

What is one way in which prokaryotes conserve energy?

Back 28

By making protiens only when they need them. This is what gene regulation is all about ! - turning on and off the making of proteins

Front 29

Name all of the ways a prokaryote can "shut off" the making of a protien (there are 5 answers).

Back 29

1. Lower the amount of mRNA created
2. Hydrolyze the mRNA - making it useless
3. Preven the translation that takes place at the ribosome
4. Hydrolyze the protein after its made - making it useless
5. Inhibit the function of the protein

Front 30

What exactly is a prokaryotic operon?

Back 30

1. It is a cluster of genes with a SINGLE promoter.
2. In our example of E.coli, there are 3 protiens involved in the metabolism of lactose (therefore it is called the lac operon)
3. Because they share the same promoter, either NONE or ALL enzymes will be made at the same exact time !!

Front 31

A typical prokaryotic operon will consist of what three things?

Back 31

1. A single promoter
2. Two or more structural genes (these are genes that collectively encode for a particular protein(s)
3. An operator (a stretch of DNA on which a regulatory protien binds in order to activate or repress transcription

Front 32

The transcription of prokaryotic operons can be controled three ways. What is one of these ways?

Back 32

1. DNA codes a repressor protien (i)
2. This repressor attaches to the operator (o)
4. Due to the repressor, normal RNA polymerase CANNOT bind
5. Transcription is blocked and NO enzymes (z,y,a) are made
NOTE: This is an example of "negative control"

Front 33

The transcription of prokaryotic operons can be controled three ways. What is a second way?

Back 33

1. An inducer molecule binds to the repressor protein
2. This makes it impossible for repressor to bind to the operator (o)
3. RNA polymerase binds to the promotoer (p)
4. RNA can then transcribe the structural genes (z,y,a)

Front 34

The transcription of prokaryotic operons can be controled three ways. What is a third way?

Back 34

Through activator protiens. The binding of an activator protien results in a more efficient binding of RNA polymerase to the promter - which causes increased transcription

Front 35

Eukaryotic gene expression can only be occur during transcription. T or F?

Back 35

False: it can occur duing both transcription and/or translation

Front 36

What is the purpose of eukaryotic gene expression?

Back 36

To regulate the proper timing and location of protien production

Front 37

What are the 8 different ways genes can be regulated in eukaryotic cells?

Back 37

1. Remodeling of chromatin
2. Transcriptional control
3. Processing control
4. Transport control
5. mRNA stability control
6. Translational control
7. Post-translational control
8. Protien dgradation

Front 38

Explain what TF's, TFIID and TATA are in eukaryotes.

Back 38

1. There are two important sequences on a promoter
2. One of these is the TATA box (a sequence of A and T nucleotides)
3. RNA polymerase CANNOT just simply bind to this promoter
4. A transcription factor (TF) must FIRST assemble onto the chromosome
5. The first TF to bind on the promoter is the protein TFIID
6. After, several other smaller TFs bind to TFIID
7. Then finally, the RNA polymerase binds to TFIID

Front 39

What are the two important sequences on a eukaryotic promoter?

Back 39

1. Recognition sequence (recognized by RNA)
2. TATA box (where DNA begins to denature and expose the template strand

Front 40

What are two examples of regulatory protiens in eukaryotic DNA?

Back 40

1. Positive regulators: aka enchancers which bind activator proteins
2. Negative regulators: silencers that bind repressor proteins

Front 41

What is this picture describing?

Back 41

The DNA is bending to bring the activator protein (pink) which is bound to the enhancer (pink DNA) into contact with the transcription complex. By this process, transcription is regulated

Front 42

Proteins do not just "randomly" bind to DNA. Protien domains bind to DNA in a special way called structural motifs. There are 4 of them. What are they?

Back 42

1. Helix-turn-helix
2. Leucine zipper
3. Zinc finger
4. Heliz-loop-heliz

Front 43

What structural motif is being shown here?

Back 43

Helix-turn-helix motif

Front 44

What structural motif is being shown here?

Back 44

Leucine zipper motif

Front 45

What sturctural motif is being shown here?

Back 45

Helix-loop-helix motif

Front 46

What structural motif is being shown here?

Back 46

Zinc finger motif

Front 47

What are three characteristics of epigenetics

Back 47

1. Changes in the expression of a gene(s) WITHOUT change in the DNA sequence
2. Heritable, stable and reversible
3. Include DNA methylation and chromosomal protein alterations

Front 48

Cytosine can be chemically modified by adding a methyl group: -CH3. What is this called?

Back 48

Methylation

Front 49

What does maintenance methylase do?

Back 49

After DNA replicates, maintenance methylase catalyzes methylation on the new strand (so both strands now have a CH3 group)

Front 50

By what process can the methyl group be REMOVED from the replicated DNA strands?

Back 50

Demethylation

Front 51

What is the effect of methylation on DNA?

Back 51

It generally REPRESSES gene transcription - thus, these genes tend to be inactive (or silenced)

Front 52

What are some environmental factors that lead to epigenetic changes?

Back 52

1. Stress - heavly methylated genes
2. Addiction (i.e. alchohol)

Front 53

What is genomic imprinting?

Back 53

When offspring inherit an inactive (methylated) copy of a gene from mom and an active (demethylated) copy of a gene from dad

Front 54

What is alternative splicing?

Back 54

1. A form of gene expression in eukaryotes AFTER transcription
2. When exons (which are NOT normally cut out) are cut out along with the introns thereby creating a completely DIFFERENT protein.
3. One gene can therefore create MANY different kinds of proteins by "cutting" it up in different ways

Front 55

Only 5 percent of the genome encodes proteins. The remaining non-coding regions can also be transcribed. What are these called?

Back 55

MicroRNAs (miRNAs)
These are TINY RNA molecules

Front 56

What are characteristics of microRNA's

Back 56

1. Only 22 bases long
2. Normal RNA folds onto itself and is cut up.
3. These cut up pieces are cleaved to form mircoRNA
4. MicroRNA targets mRNA and degrades it (breaks it down).

Front 57

Generally, what ways can translation be regulated?

Back 57

1. Either it is blocked completely or..
2. The produced protein is somehow altered

Front 58

Is there a relationship between the amount (concentration) of protien and mRNA in a cell? Why?

Back 58

Not really. Sometimes there can be LOTS of mRNA, but LITTLE to NO protein...and vice versa.
Reason: Concentrations are determined by factors acting after the mRNA is made

Front 59

Specifically, what ways can translation be regulated

Back 59

1. miRNA's inhibit translation
2. GTP cap is modified - if unmodified the no translation
3. Repressor protiens block translation directly

Front 60

A break down illustration of transcription in prokaryotes and eukaryotes

Back 60

See illustration