Cell Biology For Bme: Chapters 8 - Gene Expression

Front 1

What is Gene Expression?

Back 1

Process where a gene makes its effect on a cell or organism by directing the synthesis of proteins or RNA with characteristic activity.

Front 2

How is Cell Differentiation achieved?

Back 2

Changes in gene expression!

Front 3

In the pancreas, Beta and Alpha cells produce what, respectively?

Back 3

Beta --> insulin
Alpha --> glucagon

Front 4

What are Lymphocytes?

Back 4

White blood cells that are the only type of cells that produce antibodies

Front 5

What are Red Blood Cells?

Back 5

Cells that are solely responsible for producing O-transport protein Hemoglobin (which are made in reticulocytes)

Front 6

How can the extent of gene expression be gauged?

Back 6

By comparing protein composition using 2D gel electrophoresis

Front 7

TRUE OR FALSE: Most proteins are NOT common to all cell types. These are called housekeeping proteins.

Back 7

FALSE. Most proteins ARE common to all cell types and are called housekeeping proteins.

Front 8

What types of proteins are included in the Housekeeping Proteins?

Back 8

Structural proteins of chromosomes, RNA pols, DNA repair enzymes, ribosomal proteins, enzymes in glycolysis, metabolic process proteins, and cytoskeleton proteins

Front 9

What is Mass Spectrometry used for?

Back 9

It is used to detect rare proteins produced by certain cells and whether these proteins are covalently modified (like phosphorylation)

Front 10

Gene Expression can also be studied through monitoring what?

Back 10

the mRNAs!

Front 11

A typical human differentiated cell expresses how many genes out of how big a genome?

Back 11

Typically expresses 5000-15000 genes out of 25000 genes in the genome.

Front 12

What are Enhancers?

Back 12

DNA sites to which eucaryotic gene activators bind

Front 13

TRUE OR FALSE: Activator proteins enhance transcription even though they can be 1000 nucleotide base pairs away from the gene's promoter.

Back 13

TRUE!

Front 14

Do activator proteins work even when bound upstream or downstream from the gene?

Back 14

YES~!

Front 15

What is a Mediator?

Back 15

A protein complex that serves to link the distantly bound transcription regulators to the proteins at the promoter.

Front 16

What do Eucaryotic Repressor Proteins do?

Back 16

They decrease transcription by preventing or sabotaging the assembly of the same protein complex.

Front 17

In addition to promoting, or repressing the assembly of a transcription initiation complex, eucaryotic transcription regulators have what other mechanism of action?

Back 17

They attract proteins that modulate chromatin structure and thereby affect the accessibility of the promoter to the general transcription factors and RNA pol.

Front 18

Nucleosomes can inhibit the initiation of transcription if they are positioned over what?

Back 18

A promoter!

Front 19

Chromatin packaging may have evolved in part to prevent what?

Back 19

Leaky gene expression or the initiation of transcription in the absence of the proper activator proteins

Front 20

Many transcription activators attract histone acetylases which do what?

Back 20

Attach an acetyl group to selected lysines in the tail of histone proteins which alters chromatin structure allowing greater accessibility to the underlying DNA

Front 21

Many repressors attract histone deacetylases that do what?

Back 21

Enzymes that remove the acetyl groups from histone tails thereby reversing the positive effects that acetylation has on transcription initiation.

Front 22

What is a prerequisite for the creation of organized tissues and for the maintenance of stably differentiated cell types?

Back 22

Cell memory - cells ability to remember the changes in gene expression triggered by a transient signal

Front 23

What is Combinatorial Control?

Back 23

The way groups of regulatory proteins work together to determine the expression of a single gene.

Front 24

What is one way in which bacteria coordinate the expression of a set of genes?

Back 24

Having the genes clustered together in an operon under the control of a single promoter.

Front 25

How do eucaryotes coordinate gene expression, rather, how can it rapidly and decisively switch whole groups of genes on or off?

Back 25

While gene expression is combinatorial, the effect of a single transcription regulator can still be decisive in switching any particular gene on or off simply by completing the combination needed to activate or repress that gene.

Front 26

TRUE OR FALSE: As long as different genes contain DNA sequences recognized by the same transcription regulator, they can be switched on or off together, as a unit.

Back 26

TRUE!

Front 27

In order to bind to regulatory sites in DNA, glucocorticoid receptor protein must first form what?

Back 27

A complex with a molecule of glucocorticoid hormone!

Front 28

The ability to switch many different genes on or off using just one protein is not only useful in the day-to-day regulation of cell function but it also is one of the means by which eucaryotic cells do what?

Back 28

Differentiate into particular types of cells during embryonic development

Front 29

A mammalian skeletal muscle cell is formed by the fusion of what?

Back 29

Many muscle precursor cells called myoblasts

Front 30

What is a Reporter Gene?

Back 30

A gene encoding a protein whose activity is easy to monitor experimentally

Front 31

What is one of the simplest ways of ensuring that daughter cells "remember" what kind of cells they are supposed to be?

Back 31

A positive feedback loop!

Front 32

What are 3 ways of maintaining cell type?

Back 32

1. Positive feedback loops
2. faithful propagation of a condensed chromatin structure from parent to daughter cell.
3. DNA methylation

Front 33

What is DNA Methylation?

Back 33

Enzymatic addition of methyl groups to cytosine bases in DNA which generally turns off genes by attracting proteins that block gene expression.

Front 34

DNA methylation patterns are passed on to progeny cells by what?

Back 34

The action of an enzyme that copies the methylation pattern on the parent DNA strand to the daughter DNA strand immediately after replication.

Front 35

The three most common ways of maintaining cell type are considered forms of what?

Back 35

Epigenetic Inheritance

Front 36

What is Ey in flies or Pax-6 in vertebrates?

Back 36

Transcription regulator that is crucial for eye development.

Front 37

Ey can trigger the formation of what?

Back 37

Not just a single cell type but a whole organ-the eye-composed of different types of cells all properly organized in 3D space

Front 38

The action of just one transcription regulator can produce a cascade of regulators whose combined actions lead to what?

Back 38

The formation of an organized group of many different types of cells.

Front 39

What are Post-transcriptional Controls?

Back 39

Controls that operate after RNA polymerase has bound to a gene's promoter and started to synthesize RNA

Front 40

What provides an economical solution to Gene Regulation (think post-transcriptional control)?

Back 40

Riboswitches!

Front 41

What are Riboswitches?

Back 41

Short sequences of RNA that change their conformation when bound to small molecules such as metabolites.

Front 42

Why are Riboswitches the most economical examples of gene control devices?

Back 42

Because they bypass the need for regulatory proteins altogether!

Front 43

Once an mRNA has been synthesized, what is one of the most common ways of regulating how much of its protein product is made?

Back 43

To control the initiation of translation!

Front 44

In bacteria, how can you inhibit or promote the translation of an mRNA?

Back 44

By blocking or exposing the ribosome recognition sequence that is located a few nucleotides upstream of the AUG codon.

Front 45

In eucaryotes, mRNAs possess what that helps guide the ribosome to the first AUG?

Back 45

The 5' cap!

Front 46

In eucaryotic cells, repressors can inhibit translation by doing what?

Back 46

By binding to specific RNA sequences in the 5' untranslated region of the mRNA and keeping the ribosome from finding the first AUG.

Front 47

What are microRNAs?

Back 47

A type of non-coding RNA found in plants and animals that control gene expression by base-pairing with specific mRNAS and controlling their stability and their translation.

Front 48

miRNA is assembled with specialized proteins to form what?

Back 48

RNA-Induced Silencing Complex (RISC)

Front 49

RISC patrols the cytoplasm searching for what?

Back 49

Searching for mRNAS that are complementary to the miRNA where when it finds one, it base pairs with it and is destroyed by a nuclease present within the RISC.

Front 50

Once the RISC has taken care of an mRNA molecule what happens to it?

Back 50

It is released and is free to seek out additional mRNA molecules

Front 51

What two features of miRNA make them especially useful regulators of gene expression?

Back 51

1. a single miRNA can regulate a whole set of different mRNAs so long as the mRNAs carry a common sequence
2. gene that encodes an miRNA occupies relatively little space in the genome compared with one a transcription regulator.

Front 52

Some of the proteins that process and package miRNAs also serve as a cell defense mechanism: what do they do?

Back 52

They orchestrate the destruction of FOREIGN RNA molecules, specifically ones that are double-stranded (viruses, some transposable genetic elements)

Front 53

What is RNA interference?

Back 53

Targeted RNA degradation mechanism that helps to keep potentially dangerous invaders in check.

Front 54

The presence of foreign doublestranded RNA in the cell trigers RNAi by first attracting what?

Back 54

A protein complex containing a nuclease called Dicer

Front 55

The protein complex Dicer does what to double-stranded RNA?

Back 55

Cleaves it into short fragments called small interfering RNAs (siRNAs) which are then incorporated into RISCs

Front 56

RNAi is found in what kind of organisms?

Back 56

All kinds indicating that it is evolutionary ancient.

Front 57

In a practical sense, RNAi has become a powerful experimental tool that allows scientists to do what?

Back 57

Inactivate almost any gene in cultured cells or in some cases a whole plant or animal.

Front 58

What is the Promoter Region?

Back 58

Region that attracts RNA pol and correctly orients it to begin making RNA copy of gene

Front 59

What does the Promoter Region contain?

Back 59

Contains initiation site where transcription actually begins

Front 60

Short regulatory DNA sequences respond to how many signals to turn genes on or off?

Back 60

Usually just 1

Front 61

Long regulatory DNA sequences respond to how many signals to turn genes on or off?

Back 61

Multiple signals

Front 62

TRUE OR FALSE: Regulatory DNA sequences work alone and do not need transcription regulators which bind to DNA.

Back 62

FALSE. Regulatory DNA sequences do NOT work alone and require transcription regulators which bind to DNA.

Front 63

Why do Proteins recognize specific DNA?

Back 63

Because the surface of protein fits tightly against special surface of double helix of the region.

Front 64

Do Transcription Regulators have high or low affinity to strand surface?

Back 64

HIGH affinity to strand surface

Front 65

What kind of bonds do transcription regulators form with the strand surface?

Back 65

H Bonds, Ionic Bonds, as well as hydrophobic interactions

Front 66

Do Transcription Regulators disrupt base-pairing in DNA?

Back 66

NO!

Front 67

How many base-pairs are involved in transcription regulator binding?

Back 67

~20

Front 68

What is one of the tightest, strongest, and most specific interaction known in biology?

Back 68

Protein-DNA interaction!

Front 69

Where are DNA-Binding Motifs found?

Back 69

Found in transcription regulators

Front 70

What are the three main DNA-Binding Motifs?

Back 70

1. Homeodomain
2. Zinc Finger
3. Leucine Zipper

Front 71

What is Homeodomain?

Back 71

DNA-Binding Motif found in eucaryotic DNA-binding proteins consisting of 3 alpha helices.

Front 72

Which alpha helix in homeodomains is the most in contact with the DNA strand?

Back 72

Alpha helix #3!

Front 73

What is Zinc Finger?

Back 73

DNA-Binding Motif found in clusters covalently joined together consisting of an alpha helix, beta sheet, and one zinc molecule.

Front 74

What is a Leucine Zipper?

Back 74

DNA-Binding Motif that binds to DNA as dimers and formed by 2 alpha helices contributed by different proteins.

Front 75

What are Dimers?

Back 75

Pairs

Front 76

What does Dimerization do with DNA?

Back 76

It doubles area of contact with DNA thus increasing strength/specificity of protein-DNA interaction

Front 77

What does Dimerization allow?

Back 77

It allows many different DNA sequences to be recognized by limited #s of proteins due to 2 different protein dimer pairing combinations

Front 78

What is an Operon?

Back 78

Set of genes that are transcribed into a single mRNA.

Front 79

Operons are common in what type of cell?

Back 79

Bacterial cells. NOT EUKARYOTES.

Front 80

What is an Operator?

Back 80

Short DNA sequence recognized by transcription regulator which blocks access of RNA pol to promoter

Front 81

What is a Tryptophan Repressor?

Back 81

Repressor that can only bind to DNA if bound by tryptophan molecules.

Front 82

The tryptophan repressor is what kind of protein?

Back 82

Allosteric protein

Front 83

What does it mean to be allosteric?

Back 83

Binding of another molecule causes slight change in 3D structure of original protein.

Front 84

TRUE OR FALSE: Tryptophan Repressor is only sometimes present in the cell.

Back 84

FALSE. It is ALWAYS present in the cell!

Front 85

If Tryptophan is present, what happens?

Back 85

Tryptophan binds to repressor protein which then binds to DNA and blocks transcription from occurring.

Front 86

What is Unregulated Gene Expression called?

Back 86

Constitutive Gene Expression!

Front 87

The Trp Operon contains how many genes?

Back 87

5

Front 88

What is an Activator Protein?

Back 88

Protein that work on promoters but bind and position RNA pol poorly.

Front 89

In the Lac Operon, the activator protein CAP needs what before it can bind to DNA?

Back 89

CAP needs cyclic AMP (cAMP)

Front 90

The lac operon is controlled by what kind of proteins?

Back 90

Both activators and repressor proteins

Front 91

If both glucose and lactose are present, is the operon on or off? Is CAP bound or not bound?

Back 91

Operon is OFF and CAP is NOT bound.

Front 92

If glucose is present and lactose is not, is the operon on or off? Is CAP bound or not bound?

Back 92

Operon is OFF, Lac repressor is bound but CAP is NOT bound.

Front 93

If both glucose and lactose are not present, is the operon on or off? Is CAP bound or not bound?

Back 93

Operon is OFF. Lac repressor is BOUND.

Front 94

If glucose is not present and Lactose is, is the operon on or off? Is CAP bound or not bound?

Back 94

Operon is ON. CAP is bound.

Front 95

If Guanine is scarce, what happens?

Back 95

Riboswitch will come in and genes for purine biosynthesis are turned ON.

Front 96

If Guanine in plentiful, what happens?

Back 96

Guanine binds to riboswitch, riboswitch changes conformation, and new structure terminates transcription and thus genes for purine biosynthesis are OFF.

Front 97

How many microRNAs are known?

Back 97

400

Front 98

Is RNA interference specific or non-specific?

Back 98

NON-SPECIFIC!