Exam 3 (B302)

What are the 3 general steps of translation?

Initiation, elongation, termination

Protein folding is necessary for proper functioning of most proteins. T/F?

True

All proteins are expressed in all cell types all the time. T/F?

False

Bacterium does what to make the enzymes needed to digest food only when its available?

Express genes selectively

Gene expression is under even more what?

Elaborate control

What is achieved by changes in gene expression?

Cell differentiation

What proteins include structural proteins of chromosomes, RNA polymerases, DNA repair enzymes, ribosomal proteins, enzymes involved in glycolysis and other metabolic processes, and many cytoskeleton forming proteins?

Housekeeping proteins

Each different cell type also produces what that’s responsible for the cell’s distinctive properties?

Specialized proteins

A differentiated human cell expresses perhaps how many genes from a repertoire of about 25,000 total genes?

5k-15k genes

The main site of control is what? (step 1)

Transcriptional control

In addition to promoter, nearly all genes have what that’s used to switch the gene on or off?

Regulatory DNA sequences

Regulatory DNA sequences are recognized by proteins called what to control transcription?

Transcription regulators

A transcription regulator binds to what of a DNA helix?

Major groove

Typical protein-DNA interface would consist of 10-20 contacts each involving what?

A different amino acid and each contributing to strength of protein-DNA interaction

Features vary depending on what?

Nucleotide sequence thus different proteins will recognizee different nucleotide sequences

Protein-DNA interactions are among tightest and most of what interaction?

Specific molecular interaction

Many proteins responsible for gene regulation recognize DNA through several structural what?

Motifs

Define homeodomain.

3 consecutive alpha helices shown as cylinders (most contacts with DNA bases are made by helix 3 and the Asn contacts adenine)

Define zinc finger motif.

Built from an alpha helix and beta sheet held together by a molecule of zinc (Zinc fingers are often clustered, covalently joined together to allow the alpha helix of each finger to contact the DNA bases in major groove)

A leucine zipper motif is formed by what?

Two alpha helices, each contributed by a different protein molecule

Leucine zippers bind to DNA as what?

Dimers (gripping the double helix like a clothespin on a clothesline)

A cluster of bacterial genes can be transcribed from a what?

Single promoter

What allows cells to respond to changes in environment?

Transcription switches

All the enzymes are needed to synthesize the what?

Amino acid tryptophan

Define operon.

Each cluster of genes transcribed as a single mRNA molecule

Genes can be switched on/off with what?

Repressor proteins

Repressor protein becomes active and binds to what?

Operator (where it blocks binding of RNA polymerase to promoter)

Gene expression can also be controlled with what?

Activator proteins

Without activator, promoter does what?

Fails to initiate transcription efficiently

Bacterial what must bind cyclic AMP (cAMP) before it can bind to DNA?

Catabolic activator protein (CAP)

CAP allows genes to be what in response to increases in intracellular cAMP concentration?

Switched on

Intracellular cAMP concentration signals to bacterium that what is no longer available?

Glucose

Lac operon is controlled by what 2 signals/molecules?

Glucose and lactose

Glucose and lactose concentrations control initiation of transcription of Lac operon through effects on what?

Lac repressor protein and CAP

Lactose is absent so what happens?

Lac repressor binds Lac operator and shuts off expression of operon

Glucose is absent so what happens?

Cyclic AMP is produced by cell and CAP binds to DNA

A what protein bound to DNA attracts RNA polymerase and general transcription factors to the promoter?

Activator protein

What large protein complex serves as a go-between?

Mediator

Eukaryotic gene activator proteins can direct local what in chromatin structure?

Alterations

Many transcription activators attract what?

Histone acetylases

Histone acetylases attaches to which group?

Acetyl group, to selected lysines in tail of histone proteins

Each cell in a multicellular organism what only a fraction of its genes?

Expresses

Most transcription regulators bind to DNA using one of the DNA-binding what?

Motifs (such as homeodomain, leucine zipper and zinc finger)

Eukaryotic transcription what acts in two major ways?

Regulators

Your body is composed of numerous cell types with specific functions. These cells contain the same DNA but the cells differently express certain genes resulting in cell type differences. T/F?

True

A neuron and a white blood cell have different functions. Neurons can receives and respond to electrical signals while a white blood cell defends the body against infection. Why?

The neuron expresses some mRNAs that the white blood cell doesn’t

What is the main step that’s controlled in gene expression?

Transcription

Which motif found in transcriptional regulators contain 3 alpha helices?

Homeodomain

The simplest changes in gene expression are often what?

Transient (such as in response to signals in their environments)

Once a cell becomes what, the choice of fate is generally maintained through many subsequent cell generations?

Committed

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

Cell memory

A positive feedback loop can create what?

Cell memory

Define positive feedback loop.

A transcription regulator activates transcription of its own gene (in addition to that other cell-type-specific genes)

Protein A is a transcription regulator that does what?

Activates its own transcription

Transcription regulators work together as a what to control expression of a eukaryotic gene?

Committee

What is the same for all genes transcribed by RNA polymerase II?

General transcription factors

The transcription regulators and the locations of their binding sites relative to the promoters are what?

Different for different genes

What refers to the way that groups of regulatory proteins work together to determine the expression of a single gene?

Combinatorial control

Activator proteins bound to the regulatory region but are what to activate transcription?

Not sufficient

An additional transcription regulator (the glucocorticoid hormone) does what of transcription regulators required for efficient initiation of transcription?

Completes the combination

A decision to make a new what is made after each cell division?

Regulator

Define pluripotent stem cells.

Cells that are capable of giving rise to specialized cell types

Define iPS cells. (Induced Pluripotent Stem cells)

Cells that look and behave like pluripotent stem cells but are artificially induced in a lab

Formation of 5-methylcytosine occurs by what of a what base in the DNA double helix?

Methylation of a cytosine

In addition to the positive feedback loop to create cell memory, a second way of maintaining cell type is through the what?

Faithful propagation of a condensed chromatin structure from parent to daughter cell

A third way in which cells can transmit information about gene expression to their progeny is through what?

DNA methylation

Maintenance methyltransferase guarantees that a pattern of DNA methylation is inherited by progeny DNA - referred to as what?

Epigenetic inheritance

A what controls purine biosynthesis genes in bacteria?

Riboswitch

Majority of genes are what by switching on/off transcription initiation?

Regulated

Define riboswitches.

Short sequences where mRNA change their conformation when bound to small molecules (to regulate their own transcription and translation)

Gene expression can be controlled by what?

Regulating translation initiation

Some ribosomal proteins use this mechanism to what?

Inhibit the translation of their own mRNA

An mRNA from the pathogen ‘Listeria’ contains a what RNA sequence that controls the translation of a set of virulence genes?

Thermosensor

Binding of a small molecule to a riboswitch causes a what of the RNA?

Structural rearrangement (sequestering the ribosome recognition sequence and blocking translation initiation)

The endogenous ‘noncoding RNA’ called what is processed to form a mature miRNA?

Precursor microRNA (miRNA)

It then assembles with a set of proteins into a complex called what?

RNA induced silencing complex (RISC)

What destroys foreign RNAs?

siRNAs

Foreign double-stranded RNAs (such as from a virus) are first cleaved by a nuclease called what?

Dicer

The resulting double-stranded fragments called what are incorporated into RISCs?

Small interfering RNAs (siRNAs); (which discard one strand of the duplex and use the other strand to destroy the complementary RNAs)

This mechanism forms the basis for what in many organisms which helps eliminate potential dangerous invaders?

RNA interference (RNAi)

In regards to the trp operon, the presence of tryptophan will cause the repressor protein to release the operator region of DNA. T/F?

False

Cell membranes act as what?

Selective barriers

The plasma membrane is involved in what?

Cell communication, import/export of molecules, cell growth

What is the most common phospholipid in cell membranes?

Phosphatidylcholine

Phosphatidylcholine is built from 5 parts being what?

~Choline (hydrophilic head)

~Phosphate (links choline to glycerol)

~Glycerol (links phosphate to two hydrocarbon chains)

and two hydrocarbon chains

Because the 2-methylpropane molecule is hydrophobic, it can’t form favorable interactions with water and force adjacent water molecules to rearrange into what around it?

Cage-like structure

Amphipathic phospholipids form a what?

Bilayer in water

Phospholipid bilayers does what to form sealed compartments?

Spontaneously close in on themselves

The same forces driving amphipathic molecules to form a bilayer makes a bilayer what?

Self-sealing

The closed structure is stable because it does what to the exposure of the hydrophobic hydrocarbon tails to water?

Avoids

Pure phospholipids can formed closed and spherical what?

Liposomes

The fluidity of a cell membrane is important for membrane function and must be what?

Maintained within certain limits

What influences the fluidity of the bilayer?

~Temperature (heat increases)

~Phospholipid composition (types of hydrocarbon tails)

~Hydrocarbon tails that don’t pack closely together increases the fluidity

~Unsaturated fatty acid tails

Phospholipids and what are distributed asymmeterically in the plasma membrane lipid bilayer?

Glycolipids

The two faces of the lipid bilayer are what?

~Cytosolic side (faces cytosol)

~Non-cytosolic side (faces exterior of cell/interior of internal organelle)

What plays a role in synthesizing lipid bilayer?

Flippases

Newly synthesized phospholipid molecules are all added to the what?

Cytosolic side of the ER membrane

Define scramblases.

Responsible for the transfer of random phospholipids from one monolayer to another

What transfers specific phospholipids to the cytosolic monolayer? (Golgi Specific)

Flippases

Membranes are transported by a process of what?

Vesicle budding and fusing