BIO 1A03 Test 2

Theme 2 Modules 3/4 and All of Theme 3

molecular components of translation

messenger RNA, initation factors, elongation factors, release factors, Aminoacyl tRNA synthetases, tRNA, Ribosomal proteins and rRNA.

phosphorylation

the process of adding a phosphate group to a molecule, typically a protein, lipid, or nucleic acid.

methylation

* a process by which a methyl group (CH3) is added to a molecule, typically DNA, RNA, or protein.

acetylation

the process of adding an acetyl group to a molecule.

one gene one polypeptide hypothesis

The idea that each gene codes for a single polypeptide. This hypothesis was proposed by Beadle and Tatum in 1941 after their experiments with Neurospora crassa.

Lagging Strand

replicates in the 5’ direction in segments

Gel Electrophoresis

A process that distinguishes between the sizes of the DNA fragments

Housekeeping Genes

include that are important for structural proteins of the cell

Housekeeping Genes

Genes that are expressed in all cells and are essential for basic cellular functions like metabolism, cell cycle, and maintenance. They are used as reference genes to normalize gene expression data in experiments.

Regulation of gene expression by siRNA

inhibiting translation by degrading RNA transcripts

Insertions and deletions of single nucleotides

cause frameshift mutations

beta-galactosidase

expressed in the presence of lactose and when no glucose is available → regulating

beta-galactosidase

The enzyme that metabolizes lactose in bacteria → regulating

an operon

A group of related genes with similar functions that are found clustered together along the bacterial chromosome

Insertions and deletions that occur in multiples of three nucleotides

add or delete amino acids to/from the normal polypeptide

Both miRNA and siRNA work in conjunction with

a protein complex called RISC to bind RNA transcripts in the cytoplasm.

cis acting factors

DNA sites bound by regulatory transcription factors

kinase

An enzyme that attaches a phosphate group to another molecule

Mismatch repair, base excision repair and nucleotide excision repair

each type of repair uses an undamaged segment of DNA as the template for repair

Protein degradation of misfolded proteins is accomplished

tagging these proteins with small ubiquitin proteins that form a polyubiquitin chain

gene expression

transcription, translation and post-translational modifications of the functional gene product

PCR steps

1. Denaturing
2. Annealing
3. Extending

where are CpG islands found

found in a small region near or in the promoter site of a gene

regulating genes

Genes that are turned on and off on an as-needed basis

cyclin-CDK complex

capable of phosphorylating key proteins involved in regulating the cell cycle?

DNA Ligase

joins DNA together from different origins of replication

Lac Z

codes for beta-galactosidase → needed to split lactose into smaller sugars

LacY

codes for lactose permase transport protein

Lac I

controls the expression of the genes in the lactose operon

Negatively regulated transcription

A repressor protein will bind to the operator region of the operon → turning off transcription

Positively Regulated Transcription

A transcriptional activator protein binds to an activator binding site in DNA

Prokaryotic and Eukaryotic Transcription Similarities

1. Proteins are involved with activating repressing transcription
2. Utilize RNA polymerase to bind to promoters to initiate transcription

Shine-Delgarno Sequences

Prokaryotic transcription initiation binding site

Prokaryotic Transcription

groups related genes with similar functions that can be found clustered together into operons transcribed by a single promoter

Eukaryotic Transcription

each gene is controlled by its own promoters and enhancers. DNA is organized into chromatin.

Silencer Regions

Activated by a repressor protein where they interfere with general transcription, factor assembly and mediator activity

Location of prokaryotic Transcription and Translation

Takes place in the nucleoid region → only in prokaryotes

Gene Expression Regulation Factors

* transcription initiation
* RNA processing
* Overall stability of the RNA molecules
* protein synthesis
* protein modification and transport
* protein degradation

Multi-level regulation

allows for a cell to rapidly alter levels of active proteins in response to signals

miRNA

transcribed from protein encoding genes using the same RNA polymerase that transcribes for other RNA molecules

post-translational modifications

* cleavage
* disulphide bond formation
* acetylation
* phosphorylation
* methylation

Ubiquitin

a protein that targets proteins and tags them through an enzymatic cascade

structure of histone proteuns and its interaction with DNA

DNA is tightly wound around histone proteins due to the interactions of positively charged tails of histone proteins with the negatively charged phosphates in DNA

Proteasome

A large protein complex that degrades unneeded or damaged proteins in cells.

selective degredation

Process of breaking down specific proteins in a cell, while leaving others intact. This is achieved through the use of specialized enzymes that target specific amino acid sequences.

TATA box

Nucleotide sequence found in the promoter region of genes that indicates where RNA polymerase should bind to initiate transcription.

shine-delgarno sequences

Short nucleotide sequences found in bacterial mRNA molecules that help in the initiation of protein synthesis by aligning ribosomes with the start codon.

correct matching of tRNA and amino acids

facilitated by synthetase enzyme along with rRNA and ribosomal proteins

A cell that undergoes a great amount of protein synthesis would have

a dense rough endoplasmic reticulum netwok

Post-translational modifications of insulin

begins with the cleavage of the signal sequence in the endoplasmic reticulum

The production of the fully mature insulin protein from a single polypeptide of 110 amino acids is achieved through

post-translational modifications

A transfer RNA (#1) attached to the amino acid lysine enters the ribosome. The lysine binds to the growing polypeptide on the other tRNA (#2) in the ribosome already. Where does tRNA #2 move to after this bonding of lysine to the polypeptide?

E-site

When does translation begin in prokaryotic cells?

Once the pre-mRNA has been concerted to mRNA.

Steps to protein synthesis

1. An aminoacyl-tRNA binds to the A site


2. tRNA leaves the P site, and the P site remains vacant.
3. A peptide bond forms between the new amino acid and a polypeptide chain.
4. A small ribosomal subunit binds with mRNA.
5. tRNA translocates to the P site

The lacZ and lacY genes are transcribed when

lactose is present and glucose levels are low.

The CRP-cAMP complex binds the lactose operon when

glucose levels are low and cAMP levels are high.

As E.coli cells transition from glucose to lactose metabolism when

there is an increase in the amount of detectable lactose permease.

When glucose is no longer available as a nutrient source for bacteria, and lactose becomes the predominant nutrient source, beta-galactosidase production

is regulated at the transcriptional level.

Small interfering RNA (siRNA) regulates gene expression by

inhibiting translation by degrading RNA transcripts.

When comparing the effects of regulatory transcription factors that affect TFIID and those that affect adaptor or mediator proteins

mediator proteins allow for the binding of RNA polymerase but transcription can be prevented by transcription factors that bind to silencer regions.

Histone proteins

associated with chromatin remodeling and affect transcription.

Imagine that a eukaryotic organism failed to carry out the process of alternative splicing. Which of the \n following would be observed in that situation?

The resulting polypeptide products would not be different in their structural conformations

Alternative Splicing

enables one pre-mRNA molecules to be spliced at different junctions and results in many different mature mRNA molecules where each contain different combinations of transcribed exons

Enhancers

distant sites where activator proteins bind

when non-functional what would lead to a reduction in the total amount of functional lacZ produced by a bacterial cell?

The CRP-cAMP binding site

\n Lactose is involved in ________________ of the lac operon by __________________

positive regulation; increasing transcription.

lactose operon is transcribed when

the cyclic AMP and lactose levels are both high within the cell environment.

tagging of ubiquitin on the human lactase gene

example of post-translational regulation of the lactase enzyme gene expression

regulation of eukaryotic gene expression example

RNA polymerase binds to undermethylated promoters

in situ hybridization

used to determine when DNA is being expressed in tissues

siRNAs are able to regulate gene expression by

degrading target mRNA

During the process of translation, which of the following describes what occurs once the ribosomal \n translation complex is completely assembled?

The initiation factors are then released.

Consider the biochemical pathway of the synthesis of arginine. If similar protocols were implemented to \n that of researchers Beadle & Tatum and Srb & Horowitz, which used Neurospora crassa, what would be \n observed for the arg 2 mutant that is placed solely on minimal medium

No growth would be observed on the minimal medium alone.

structural components present in mature insulin

Chain A and Chain B

Alternative Splicing

produces mRNA molecules with different combinations of exons

The binding of the insulin ligand to insulin receptor kinases

enables the phosphorylation of cytoplasmic proteins.