Lecture 9: Gene To Protein

Question 1

What is gene expression?

Answer 1

The process of going from DNA to a functional product.

The Central Dogma
DNA -> RNA -> Protein

Question 2

What are the DNA and mRNA bases?

Answer 2

Adenine, Guanine, Thymine, Cytosine and Uracil.
Uracil is easier to make than Thymine.
Thymine is more stable -> DNA is the inherited material hence needs to be more stable

A-T/U
C-G

Question 3

What is the genotype?

Answer 3

An organism’s hereditary information.

Question 4

What is the phenotype?

Answer 4

Actual observable or physiological traits.

Question 5

How do genotype and environment interact?

Answer 5

They determine our phenotype.

Question 6

What is DNA?

Answer 6

Deoxyribonucleic acid, the heritable material that stores and transmits information.

Question 7

What is RNA?

Answer 7

Ribonucleic acid, which acts as a messenger to make proteins from DNA information.

Question 8

What are the three main steps of protein synthesis?

Answer 8

Transcription of RNA from DNA

Processing of pre-mRNA to mature mRNA

Translation of mRNA to protein

Question 9

What occurs during transcription?

Answer 9

RNA is synthesized from a DNA template.

Question 10

What are the three phases of Transcription?

Answer 10

Initiation -> polymerase binds to promoter
Elongation -> moves downstream through the gene, transcribing RNA
Termination -> detaches after terminator reached

Question 11

What is the role of RNA polymerase during transcription?

Answer 11

It binds to the promoter region along with other transcription factors to form the transcription initiation complex and synthesizes RNA.

Question 12

Why is it called the 3’ or 5’ ends?

Answer 12

Due to phosphate group connecting to the 3’ or 5’ carbon

Question 13

What is the TATA box?

Answer 13

A sequence of DNA found in the promoter region which marks where transcription should be initiated

The typical promoter element ~25nt upstream of the transcription start site.

Question 14

What is TBP?

Answer 14

TATA box binding protein is a transcription factor that binds to the TATA box of the promoter region forming transcription initiation complex.

Question 15

What is the role of transcription factors?

Answer 15

They are required for the assembly of the transcription initiation complex.

Question 16

What is the process of initiation in transcription?

Answer 16

Initiation is the assembly of proteins required before transcription can commence

Eukaryotic Primer - DNA contains a promoter region in which the TATA box can be found

Several Transcription factors bind to promoter region - Assembly of several transcription factors including the TATA box binding protein (TBP)

Transcription initiation complex - This changes the shape of the promoter, RNA Polymerase II can now bind along with more transcription factors to form the transcription initiation complex

Question 17

What is the polyadenylation signal?

Answer 17

A sequence of nucleotide bases that signal the termination of transcription hence the release of pre-mRNA and RNA polymerase

Question 18

What is the process of elongation in transcription?

Answer 18

10-20 nucleotides exposed at a time when DNA unwound, allowing RNA
Nucleotides to come in and bond to their basepair. Producing a phosphodiester bond (strong) between the RNA nucleotides

Moves downstream through the gene, transcribing RNA

Complementary RNA nucleotides added to 3’ end of growing transcript (3’OH of transcript binds with 5’ phosphate of incoming nucleotide)

Double helix reforms as transcript leaves the template strand

Question 19

What is the process of termination in transcription?

Answer 19

Detaches after terminator reached after transcription of the polyadenylation signal (AAUAAA) nuclear enzymes release the pre-mRNA and RNA polymerase then dissociates from the DNA

The polyadenylation signal (AAUAAA) indicates where transcription ends.

Question 20

What are the 3 steps to processing stage of gene expression?

Answer 20

Capping, tailing, splicing

Question 21

What is capping in mRNA processing? Why?

Answer 21

A modified guanine nucleotide is added to the 5’ end.

Capping and tailing are thought to facilitate export, confer stability and facilitate ribosome binding in cytoplasm
RNA rapidly degrades

Question 22

What is tailing in mRNA processing? Why?

Answer 22

50-250 adenine nucleotides (polyA) are added to the 3’ end.

Capping and tailing are thought to facilitate export, confer stability and facilitate ribosome binding in cytoplasm
RNA rapidly degrades

Question 23

What are exons?

Answer 23

Regions that remain in mature RNA.

Question 24

What are introns?

Answer 24

Intervening regions that do not remain in mature RNA.

Question 25

What are UTRs?

Answer 25

Untranslated regions at 5’ and 3’ ends of mRNA

Question 26

What is splicing?

Answer 26

Introns are removed from the transcript

Question 27

What is a spliceosome?

Answer 27

A large complex of proteins and small RNAs, removes introns and joins exons to form mature mRNA.

Question 28

What is alternative splicing?

Answer 28

A process that allows different combinations of exons to produce multiple mRNA forms.

Question 29

Why do we have alternative splicing/introns?

Answer 29

Larger organisms have introns, allowing for much higher complexity and variation Alternative splicing allows for multiple gene products from the same gene ~20,000 genes, there could be many times that number of proteins!!

Question 30

What are codons?

Answer 30

Groups of three mRNA bases in a row that code for a specific amino acid

Question 31

What is the relationship between codons and amino acids?

Answer 31

Codons are translated into amino acids during protein synthesis.

Question 32

What is the role of tRNA in translation?

Answer 32

tRNA molecules within the cytosol with specific anticodons carry corresponding amino acids to the ribosome and matches them to the mRNA codons.

Question 33

What are the three sites in the ribosome?

Answer 33

* A site (Aminoacyl-tRNA binding site) * P site (Peptidyl-tRNA binding site) * E site (Exit site)

Question 34

How do amino acids connect to growing polypeptide chain?

Answer 34

The amino acid is added via peptide bonds to the growing polypeptide chain

Question 35

What initiates translation?

Answer 35

The small ribosomal subunit with the initiator tRNA already attached binds with mRNA and scans for the start codon (AUG).

Question 36

What is tRNA's function?

Answer 36

tRNA is the physical link between the mRNA and the amino acid sequence of proteins

Question 37

What is required for the assembly of the translation initiation complex?

Answer 37

Energy in the form of GTP (Guanosine triphosphate)

Question 38

What happens during elongation in translation?

Answer 38

tRNA recognizes codon, tRNA translocates from A to P site. The large subunit of the ribosome catalyses peptide bond formation, removes it from tRNA in P site tRNA in P site moves to E and is released Energy is required (GTP)

Question 39

What signals termination in translation?

Answer 39

Recognition of a stop codon (UAG, UAA, UGA) in the A site by a release factor Release factor promotes hydrolysis Bond between p-site tRNA and last amino acid is hydrolyzed, releasing polypeptide chain Ribosomal subunits and other components dissociate Hydrolysis of two GTP molecules required

Question 40

What are the control points of Gene to Protein?

Answer 40

Transcription factors need to assemble, and DNA needs to be accessible Capping, extent of polyadenylation, alternate splicing, producing an mRNA able to be translated specific proteins assist in nuclear export of mRNA regulatory proteins can block translation, variable mRNA life-spans

Question 41

What is the importance of gene expression regulation?

Answer 41

To achieve the right function at the right time and place (temporal and spatial control)

Question 42

What are housekeeping proteins?

Answer 42

Proteins that are continuously produced * protein and mRNA are present in large quantities (e.g. Tubulin) * typically, have longer “half life” in cells

Question 43

What are temporary proteins?

Answer 43

Produced by cell signaling (e.g. ligand binding a cell surface receptor, or activating an intracellular receptor) Signal transduced and may enter nucleus to activate transcription Results in the production of a short-lived protein to carry out the required function

Question 44

What are the properties of an Animo acid?

Answer 44

Has a Amino group, and Carboxyl group, and a side chain. The side chains (R groups) determine the properties of each amino acid

Question 45

What are signal peptides?

Answer 45

Short sequences that direct ribosomes to the endoplasmic reticulum.

Question 46

What is post-translational modification?

Answer 46

Chemical changes to a protein after translation that can affect its activity.

Question 47

What are some common post-translational modifications?

Answer 47

* Phosphorylation * Methylation * Acetylation * Biotinylation * Carboxylation * Carbohydrate addition * Cleavage * Ubiquitination

Question 48

What is the primary structure of a protein?

Answer 48

The sequence of amino acids determined by DNA.

Question 49

What forms secondary structure in proteins?

Answer 49

Hydrogen bonds forming alpha helices and beta sheets.

Question 50

What stabilizes tertiary structure in proteins?

Answer 50

Interactions between side chains (R groups).

Question 51

What characterizes quaternary structure?

Answer 51

Multiple proteins associating together to form a functional protein. Not all proteins form quaternary structures

Question 52

What are the terminus ends of the primary structure?

Answer 52

N – Terminus is the amino end (5’) C – Terminus is the carboxyl end (3’)

Question 53

Where does Transcription and Processing occur?

Answer 53

Nucleus

Question 54

Where does Translation occur?

Answer 54

Cytosol