Exam 3

Question 1

Acetylation

Answer 1

-Covalent modification
Acetylation of lysine weakens DNA-histone interaction
Easier for transcription factors to access cytosine
Transcription factor for RNA polymerase
Uses histone acetyl transferases (HATs)

Question 2

Euchromatin

Answer 2

loosely packed
Transcriptionally active
Gene sequence available to RNA polymerases

Question 3

DNA Methylation

Answer 3

DNA methylation restricts differentiation potential of a cell.
Increase DNA methylation = decrease cell potential
Also, the presence of “CG” patterns increases the chance of methylation
DNA methylation changes throughout development

Question 4

Base Pairings

Answer 4

C-G and T-A unless it is transcription then T is replaced with U

Question 5

Bidirectional

Answer 5

Bidirectional with multiple origins
Starts at several points (origins)
Replication “bubble” is formed

Question 6

Read from 5’-3’

Answer 6

Translation uses mRNA which is read 5’-3’
Parental strand reads from 3’-5’
Synthesized 5’-3’

Question 7

RNA primers are used in which process?

Answer 7

DNA replication

Question 8

Ligase

Answer 8

DNA ligase joins nucleotides in fragments by forming phosphodiester bonds
REQUIRES ATP
Connect Okazaki fragments

Question 9

Replication Fork

Answer 9

Homologous recombination = uses info from unaffected chromosome to fix; usually if error at replication fork
Replication fork
Unwound by helicase which needs ATP.

What functions ahead of the replication fork?
Answer: Topoisomerases (Chap. 7 slide 16)

Question 10

During DNA replication, nucleotides are added to the ________ end

Answer 10

3’

Question 11

“__________ transcription factors regulate the number of RNA polymerases transcribing simultaneously”

Answer 11

Specific

Question 12

Transcription complex assemble on the DNA strand

Answer 12

TATA

Question 13

Initiating Transcription

Answer 13

TFIIH phosphorylates RNA polymerase II causing a conformational change which initiates transcription

Question 14

… is added to mRNA to prevent…

Answer 14

5’ cap
The 5’ end of RNA is capped with a methyl guanosine (AKA 5’-Cap)
These prevent degradation by exonucleases

Question 15

___________ is a complex of proteins found in the nucleus used in mRNA production.

Answer 15

Spliceosome

Question 16

3rd position in Wobble Hypothesis

Answer 16

The 3rd base on the codon binds with the 1st base of the anti-codon and determines the amino acid
Look at Genetic Code Chart (nonsense, missense, silent mutation)

Question 17

TATA

Answer 17

During transcription the promotor region is often a TATA sequence called a TATA box
TATA box directs RNA polymerase II
TATA binding protein binds to TATA box

Question 18

Is read in the ______ direction

Answer 18

3’ to the 5’ end

mRNA is read in the 5’-3’ direction during translation

Question 19

Results in a codon that codes for ___________ instead of _________

Answer 19

A stop codon An amino acid

An example of when this happens is sickle cell anemia (nonsense mutation)

Question 20

Anticodon

Answer 20

Recognizes a codon for a specific amino acid
Flipped 3’-5’ to pair, but always written 5’-3’
First base in anticodon can pair with multiple options

Question 21

“Which amino acid is most likely to be found at the N-Terminal of all newly synthesized proteins?”

Answer 21

Methionine

Question 22

Movement of ribosomes

Answer 22

5’-3’ on mRNA
Directed by signal sequence on protein to the ER or to be free (lacking signal)
Composed of rRNA

Question 23

“Which of the following would cause the termination of translation”

Answer 23

UGA at the A site

Termination of translation would result from the stop codon UAG, UGA, or UAA at the A site.

Question 24

Post-translational

Answer 24

Changes controlled by miRNA

Generally active

Trimming- Slicing of a protein using endoprotease to make it active

Covalent modification-
phosphorylation, glycosylation, hydroxylation, carboxylation or acetylation

Can begin while still being synthesized by ribosome

Medial Golgi complex adds tags for lysosome

Question 25

Bud off vesicles

Answer 25

Vesicles with secretory proteins bud off from golgi complex (constitutive secretion)

Vesicles with regulatory proteins bud off from golgi complex (regulated secretion)

Lysosomal trafficking: Protein buds off from golgi complex

Question 26

From the same gene

Answer 26

Alternative splicing = taking out different introns

Make multiple proteins from a single gene

Question 27

The shorter the half-life.

Answer 27

Proteosomal protein degradation
Degrades proteins with shorter half life
Enzymes of the proteosome use which part of a protein to identify its half-life?
N-terminal amino acid
Proline, Glucine, Serine, Threonine degrade fastest

Question 28

Proteins Targeted

Answer 28

Proteins targeted to the ER have a special sequence located where? N-Terminal
Possible Extra Credit: (Chap. 11 Slide 22) Zellweger Syndrome

Question 29

Where modification occurs

Answer 29

Called cotranslational modification (occurs while translation is still happening) 
Trimming
Covalent (just need to know what they add)
Phosphorylation (phosphate)
Glycosylation (glucose/sugar)
Produces glycoproteins = specificity
O-linked
N-linked- occurs in the Golgi complex / RER
Hydroxylation (hydroxyl group, -OH)
Proline and lysine in collagen
Vit C
Carboxylation (Carboxyl group, -COOH)
Vit K needed
Clotting, bone formation
Acetylation (acetyl group, -OCH3)
Lysine on histones

Question 30

before it will be active

Answer 30

A protein must undergo post translational modification before it will be active
Trimming

Question 31

Mitochondria

Answer 31

Which protein is required for transport of translated protein into the mitochondria? (translocase)
y (gamma) DNA polymerase is located in the mitochondria and has both 5’-3’ polymerase function and 3-5 exonuclease function
Free ribosomes synthesize proteins for mitochondria

Question 32

What is the minimum number of ubiquitins necessary to be recognized by the regulatory protein of the proteasome?

Answer 32

4

Determine half-life by the N-terminal of the Amino Acid

Question 33

Which of the following is not typically degraded by lysosomes?

Answer 33

Improperly folded proteins

Question 34

INTO THE NUCLEUS

Answer 34

proteins made in the nucleus usually go to the cytosol but can go in the nucleus- Nuclear proteins, nucleus requires enzymes for DNA replicatoin and transcription must contain nuclear localisation signal transcription which allows protein to pass through nuclear pore with help from importin which is released after the protein is inside the nuclear envelope.

Question 35

rRNA

Answer 35

Each ribosome contains 4 rRNA
3 located in larger subunit
1 located in smaller subunit

Question 36

Too many repeats

Answer 36

Trinucleotide repeat expansion: too many repeats are added, so final protein has extra copies of AA

Question 37

“The default pathway for proteins that are made by free/cytosolic ribosomes is to send them to the _______.”

Answer 37

The default pathway of protein trafficking is from the ribosome to the cytosol.

Question 38

DNA repeats, present at the ends of chromosomes, that act to protect it from degradation are called:

Answer 38

Telomeres

Question 39

Enzymes of the proteosome use which part of a protein to identify its half-life?

Answer 39

N-Terminal Amino Acid

Question 40

In regulated secretion, proteins made at the RER are

Answer 40

Stored in granules in the cytosol for later release