exam 3- ta review

Question 1

Virulent Phage

Answer 1

A bacteriophage that only has a lytic cycle as a means of reproduction

Question 2

Temperate Phage

Answer 2

A bacteriophage that has both lytic and lysogenic cycles as a means of reproduction

Question 3

Prophage/ Provirus

Answer 3

A virus that is experiencing latency–the inactive stage of a virus integrated into the host cell genome.

Question 4

What are the six general steps of the viral reproduction cycle?

Answer 4

Attachment–the use of binding receptors to attach to a cell’s outer membrane
Entry–viral materials enter the cell’s cytoplasm
Integration–INTEGRASE enzyme
Synthesis–the production/replication of viral material
Viral Assembly–the assembly of all viral material
Release–Lysis (the rupture of the cell)

Question 5

What key enzymes are important to viral reproduction?

Answer 5

Integrase, Reverse transcriptase

Question 6

reproductive cycles of HIV

Answer 6

Attachment
-Spike glycoproteins bind to cell membrane’s receptors
Entry
-Viral envelope fuses with cell membrane
-Some capsid proteins are removed (uncoating) which releases viral content: RNA, reverse transcriptase, and integrase

Integration
-RNA is reverse transcribed into DNA
-Viral DNA integrated into cell genome via integrase→provirus/lysogenic

Question 7

reproductive cycle of Phage Lambda

Answer 7

Attachment
-Proteins bind to the cell’s membrane

Entry
-Viral DNA is injected into cytoplasm

Integration
-Viral DNA is integrated via integrase
-Can either: go into lysogenic cycle, start lysogenic cycle then switch lytic, or skip lysogenic and go into lytic

Question 8

Phosphodiester linkage

Answer 8

The element of DNA’s backbone in which nucleotides are covalently linked together

Question 9

Ester bonds

Answer 9

Bonds present in phosphorus groups that make up the backbone of DNA

Question 10

Nucleotide (and it’s components)

Answer 10

The fundamental unit of DNA composed of a phosphorous group, sugar, and nitrogenous base

Question 11

What is Chargaff’s rule?

Answer 11

A bonds w/ T; C bonds w/ G
Amount of A = Amount of T; Amount of C = Amount of G

Question 12

One strand of DNA is 5’ GCCTAGGATC 3’. What is the opposing strand? How many hydrogen bonds are present between the two strands?

Answer 12

3’ CGGATCCTAG 5’
A–T 2 bonds, C–G 3 bonds →26 bonds

Question 13

What are the key differences between DNA and RNA?

Answer 13

A DNA nucleotide has a deoxyribose sugar while a RNA nucleotide has a ribose sugar

Question 14

Two strands of DNA, forming a double helix, can be described as…?

Answer 14

Antiparallel (complementary and oriented in opposite directions)

Question 15

Euchromatin

Answer 15

Less condensed regions of chromosomes, transcriptionally active

Question 16

Heterochromatin

Answer 16

Tightly compacted regions of chromosomes, generally transcriptionally inactive

Question 17

Loop Domains

Answer 17

Loops formed as the third level of compaction via CTCF and SMC proteins

Question 18

Transposon

Answer 18

A short segment of DNA that can move within the genome via simple transposition; “jumping genes”

Question 19

Retrotransposon

Answer 19

A transposable element that moves via transposition → transcribed into RNA then reverse transcriptase makes a second copy in DNA

Question 20

7 copies of a retrotransposon are created and integrated into the genome. What is the result or outcome of this retrotransposition event?

Answer 20

8!! 1 original copy + 7 copies produced via retrotransposition

Question 21

What are the levels of DNA compaction (least compacted to most compacted)?

Answer 21

1. DNA double helix
2. Nucleosomes (“beads on a string”)
3. 30 nm fiber
4. Loop domains
5. Metaphase chromosome

Question 22

Topoisomerase II

Answer 22

(aka DNA gyrase) Relaxes supercoiling ahead of the replication fork

Question 23

Single-strand binding protein

Answer 23

Binds to single-stranded DNA to keep the two strands separated during replication

Question 24

Primase

Answer 24

Synthesizes RNA primers that are used to build new DNA strands.

Question 25

DNA polymerase III

Answer 25

Synthesizes the DNA in the leading and lagging strands

Question 26

DNA polymerase I

Answer 26

Removes RNA primers in bacteria and fills in the gaps with DNA

Question 27

Flap endonuclease

Answer 27

Removes RNA primers in eukaryotes

Question 28

Okazaki fragments

Answer 28

Short segments of newly synthesized DNA made on the lagging strand so that DNA is made 5’ to 3’ but moves away from the replication fork

Question 29

What enzymes or biological molecules make up a primosome?

Answer 29

Primase (synthesizes RNA primers) + Helicase (unwinds DNA)

Question 30

DNA is synthesized in the ___ direction, while DNA is proofread in the ____ direction.

Answer 30

5’ 3’ , 3’ to 5’

Question 31

What is the difference between the DNA polymerases used in prokaryotes and eukaryotes for the replication of DNA?

Answer 31

In prokaryotes, DNA polymerase III is the major/sole enzyme that handles DNA synthesis on both leading and lagging strands. In eukaryotes, two DNA polymerases assist with the synthesis of the leading and lagging strand (epsilon “ε” and delta “δ”)

Question 32

Introns

Answer 32

Non-coding sequences present in mRNA→do not lead to any protein production

Question 33

Exons

Answer 33

Functional or coding sequences present in mRNA→leads to protein production (gene expression)

Question 34

Alternative splicing

Answer 34

Exons from the same gene are joined together in different combinations, leading to a variety in protein “outcomes” from a single gene

Question 35

Tailing (in RNA Modification)

Answer 35

In eukaryotes, added to the 3’ end to promote stability

Question 36

TFIIH

Answer 36

A multisubunit protein… (a) Certain subunits that act as helicases to promote formation of the open complex. (b) Other subunits phosphorylate the carboxyl terminal domain (CTD) of RNA polymerase II which leads to elongation phase

Question 37

One DNA strand is 5’ ACAATTCGAA 3’ What is the complementary RNA strand?

Answer 37

CALLED THE TEMPLATE STRAND, 3’ UGUUAAGCUU 5’

Question 38

What are the three steps of transcription?

Answer 38

1. Initiation-RNA polymerase binds to DNA 2. Elongation-RNA polymerase synthesizes RNA (open complex is formed) 3.Termination-RNA polymerase stops synthesizing RNA

Question 39

Protein

Answer 39

A sequence of amino acids that serve in cell structure and function.

Question 40

tRNA

Answer 40

RNA molecule that carries the amino acids that correspond to codons in the mRNA. A tRNA molecule has an anticodon to pair with specific trinucleotide sequences

Question 41

Charged tRNA

Answer 41

A tRNA with an amino acid attached to it

Question 42

Ribosomes

Answer 42

The large macromolecular complex that performs translation and composed of two subunits.

Question 43

Nucleolus

Answer 43

A region of the nucleus that produces and assembles ribosomal subunits

Question 44

Shine-Dalgarno sequence

Answer 44

Ribosomal-binding site that facilitates the binding of mRNA to the 30S subunit

Question 45

Peptidyl transferase complex

Answer 45

A part of the 50S subunit, catalyzes the peptidyl transfer reaction in which the polypeptide in the P site is moved to the amino acid of the A site

Question 46

What are the three sites of a ribosome? What is the function/purpose of each site?

Answer 46

1. E–“Exit site” The site that allows for the exit of a tRNA molecule 2. P– “Passing Peptide site” The site that holds the growing polypeptide chain 3. A–“new Amino site” The site that accepts new amino acids attached to tRNA

Question 47

Describe Kozak’s rules.

Answer 47

Rules for optimal translation → -3 to +4

Question 48

The ribosome is composed of multiple subunits. Belonging to the 30S ribosomal subunit, what is the role of 16S rRNA.

Answer 48

Plays a key role in codon-anticodon recognition, detecting an incorrect tRNA bound a the A site