RNA and viruses

Question 1

What are ribozymes?

Answer 1

Enzymes that catalyze RNA cleavage

Question 2

What are the key features of tRNA?

Answer 2

Cloverleaf structure
key features
– 3’ end covalently attached to
specific amino acid
– anti-codon loop – 3 nucleotides binds to codon in mRNA
– other loops for recognition – aa tRNA synthase, ribosome

Question 3

What is the most abundant RNA? What are its features?

Answer 3

most abundant RNA – complex structure

3D structure is conserved, sequence is not
• component of ribosomes – 2 subunits, each
has several RNAs and 20-50 proteins
• rRNA is scaffold for proteins to bind
• catalytic activity of the
ribosome is in the rRNA

Question 4

What is an ORF?

Answer 4

open reading frame (ORF) – part of the mRNA

coding for a protein

Question 5

What are the characteristics of prokaryotic mRNAS?

Answer 5

prokaryotic mRNAs
– can be polycistronic – encode >1 protein
– not modified
– translated during or shortly after it is made

Question 6

What are the characteristics of eukaryotic mRNAs?

Answer 6

eukaryotic mRNAs
– generally monocistronic
– extensively modified – including splicing
– transcribed in nucleus, translated in cytoplasm

Question 7

What are miRNAs?

Answer 7

miRNA – microRNAs – 22-26 nucleotides
– gene expression regulation
– assemble into RISC complex – bind mRNA and block
translation

Question 8

What are snoRNAs?

Answer 8

snoRNA – small nucleolar RNA – 70-300 nucleotides
– facilitate chemical modification of rRNA
– encoded with rRNA genes
– component of snoRNP – small nucleolar ribonucleoprotein
– snoRNA guides snRNP to correct site on rRNA via base
pairing

Question 9

What are siRNAs?

Answer 9

siRNA – small interfering RNAs - 21-23 nucleotides

– bind mRNA and induce mRNA degradation

Question 10

What are snRNAs?

Answer 10

snRNA - small nuclear RNAs – 100-300
nucleotides – called U1, U2, U4, U5, U6
– bind proteins to form snRNPs – small nuclear ribonucleoproteins
– involved in mRNA splicing – component of the spliceosome

Question 11

What are lncRNAs?

Answer 11

lncRNA – long noncoding RNA
– long RNAs that do not encode proteins and play a role
in the regulation of gene expression
– e.g. Xist – a 17,000 – 20,000 nucleotide RNA that
functions in inactivation of the X chromosome

Question 12

What is the difference between + and - ssRNA viruses?

Answer 12

+ve stranded – the viral genome is the same as mRNA

-ve stranded – the viral genome is complementary to mRNA

Question 13

What happens when a virus hijacks a cell?

Answer 13

Virus infects a cell – hijacks cell machinery to make
more virus
– to make viral RNA
– to make viral protein
– to replicate genetic material
– to alter metabolism of the cell to favor viral production

Question 14

What is the structure of a T4 phage?

Answer 14

viral anatomy
– head – capsid – contains ds DNA
– tail – attaches to host bacteria

Question 15

What happens when a T4 phage infects a bacteria?

Answer 15

viral infection
– DNA injected into bacteria
– within minutes synthesis of bacterial DNA, RNA and protein STOPS
– phage mRNA synthesis begins
• virulent or lytic cycle
– phage protein synthesis occurs
• capsid proteins
• enzymes for DNA replication
• proteins to help assemble new phage
• proteins to help the mature virus escape
– replication of genetic material
– assembly of new phage
– bacterial lysis and release of the new phage

Question 16

What is a temperate phage?

Answer 16

rather than making new phage, the phage genome
integrates into the host DNA

aka lysogenic

Question 17

What is a prophage?

Answer 17

prophage – integrated phage genome
– prophage is replicated as part of the host DNA,
but does not produce RNA, proteins and genetic
material to make new phage

Question 18

Where do eukaryotic cell-infecting viruses replicate?

Answer 18

Some in cytoplasm, some in nucleus

Question 19

What are the features of Zika virus?

Answer 19

Zika virus is a ss +stranded RNA virus and it is enveloped

Question 20

What important proteins are involved in Zika virus activity?

Answer 20

Capsid protein - binds RNA – assembles viral particle
• M protein – transmembrane protein
• E protein – transmembrane protein, receptor for the
cell – mediates membrane fusion
• Replicase complex – comprised of 5 nonstructural
proteins – has RNA-dependent RNA polymerase

Question 21

What is the function of Zika E protein?

Answer 21

• E protein – transmembrane protein, receptor for the

cell – mediates membrane fusion

Question 22

What are the steps in Zika infection?

Answer 22

1) virus attaches to cell surface receptor
2) endocytosis–virus enveloped in vesicle
3) vesicle pH lowers
4) viral envelope fuses with vesicle membrane, releasing capsid/genome
5) caspid is disassembled, viral genome translated, viruses produced

Question 23

What are the steps in Zika viral genome expression?

Answer 23

1) existing +stranded ssRNA can be directly translated into mRNA
3) Replicase complex synthesizes second RNA strand complementary to +ssRNA, then uses it as template to synthesize many new copies of +ssRNA

Question 24

Where does Zika viral replication occur?

Answer 24

Close to the ER

Question 25

How are Zika viral particles assembled?

Answer 25

1) +ssRNA encapsulated by capsid
2) Capsid associates with E and M proteins in ER membrane
3) Viral particles bud into ER and use section of membrane with E/M proteins to make envelope
4) Exocytosis

Question 26

What is the structure of HIV?

Answer 26

capsid – cylindrical core
genome – 2 copies of a ssRNA
molecule
envelope – contains viral and cell encoded
glycoproteins

Question 27

What proteins are important to HIV function?

Answer 27

reverse transcriptase – enzyme that makes dsDNA copy of ssRNA genome

integrase – enzyme that catalyzes integration of
dsDNA (viral) into host DNA

protease

RNase

Question 28

How does HIV enter the cell?

Answer 28

Virus binds to the host
– viral glycoproteins (gp120) bind cell surface receptor
– CD4 (on T cells) is cell receptor – CCR5 and CXCR4
are co-receptors
• viral envelope fuses with cell membrane
releasing capsid into cytoplasm

Question 29

How does HIV genetic material integrate into the cell’s genome?

Answer 29

reverse transcriptase makes a dsDNA copy of the ssRNA genome

dsDNA translocates to nucleus and integrates into
host genome (provirus)

Question 30

What is a provirus?

Answer 30

Copy of viral genome that is integrated into a host genome–similar to a prophage

Function is to be transcribed/translated along with the host genome to produce new viruses, which are then released from the cell

Question 31

What cells does HIV affect?

Answer 31

Helper T cells–can cause apoptosis or damage cells due to hijacking/viral production

Question 32

What are the five components of HAART?

Answer 32

1) nucleoside inhibitors (e.g. chain terminators) of
reverse transcriptase

2) non-nucleoside inhibitors (e.g. allosteric) of reverse transcriptase
3) protease inhibitors
4) integrase inhibitors
5) CCR5 antagonists

Question 33

What class of drug is AZT?

Answer 33

Nucleoside inhibitor of reverse transcriptase

Question 34

What class of drug is efavinenz?

Answer 34

nonnucleoside inhibitor of RT

Question 35

What class of drug is indinavir?

Answer 35

protease inhibitor

Question 36

What class of drug is raltegravir?

Answer 36

integrase inhibitor

Question 37

What class of drug is maravinoc?

Answer 37

CCR5 antagonist