Molecular Biology Review (Lecture 5)

Question 1

What are the goals of viruses and how do they achieve that?

Answer 1

replicate its genome and assemble new progeny by taking over host cell’s cellular processes and have it focus on the virus’s goals

Question 2

What does it mean that cellular processes are localized?

Answer 2

there is a specific place where only these processes (DNA replication, transcription, translation) can occur

Question 3

In which direction is DNA read and then synthesized?

Answer 3

read 3’-5’ and synthesized 5’-3’ (bottom strand = leading)

Question 4

What type of bond are between nucleotides?

Answer 4

phosphodiester bond

Question 5

What are non-coding RNAs?

Answer 5

tRNAs and rRNA types of RNA

Question 6

What are enhancer proteins?

Answer 6

help the transcription of the genes

Question 7

Which type of polymerase binds to promoter sequences on the DNA?

Answer 7

DNA-dependent RNA polymerase

Question 8

How much of our genes are actually made into proteins?

Answer 8

1.5%

Question 9

What is the enzyme that replicates DNA?

Answer 9

DNA-dependent DNA polymerase

Question 10

Where does the DdDp bind to on the DNA?

Answer 10

origin of replication (ORI)

Question 11

What enzyme puts down the RNA primer needed for DNA replication?

Answer 11

DNA-dependent RNA polymerase

Question 12

Which enzyme binds to DNA right after the DdDp sits on the DNA? And why?

Answer 12

helicase to unwind the DNA

Question 13

What are the 3 important properties of DNA-dependent DNA polymerase?

Answer 13

requires RNA primer, high fidelity of copying (resistant to error), proofreading ability

Question 14

What is the proofreading ability of DdDp attributed to?

Answer 14

exonuclease activity 3’-5’

Question 15

Why does DdDp need an RNA primer?

Answer 15

cannot initiate de novo synthesis because DNA nucleotides don’t have a free 3’OH group

Question 16

What does “de novo” mean?

Answer 16

synthesize on its own, “from new”

Question 17

What is the enzyme needed for transcription?

Answer 17

DNA-dependent RNA polymerase

Question 18

What are the 4 important properties of DNA-dependent RNA polymerase?

Answer 18

binds to the promoter region of DNA, built-in helicase activity, de novo synthesis of RNA, NO proofreading ability

Question 19

What is the difference between preliminary mRNA and mature mRNA?

Answer 19

depending if it had gone through the 3 necessary modifications

Question 20

What are the necessary 3 modifications of preliminary mRNA in order for it to leave the nucleus?

Answer 20

5’ cap, poly (A) tail, and RNA splicing

Question 21

What are the 3 important reasons why mRNA needs a 5’ cap?

Answer 21

help mRNA get out of nucleus, prevent it from degradation of RNases, translation initiation complex recognizes 5’ cap to start translation

Question 22

What is the “Initiation” step of translation?

Answer 22

initiation complex forms when it recognizes the 5’ cap

Question 23

What makes up the initiation complex?

Answer 23

small subunit and tRNA molecule that recognizes the start codon –> large subunit goes on top of it

Question 24

What step in translation is the key step for viruses?

Answer 24

initiation since the viruses need to get their transcripts recognized by the host cell translation machinery

Question 25

What is the difference between monocistronic and polycistronic?

Answer 25

monocistronic transcripts can code for ONLY ONE protein /polypeptide | polycistronic transcripts can code for MORE THAN ONE different protein off of the same transcript

Question 26

Which organisms have monocistronic transcripts?

Answer 26

eukaryotes

Question 27

Which organisms have polycistronic transcripts?

Answer 27

prokaryotes and viruses

Question 28

Which type of transcripts do eukaryotic translation machinery only recognize?

Answer 28

monocistronic

Question 29

What is the role of the ER?

Answer 29

protein folding, packaging, and some modification

Question 30

What is the role of the Golgi?

Answer 30

modification of proteins and transport them out

Question 31

What is the exocytic pathway?

Answer 31

proteins that get secreted by the cell

Question 32

Where does the Golgi direct proteins when they need to be degraded?

Answer 32

lysosome

Question 33

What are the 3 endocytic pathways?

Answer 33

phagocytosis, pinocytosis, and receptor-mediated endocytosis

Question 34

What is phagocytosis?

Answer 34

"cell eating"; constantly taking in molecules from the environment; ex of phagocytic cell = immunological cells

Question 35

What is pinocytosis?

Answer 35

cell-drinking, taking up fluids

Question 36

What cytoskeleton element mediates phagocytosis and pinocytosis and why?

Answer 36

actin because these cells are constantly stretching

Question 37

What is receptor-mediated endocytosis?

Answer 37

use of receptors to get inside the cell (mode of entry with viruses)

Question 38

What specific type of protein mediates the receptor-mediated endocytosis and how?

Answer 38

clathrin-coated proteins that assemble under the receptor-endocytic area of the membrane to take substance in

Question 39

What are the 4 roles the cytoskeleton?

Answer 39

cell movement, chromosome separation, transport of organelles/things inside cell, provides shape and mechanical strength

Question 40

What are microtubules and what does it establish in the cell?

Answer 40

cytoskeleton element made up of tubulin; establishes polarity in the cell (gives direction of transport)

Question 41

Where is actin usually located within the cell and what is it's role?

Answer 41

usually around the plasma membrane and is involved with the movement of the plasma membrane and other vesicles

Question 42

What is the role of intermediate filaments?

Answer 42

provide cell structure and help cells adhere to neighboring cells

Question 43

What are the 4 hurdles that viruses face after attachment?

Answer 43

receptors and polymerases, actin remodeling, ribosomes and viral mRNA compatibility, and viral-host cell mRNA competition

Question 44

How are receptors and polymerases a hurdle for the virus to enter the host cell?

Answer 44

receptors = virus needs to have a receptor to be readily available and exposed to bind with to get into cell ||| polymerase = (depending on nature of nucleic acid) DdDp needs to be active/available for DNA viruses or same with RdRp for RNA viruses

Question 45

How is actin a hurdle for the virus and what will it do to overcome this in order to enter the host cell?

Answer 45

actin (present on cell membrane) serves as a blockage for viral entry so virus needs to remodel actin via receptor-mediated endocytosis or cause it to remodel to bring virus in

Question 46

How are ribosomes and viral mRNA compatibility hurdles for the virus?

Answer 46

viral mRNA do not have 5'cap = need to get it or find a way for ribosomes to recognize viral mRNA

Question 47

How does the competition against host cell mRNA affect the virus?

Answer 47

virus only want their genome and transcripts to be translated and replicated = need to use up all of host-cell's resources and can't share with host cell mRNA