MM 5-6

Question 1

What is DNA replication and when does it occur in the cell cycle?

Answer 1

DNA replication occurs in during S phase of interphase. Editing of DNA happens during G2 phase. It is Semi-conservative, so each copied strand of DNA has one parent strand.

Question 2

Topoisomerase

Answer 2

Topoisomerase unwinds the supercoil during DNA replication and transcription.

Topoisomerase bind to double-stranded DNA and cut the phosphate backbone of either one or both the DNA strands. This intermediate break allows the DNA to be untangled or unwound, and, at the end of these processes, the DNA backbone is resealed again.

Question 3

Helicase

Answer 3

Helicases are motor proteins that move directionally along a nucleic acid backbone, separating two annealed nucleic acid strands using energy derived from ATP hydrolysis. Many cellular processes, such as DNA replication, transcription, recombination, and DNA repair involve the separation of nucleic acid strands that necessitates the use of helicases.

Question 4

Single-Strand Binding Proteins

Answer 4

Single-Strand Binding Proteins attach to single strands to prevent strands from re-associating.

Question 5

primase

Answer 5

Primase makes a small RNA primer that is 5 bases long and runs complimentary to the template. This occurs because DNA polymerase cannot extend a chain from scratch. After replication, the primer is removed and replaced by DNA Polymerase.

Question 6

DNA Polymerase

Answer 6

DNA polymerase reads in a 3-5 direction and replicates in a 5-3 direction by adding nucleotides with Watson Crick base pairing and catalyzing the phosphodiester bonds.

Question 7

Proliferating Cell nuclear antigen (PCNA)

Answer 7

Proliferating Cell nuclear antigen (PCNA) keeps DNA polymerase bound to the template like a sliding clamp.

Question 8

DNA Polymerase alpha:

Answer 8

DNA Polymerase alpha: involved with initiation but lacks proofreading, later replaced by sigma or epsilon.

Question 9

DNA Polymerase sigma:

Answer 9

DNA Polymerase sigma: Lagging strand synthesis and fills gaps

Question 10

DNA Polymerase epsilon

Answer 10

DNA Polymerase epsilon: Leading strand synthesis and fills gaps

Question 11

DNA Polymerase beta:

Answer 11

DNA Polymerase beta: involved in DNA repair. Performs base excision repair required for DNA maintenance, replication, recombination.

Question 12

DNA Polymerase gamma:

Answer 12

DNA Polymerase gamma: Replicates mitochondrial DNA

Question 13

Okazaki fragments

Answer 13

segments on the lagging strand, separated by primer.

Question 14

Telomeres

Answer 14

Telomeres (TTAGGG): thousands of repeated sequences that are synthesized and maintained by Telomerase. Telomerase exists in rapidly dividing single cells and germ line cells. It is absent in most somatic cells, so they get shorter through time

Question 15

Types of DNA editing

Answer 15

Mismatch repair, base excision repair, nucleotide excision repair, recombination repair.

Question 16

Transcription

Answer 16

Transcription makes RNA. Thymine is replaced with Uracil. Single stranded. Start (promoter) and stop (terminator) signals area of transcription. Occurs in nucleus and then RNA is transported through nuclear membrane to ribosomes.

Question 17

rRNA

Answer 17

rRNA: Ribosomal RNA. Accounts for 80-90% of RNA in cells. It is produced by transcription but not translated. It plays a structural and enzymatic role in ribosomes.

Question 18

tRNA

Answer 18

tRNA: Transfer RNA. Transcribed but not translated. Covalently bind Amino acids and transports them to ribosome.

Question 19

mRNA

Answer 19

mRNA: Messenger RNA is translated and contains instructions for protein synthesis.

Question 20

RNA Polymerase

Answer 20

RNA Polymerase (RNAP): Produces primary transcript RNA. Reads DNA coding (sense) strand in 3-5 direction (only). Produces RNA template (antisense) strand in 5-3 direction. Does not need primer.

Question 21

sense/antisense strands

Answer 21

sense = template (DNA) strand
antisense = coding (RNA) strand

Question 22

RNAP 2

Answer 22

RNAP 2: makes mRNA

Question 23

RNAP 1

Answer 23

RNAP 1: makes rRNA

Question 24

RNAP 3

Answer 24

RNAP 3: makes tRNA

Question 25

endonuclease

Answer 25

Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. RNA is transcribed beyond the translated region so that endonuclease has room to cleave the RNA

Question 26

post-transcriptional mRNA processing

Answer 26

Post-transcriptional mRNA processing: The product of RNAP2 transcription, called heterogeneous RNA (hnRNA), is unfinished and unedited. Only after 5’capping, splicing, and 3’ poly(A) tailing do we have finished mRNA.

Question 27

5’ Capping

Answer 27

5’ Capping: the 5’ end gets capped with 7-methyl-guanosine , which attracts proteins that protect the hnRNA from nucleases.

Question 28

Poly(A) polymerase

Answer 28

Poly(A) polymerase adds sequences of adenine to the 3’ end, to which proteins bind, protecting it from rapid destruction in the cytosol so that the mRNA may be translated many times.

Question 29

Differential Splicing

Answer 29

Differential Splicing: introns are removed by the spliceosome in collaboration with Small Nuclear RiboNucloeProteins (snRNP). Introns removed in lariat shape and exons merged. One hnRNA can make several different mRNAs depending on how it is spliced. Splice variants normally occur in different tissues. Therefore, an intron in one primary transcript may be an exon in another. This is how 30,000 genes code for 100,000 proteins.

Question 30

RNA editing

Answer 30

Editing events may include the insertion, deletion, and base substitution of nucleotides within an RNA molecule. RNA editing also allows for different proteins being made by the same primary transcript by adding a stop codon into the sequence of the final RNA, making the amino acid sequence shorter, the protein smaller.