Smith Molecular Genetics 2-6

Question 1

What is DNA replication and what stage does it take place?

Answer 1

the process in cells that produces two identical copies of DNA from one original DNA molecule
S phase of interphase

Question 2

What are three models of DNA replication that have been considered in the late 1950s?

Answer 2

Conservative mechanism: after the first replication of the two DNA molecules, one retained the old two parental strands. In the end 3/4 are new and 1/4 are the old strands

Semiconservative mechanism: the first replication creates two mixed strands and the second creates two new and two mixed strands

Dispersive mechanism: results in all strands having interspersed segments of both parental and replicated DNA

Question 3

Out of the three considered models for DNA replication, which one is correct? And what experiment confirmed this?

Answer 3

Semiconservative mechanism

Meselson and Stahl’s experiment

Question 4

Separation of the parental strands begins at ______ origins of replication in each chromosome. Thus, replication is _______.

Answer 4

several, bidirectional

Question 5

What are the four deoxynucleoside triphosphates used in DNA synthesis?

Answer 5

dATP, dGTP, TdTP, and dCTP

Question 6

Enzyme DNA ______, which synthesizes the new DNA strands, can only add nucleotides onto the __ end of a new daughter strand; the direction of synthesis is in the 5’ to 3’ direction

Answer 6

polymerase, 3’

Question 7

The addition of nucleotides to the daughter strand requires energy. Where is this energy from?

Answer 7

Bonds between the phosphates is broken (when pyrophosphate is removed) releasing energy used to form a bond between the incoming nucleotide and the growing chain

Question 8

At each replication fork, one strand is synthesized continuously 3’ to 5’ and the other strand is synthesized ____ from the replication fork along the _____ strand template in fragments called _________ _______.

Answer 8

away, lagging, Okazaki fragments

Question 9

Describe the role of helicase.

Answer 9

Unwinds the double helix by breaking hydrogen bonds; this has the effect of twisting the double helix in front more tightly

Question 10

Describe the role of Topoisomerase and Single-Binding proteins

Answer 10

Topoisomerase’s (gyrase’s) role is to alleviate additional coiling by breaking, swivelling, and rejoining the DNA strands ahead of the replication fork
Single-stranded binding proteins prevent separated strands from coming together again behind DNA helicase

Question 11

Describe the role of primase.

Answer 11

associate with a bare template strand and build a complementary RNA primer consisting of 5 to 10 nucleotides

Question 12

Describe the role of DNA polymerase III

Answer 12

removes single-stranded binding proteins and begins to build a daughter strand by adding DNA nucleotides to the daughter strand
-AT/GC rule

Question 13

What is the purpose of the sliding clamp?

Answer 13

holds DNA polymerase III onto the template strand

Question 14

What is lagging strand synthesis?

Answer 14

DNA polymerase III has to detach from the fragment it’s synthesizing because it encounters the RNA primer of a previously synthesized Okazaki fragment, so it releases from the fragment leaving a fragment in place.
The short Okazaki fragments are parts of what is called the lagging strand.
Therefore, synthesis of the lagging strand is by discontinuous replication

Question 15

Describe the role of DNA polymerase I

Answer 15

Attaches to a fragment at it’s 3’ end and removes the RNA primer nucleotides of the neighbouring fragment, replacing them with DNA nucleotides in the 5’ to 3’ direction
Note: a nick remains in the sugar phosphate backbone between the fragments

Question 16

Describe the role of ligase.

Answer 16

Enzyme is needed to complete the covalent phosphodiester bond that will repair the nick left by DNA polymerase I

Question 17

In prophase, each condensed chromosome consists of one old _____ strand and one new ______ strand

Answer 17

parental, daughter

Question 18

True or false? Smaller simpler bacterial chromosome requires only a single origin of replication called the _____.

Answer 18

True, ori

Question 19

What is the central dogma of molecular biology?

Answer 19

DNA codes for RNA (transcription)
RNA codes for proteins (translation)
Proteins do not code for DNA or RNA
-flow of genetic information is one way-

Question 20

What is transcription?

Answer 20

The synthesis of an RNA molecule complementary to a portion of a strand of DNA acting as a template

Question 21

Describe initiation (the first stage of transcription) in eukaryotes.

Answer 21

The TATA box in the promoter unit of a gene consists of 30 base pairs of Ts and As upstream the transcription start point.
First transcriptor proteins binds to the promoter, that recruit the RNA polymerase to the beginning of the transcription unit.
This altogether forms the transcription initiation complex

Question 22

Describe elongation (the second stage of transcription) in eukaryotes

Answer 22

As RNA polymerase reads the nucleotides on the DNA template strand, it uses complementary base-pairing to form the new RNA molecule from ribonucleotide triphosphates (AG/CU)

Question 23

When calculating the complementary RNA sequence to a given DNA sequence what technique should be used?

Answer 23

(1) rewrite the DNA sequence so that it is antiparallel (from 5’to3’ to 3’to5’)
(2)Then write the corresponding nucleotide
(G-C, C-G, A-U, T-A)

Question 24

Describe termination (the third and final stage of transcription) in eukaryotes

Answer 24

When RNA polymerase reaches the end of the gene, it encounters a terminator sequence of nucleotides; the RNA polymerase and the RNA transcript are released from the DNA

Question 25

What is the function of messenger RNA (mRNA)?

Answer 25

possesses the code for a particular polypeptide chain, three nucleotides in length (called codons); code for amino acids

Question 26

How many codons and amino acids are there?

Answer 26

64 codons and 20 amino acids; 18 of the amino acids are coded for by more than one codon

Question 27

What are the start (1) and stop (3) codons?

Answer 27

Start: AUG
Stop: UAA, UAG, UGA

Question 28

Describe the function of transfer RNAs (tRNAs).

Answer 28

Possess the anticodon for the amino acids to be transfered

Aminoacyl-tRNA synthetase enzymes in the cytosol add the correct amino acid onto the tRNA with the appropriate anticodon

Question 29

What is translation?

and what are it’s three stages?

Answer 29

Translation is the synthesis of a polypeptide on a ribosome using the code on an mRNA;
Occurs in the cytosol in both eukaryotes and prokaryotes
Stages: Initiation, Elongation, Termination

Question 30

Describe the Initiation stage of translation.

Answer 30

ribosomal RNAs (rRNAs) act as ribozymes and catalyze protein synthesis.
tRNA and mRNA bind in the small ribosomal subunit and finds the start codon on the mRNA.
A large ribosomal subunit now binds onto the small subunit.
Now there are E, P and A sites for tRNA accommodation

Question 31

Describe the elongation stage of translation

Answer 31

Involves an elongation cycle that adds one new amino acid at a time to the new forming polypeptide chain
At the beginning of each cycle, the polypeptide chain is held by the tRNA in the P site
At the end of the cycle, the polypeptide chain is again held by a new tRNA in the P site.

Question 32

What is the purpose of peptidyl transferase in the elongation stage of translation?

Answer 32

Peptidyl transferase in the large subunit catalyzes the formation of a peptide bond between the two amino acids attached to the two tRNAs held in the P and A sites

Question 33

Describe the termination stage of translation

Answer 33

When a stop codons on the mRNA is encountered in the A site translation is terminated
No tRNAs have an anticodon complementary to the stop codons.
Instead, stop codons in the empty A site are recognized by release factor proteins

Question 34

True or false? several ribosomes migrate along an mRNA at the same time, speeding up the synthesis of the required polypeptide

Answer 34

True

Question 35

What are mutations?

Answer 35

several ribosomes migrate along an mRNA at the same time, speeding up the synthesis of the required polypeptide

Question 36

What are the different kinds of small scale mutations?

Answer 36

(1) Point Mutations- Affect only one base pair in the DNA
(2) Base Subsitution Mutations- An incorrect base is substituted which then results in a change in the base sequence on both DNA strands
[silent mutation, missense mutation, nonsense mutation]
(3) Deletions or insertions- Mutations caused by an insertion or a deletion of a nucleotide within in a gene; results in a frameshift