DNA replication and gene expression

Question 1

DNA double helix stability is affected by

Answer 1

-temperature
denaturation or melting of the helix
 cations
stabilize the helix; reduce charge repulsion of the two
strands
 base mismatches
destabilize the helix
 length of the helix
longer helices are more stable
 proteins
histones – positively charged proteins

Question 2

Eukaryote DNA structure: nucleosome

Answer 2

-Complex of DNA double helix and proteins called histones
 Loosely packed form of DNA
 DNA replication and gene expression

Question 3

Bacterial DNA structure

Answer 3

 circular

 supercoiled

Question 4

DNA Replication- What? When? where?

Answer 4

What: the copying of DNA sequence

 When: before the cell divides (S phase)
some repair-associated DNA replication can go on
throughout the cell cycle

 Where: nucleus, mitochondrion, chloroplast
and also in test tubes
DNA replication in the mitochondrion and
chloroplast is not usually tied to cell division

Question 5

DNA replication requirements

Answer 5

it must be coordinated with cell cycle
 fidelity of replication must be very high
mistakes are mutation

Question 6

DNA replication how it happens ?

- replication is semi-conservative

Answer 6

replication is semi-conservative
 each daughter helix has one old strand, one newly
synthesized strand
- new nucleotides are added according to the WatsonCrick
pairing rules

Question 7

DNA replication materials needed

Answer 7

-Helicase: unwind parental double helix
 Single-strand binding protein: maintains ssDNA
 Topoisomerase: prevents ‘overwinding’ ahead of
replication fork
 Primase: synthesizes RNA primer
 DNA polymerase III: elongates DNA by adding to
primer
 DNA polymerase I: removes RNA primer from 5’
end and replaces it with DNA
 DNA ligase: joins strands of DNA

Question 8

How DNA replicates events

Answer 8

the helix is unwound
 helicase unwinds helix ahead of the fork
 Initiates at the origin of replication

the helix is unwound at the origin of replication
 short RNA primers are made

 the primers are extended by DNA polymerase
 the region where replication is going on is called a
replication fork

 DNA polymerase
has directionality
 can synthesize new DNA
only in the 5’  3’
direction (on the new
strand)
 must have a 3’-OH on
which to attach a new
nucleotide 

on the leading strand, synthesis is continuous
 on the lagging strand, synthesis is discontinuous
 Okazaki fragments
 helicase unwinds more helix ahead of the fork
 overwinding is resolved by topoisomerase

Question 9

Correction of errors

Answer 9

errors are mispairings (potential mutations)
 non-Watson/Crick pairings
 an uncorrected base-pairing error through another replication
cycle
AT  AC AT
AC  AT GC
so, in one lineage, an AT pair gets converted to a GC pair
 DNA polymerase corrects mispairings before proceeding
 this is the proofreading function
 it explains why DNA polymerase needs an end to work with - it
needs an end of a correctly-paired nucleotide residue
 paired bases that do not fit the active site, that do not have the
common geometry of AT and CG pairs are fixed
 the finished helix is scanned for mispairings

Question 10

Mutations in humans

Answer 10

Sickle cell anemia
 Point mutation in hemoglobin

Huntington’s disease
 CAG repeat in protein-coding gene

Question 11

Genetically modified crops

Answer 11

 Nutrition, disease resistance and
pharmaceuticals
 “Golden” rice or plants with
genetically-engineered resistance to
diseases, or containing Vitamin A,
edible vaccines
 Herbicide resistance
 Allows farmers to spray crop
to kill only the weeds
 Pesticide resistance
 Kills insects that feed on crops
 Faster growth rate

Question 12

Genetically modified salmon

Answer 12

First genetically modified animal
 Recently received FDA and Health Canada approval for
human consumption

Question 13

From gene to protein

Answer 13

What: transcription of DNA
to RNA; translation of
RNA to protein
 Where: nucleus, cytoplasm,
ER, golgi in eukaryotes;
cytoplasm in bacteria

Question 14

From gene to protein - requirements

Answer 14

 fidelity of mRNA transcript must be very high
mistakes are mutations
 fidelity of protein sequence must be very high

Question 15

From gene to protein - Principles

Answer 15

Information in DNA, RNA and protein is colinear
linear sequence of nucleotides in the coding portion
of a gene
 linear sequence of nucleotides in mRNA
 linear sequence of amino acids in a polypeptide

Question 16

From gene to messenger RNA - material needed

Answer 16

RNA polymerase: joins complimentary RNA
nucleotides to the 3’ end of RNA transcript
 mRNA: synthesized by RNA polymerase, codes for
protein sequence

Question 17

Transcription events

Answer 17

 Initiation, elongation, termination
 the helix is unwound
 RNA nucleotides are extended by RNA polymerase
 Assembled in the 5’  3’ direction
 mRNA transcript is created

Question 18

Transcription initiation

Answer 18

 In bacteria
 RNA polymerase binds to promoter
 In eukaryotes
 RNA polymerase binds to transcription factors that are bound to the
promoter

Question 19

Elongation of transcript

Answer 19

10 – 20 DNA nucleotides are exposed at one time
 DNA nucleotides pair with RNA nucleotides
 Progresses at a rate of 40 nucleotides/second in eukaryotes

Question 20

Transcript termination

Answer 20

In bacteria:
 Proceeds through
terminator
sequence in the
DNA and signals
the end of
transcription
 In eukaryotes:
 Proceeds through
the
polyadenylation
signal in the premRNA;
this is later
cleaved off

Question 21

Split Genes and RNA Splicing

Answer 21

Most eukaryotic genes and their RNA transcripts have long
noncoding stretches of nucleotides that lie between coding
regions
 These noncoding regions are called intervening sequences, or
introns
 The other regions are called exons because they are eventually
expressed, usually translated into amino acid sequences
 RNA splicing removes introns and joins exons, creating an
mRNA molecule with a continuous coding sequence

Question 22

Alteration of mRNA ends

Answer 22

 Each end of a pre-mRNA molecule is modified in a
particular way
 The 5 end receives a modified nucleotide 5 cap
 The 3 end receives a poly-A tail
 These modifications share several functions
 They seem to facilitate the export of mRNA
 They protect mRNA from hydrolytic enzymes
 They help ribosomes attach to the 5 end

Question 23

From mRNA to protein - material needed

Answer 23

mRNA: synthesized by RNA polymerase, codes for
protein sequence
 The genetic code is a triplet code
 Codon: three-nucleotide sequence that specifies a
particular amino acid; basic unit of the genetic code
 linear: bases of mRNA = letters
 unambiguous: each codon specifies only 1 amino acid
 redundant: 18 of 20 amino acids encoded by more than
one codon
 universal: same code used by all organisms, with few
differences

Question 24

From mRNA to protein

- material needed

Answer 24

 mRNA: synthesized by RNA polymerase, codes for
protein sequence
 tRNA: molecule containing anticodon and amino
acid
 Anticodons: specific sequence of three
nucleotides on tRNA; complementary to a codon
triplet on mRNA
 rRNA: together with protein makes up ribosome
 Ribosome: facilitates coupling of tRNA anticodons
with mRNA

Question 25

Ribosomes

Answer 25

The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rRNA)  Bacterial and eukaryotic ribosomes are somewhat similar but have significant differences: some antibiotic drugs specifically target bacterial ribosomes without harming eukaryotic ribosomes

Question 26

Elongation of the Polypeptide Chain

Answer 26

During the elongation stage, amino acids are added one by one to the preceding amino acid at the C-terminus of the growing chain  Each addition involves proteins called elongation factors and occurs in three steps: codon recognition, peptide bond formation, and translocation  Translation proceeds along the mRNA in a 5′ to 3′ direction

Question 27

Termination of Translation

Answer 27

Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome  The A site accepts a protein called a release factor  The release factor causes the addition of a water molecule instead of an amino acid  This reaction releases the polypeptide, and the translation assembly then comes apart