UNIVERSITY OF THE WITWATERSRAND
DEPARTMENT OF MOLECULAR MEDICINE AND HAEMATOLOGY
Dr Natalie Whalley, HAEM2000, Revision Tutorial
Tutorial 2: DNA, RNA and Protein structure, DNA replication, Transcription
and Translation
Define: Polymer, Nucleotide, Gene, Exon, Promoter, polymerisation
Polymer: this is a molecule comprising of many repeating units called monomers.
Nucleotide: a molecule made of a 5- carbon sugar, 1’ carbon has a nucleobase
attached ( guanine, cytosine, thymine, adenine and uridine in RNA), 5’ carbon has a
phosphate group attached.
Gene: the fundamental unit of information in living life. A segment of DNA that is
expressed to yield a functional product, RNA or Protein.
Protein Structure: this refers to the primary, secondary, tertiary and quaternary
structures that fold a protein.
DNA Replication: this is the process of taking 1 DNA strand and forming two in order
for the cell to divide into two daughter cells.
Transcription: this is the process of forming an RNA strand from a DNA strand.
Translation: this is the process of forming the primary structure of protein from mRNA
using a ribosome
QUESTION 1: Compare DNA, RNA and protein structure using the table below
DNA RNA Protein
Basic unit/ Deoxynucleoside Nucleotide monophosphates Amino acids
building monophosphates
block
Bonds found Phosphodiester bonds Phosphodiester bonds Peptide bonds
Structure Double stranded and linear Depends on what type of Primary,
helix. RNA it is secondary
, tertiary,
quaternary
Direction of 5’ to 3’ 5’ to 3’ 5’ to 3’
synthesis
QUESTION 2: Below is a diagram of a cellular protein
2. a Name the structures represented by A and B? What level of protein
structure is represented by A and B in the diagram. What bonds form the
structures A and B in the diagram?
A- alpha helix
B- beta pleated sheet
2.b What level of protein structure depicted in the whole diagram?
Tertiary structure
2.c If the protein is a dimer of the given structure, what level of structure would
this then be?
Quaternary structure
2.d What bonds could play a role in the folding of the protein?
Hydrogen bonds
Van der vaals forces
Electrostatic attraction
Sulphur bonds
2.e Is it a globular or fibrous protein?
Globular
2.f What substructures could be found in this protein?
Amino acids?
MCQs
1. Deoxyribonucleic acid
Ta. as a helix, exists as a pair of deoxyribonucleic acid polymers which run anti-
parallel
Fb. is made up of 21 basic building blocks, examples of which are leucine and
threonine
Tc. base pairing always constitutes a pyrimidine pairing with a purine
Fd. is arranged as a circular molecule in the nucleus of eukaryotic cells
Te. has an identical composition and function across all species
2. A gene promoter:
Fa. regulates a gene’s function
Tb. is a binding region for transcription factors and other proteins, including
RNA polymerase
?c. is found on the opposite strand (in trans) to its gene being transcribed
Td. usually contains conserved sequences, for example TATA
Fe. is contained within the first exon of a gene
3. RNA is characterised by
Ta. a backbone consisting of sugar and phosphate
Tb. the sugar ribose
Fc. having peptide bonds between RNA bases
Td. a hydroxyl group on the 2’ carbon of the sugar
Fe. the base thymine
4. With regards to protein structure,
Fa. peptide bonds form secondary structure
Tb. primary structure is the sequence of amino acids
F c. alpha helices are tertiary structures
Td. proteins with subunits have quaternary structure
Te. structure determines function
5. With respect to proteins
a. hydrogen bonds maintain secondary structure T
b. peptide bonds form primary structures T
c. quaternary structure is the sequence of amino acids F
d. tertiary structure refers to proteins with subunits F
e. domains are substructures T
Define: Translation, Transcription, Ribosome, Codon, Anticodon,
Central Dogma
Ribosome: a cytoplasmic nucleoprotein which is the cellular machinery that translate
mRNA into proteins.
Codon: the coding sequence on mRNA strands that code for specific amino acid
sequences. They consist of 3 bases.
Anticodon: this is the complementary codon sequence that exists on a tRNA molecule.
This binds to the codon in the A-Site of the ribosome during translation
Central Dogma: this is the molecular biology statement that says the DNA forms mRNA
which in turn forms Proteins
QUESTION 3: Compare DNA Replication and Transcription by completing the
following table
DNA Replication Transcription Translation
What is Dna is being replicated DNA is being mRNA is being
happening to from 2 dsDNA transcribed to mRNA translated into a
molecules primary protein
structure mad of amino
acids
Where in cell nucleus nucleus Cytoplasm
does it happen
Enzymes used DNA polymerase, RNA poly I, II, III Ribosome
and function topoisomerase,
helicase, single-
stranded DNA binding
protein, primase, DNA
ligase, exonuclease
Direction of
synthesis
When does it
happen
QUESTION 4: Label the following diagram of a replication fork
A- DNA Polymerase
B- Leading strand
C- Helicase
D- Topoisomerase
E- Primase or DNA Polymerase
F- Lagging strand
G- Okazaki fragment
H- DNA ligase
QUESTION 5:
One strand of a coding DNA isolated from mammalian cells reads:
5’ –GTAGCCTACCCATAG-3’
a) If deoxyribonucleotide polymerisation occurs (assume no primer is
required), what would the sequence of the resulting DNA strand be? Give
another name for this process.
3’ – CATCGGATGGGTATC- 5’
DNA replication
b) If ribonucleotide polymerisation to form mRNA occurs using the DNA
strand produced in a), what would the sequence of the mRNA be? What is
another name for this process? What is the name of the strand produced
in a)
5’ -GUAGCCUACCCAUAG- 3’
Transcription
Template or anti-sense strand
c) Using the Table below, what peptide would be made if translation started
exactly at the 5’ end of this mRNA and give the codon used for each
amino acid ? (Assume no start codon required) Give the sequence of the
5 anticodons that would be found on tRNA
Val-Ala-Tyr-Pro- stop
d) Would the same peptides be made if the original DNA sequence served
as the template for transcription?
no
e) Could this section of DNA be from the beginning, middle or end of a gene?
End of a gene has UAG sequence which is a stop codon
QUESTION 6:
Using the table below, determine the amino acid sequence of the normal and
abnormal β-globin proteins and indicate the amino acid substitution.
MCQs
1 With respect to DNA replication in human cells:
a. replication is “bi-directional”
b. replication is “conservative”
c. DNA Topoisomerase is necessary to prevent tension or “supercoiling” at the
replication fork
d .leading strand synthesis proceeds in the 5’ to 3’ direction and lagging strand
synthesis in the 3’ to 5’ direction
e. lagging strand replication is “discontinuous”
2. Transcription
a. does not require a primer
b. involves RNA elongation in a 3’ to 5’ direction
c. follows Watson – Crick base pairing rules
d. is regulated by transcription factors binding to the promoter
e. is catalysed by DNA polymerase
3. Translation
a. is the synthesis of protein from carboxyl to amine terminal
b. occurs on ribosomes in the cytoplasm
c. begins at start codon AUG (methionine)
d. requires rRNA with amino acid attached
e. requires mRNA containing anti-codons
4. With regards to gene transcription:
a. euchromatin is tightly packed DNA and is usually not involved in transcription
b. a splice site is a specific sequence occurring at the exon/intron boundary
c. termination of transcription occurs randomly when the RNA polymerase falls
off the strand being read
d. transcription happens in the nucleus only
e. the end product of transcription is an amino acid chain (a protein)
5. Translation requires
a. codons on mRNA
b. chain initiation codon AUG
c. an unwound DNA strand
d. attachment of amino acids to rRNA
e. base pairing between codons and anti-codons
6. Transcription
a. is catalysed by DNA polymerase
b. is the synthesis of RNA from a DNA template
c. requires thymidine triphosphate
d. requires no primer
e. is regulated by enhancer regions in DNA
7. RNA may be processed by
a. polyadenylation of 3’ end
b. phosphorylation of uracil
c. removal of exons by spliceosome
d. methylguanosine cap of 5’end
e. methylation of bases
8. Exonic sequences (exons):
a. need to be removed from the initial mRNA transcript
b. are small, about 100-250bp in size
c. represent the mature mRNA sequence
d. make up a large percentage of the human genome
e. are interrupted by introns, which are generally much larger than the exons
9. The following are examples of post translational modifications
a. Glycosylation
b. Carbonylation
c. Phosphorylation
d. Methylation
e. Esterification
10. Proteins can be post translationally modified by:
a. phosphorylation of serine amino acids
b. polyadenyaltion of their carboxy termini
c. polyubiquitination of lysine amino acids
d. acetylation of lysine amino acids
e. ketonisation of glycine amino acids
