Download Notes 1 DNA and RNA

1.1 Introduction
In this Topic the structure of DNA will be described and the DNA replication explained.
(a) Chromosomes
 Chromosomes threadlike structures located in the nucleus of all cells (except red blood cells).
 Chromosomes contain the genetic material that determines the characteristics of a living thing.
 All cells store their genetic information within chromosomes in the base sequence of DNA
(b) Genes
Gene: Sequence of 3 bases on the DNA.
Genotype (pattern of genes on a chromosome)
is determined by the sequence of bases.
Phenotype is determined by the proteins made
by the instructions encoded on DNA.
DNA chemical sequence is unique to all
individuals (except identical twins). DNA can be
cut up and separated, forming a sort of
individual 'bar code'. This is why people can be
identified using DNA fingerprinting.
(c) DNA




Deoxyribonucleic acid or DNA codes for proteins in the cell.
During cell division DNA must be replicated so that daughter cells carry an identical set of
instructions to those in the parent cell.
DNA molecules are large and complex.
DNA is inherited.
QUESTIONS
Q1: Give another name for the type of cell division described in part (c) DNA.
Q2: State where within chromosomes all cells store their genetic information.
Q3: How does the genetic information on the DNA determine the phenotype?
Q4: Which organelle in the cell contains DNA?
a) Golgi apparatus
b) Endoplasmic reticulum
c) Lysosome
d) Nucleus
Q5: DNA is a component of which structures?
1.2 DNA Structure and replication
DNA STRUCTURE
DNA is an example of a ______________ acid.
DNA is a long chemical sequence and this sequence contains the
information needed for that living thing to develop, survive and
pass its genetic information on to the next generation.
DNA is a DOUBLE HELIX characterised by the following:
(I) Nucleotides
Nucleotides are organic molecules that act as monomers (or subunits) of nucleic acids like DNA.
Nucleic acids like DNA are made from repeating units
called __________________________.
NUCLEOTIDES are the building blocks
of nucleic acids and are composed of:
- nitrogenous base ,
- deoxyribose sugar (five-carbon sugar)
- phosphate group
Activity: COMPLETE THE NUCLEOTIDE DIAGRAM
YOU MUST BE ABLE TO DRAW A NUCLEOTIDE IN THE EXAM!
(II) Sugar–phosphate backbone
Nucleotides join together to form chains.
The bonds between nucleotide are called strong
deoxyribose sugar-phosphate bonds.
When a chain of nucleotides join through sugar
phosphate bonds this forms the
deoxyribose sugar-phosphate backbone.
Activity:
1. Draw the strong deoxyribose-phosphate
bonds between the nucleotides.
2. Write 3’ and 5’ at the correct end of the
strand.
(III) HYDROGEN BONDS between nitrogenous bases

DNA encodes hereditary information in a chemical language.

There are 4 nitrogenous bases:
Adenine, Thymine, Cytosine and Guanine.
(IV) Base pairing is specific in the pattern:
Adenine ====== Thymine
Guanine ====== Cytosine
(V) Double stranded antiparallel structure:
 DNA is composed of 2 polynucleotide
chains

The two polynucleotide chains run
antiparallel with a deoxyribose sugar at the
3’ end and phosphate group at the 5’
(VI) Each chain is joins to a COMPLIMENTARY
chain by weak HYDROGEN BONDS between
nitrogenous bases. The DNA structure is a
antiparallel stranded double helix.
The four bases in DNA. The complimentary bases are:
____________ and ____________,
____________ and ______________.
It is only the bases which makes one nucleotide different from another.
Since there are only four different bases, there can only be four
_________________ in DNA .
different
Nucleotides join together by ______________ bonds to form a sugar-phosphate backbone.
The bases pair off and are held together by weak _______________ bonds, forming a
twisted double
___________. Adenine is always opposite
____________ ;
____________ is always opposite cytosine. The paired antiparallel strands coil forming a
_______________ _______________.
Web site http://www.youtube.com/watch?v=BmDG_fKUTR8
ACTIVITIES
Learner activity 1:
DNA – True or False
Learner activity 2: Short questions
Create your own DNA! Using cutting and pasting
Learner activity 3: DNA extraction. Collect a worksheet.
Learner activity 4: Discovering the structure of DNA. Collect a summary sheet.
Learner activity 5: How the structure of DNA was discovered. Case study.
Learner activity 6: Answer question set B
Learner activity 1: TRUE or FALSE
1. DNA is found in some living cells
2. DNA is the heredity material – it is passed on from one generation to the next.
3. Your DNA is the same as the DNA of the person sitting next to you.
4. DNA is found in the cytoplasm of the cell.
5. The DNA sequence – the chemical language – doesn’t matter as it doesn’t change anything
about the living thing.
Learner activity 2: SHORT QUESTIONS
1. What is a "strand" of DNA?
2. How many strands make up a DNA double helix?
3. Each strand is made up of two zones or regions. One zone of each strand is made up of
…identical repeating units, while another zone is made up of differing units.
…What are the zones of each strand called?
4. The DNA double helix looks like a twisted ladder. What makes up each rung of the ladder?
5. What holds the rungs together at the sides?
6. What holds one strand against the other in the double helix?
7. What are the four pairs of DNA bases that form in the double helix?
8. How can A distinguish T from C?
9. Which DNA double helix do you think would be harder to separate into two strands: DNA
……...composed predominantly of AT base pairs, or of GC base pairs? Why?
10. What is a mutation?
DNA HISTORY FOR CASE STUDY
At the turn of the 20th century scientists new that chromosomes contained the ‘genetic material’
that enabled organisms to pass on hereditary material or ‘genes’ to the next generation. Over the
next 50 years six scientists research elucidation of the structure of DNA and reveal the following:
.
Research conclusion:
Scientist(s)
.
1. DNA that was the ‘genetic material’,
Griffiths and Avery et al.,
2. Nucleic acid bases of DNA were found in set ratios, Chargaff
3. DNA was a double helix, composed of paired
Franklin & Wilkin : Watson & Crick
bases along two sugar phosphate backbones,
running parallel but in opposite directions
Over the next 30 years further research proved
1. ‘genetic material’ was composed of: 1.DNA with protein, 2. RNA
2. The DNA made into protein using RNA as a messenger.
3. There is a vast number of possible amino acid combinations in proteins as:
a. The 4 bases in DNA can be arranged in any combination
b. The 20 amino acids which can be arranged in any order.
RESEARCH HISTORY FOR CASE STUDY
Griffiths:
Experimental evidence from Bacterial transformation
Conclusion: A material from a virus which was heat stable and not protein could be transformed
………………….into and between mice.
Fig.1. Griffith’s experiment showing
the fate of mice when infected with
different strains or strain combinations
of the Streptococcus pneumonia virus.
The experiment in the final column
revealed to Griffith’s that there exists a
‘transforming principle ‘which he
assumed to be protein.
Avery et al.,:
Experimental evidence to identify the transforming agent.
Conclusion: Avery deduced which of the macromolecules (polysaccharide, protein, RNA or DNA)
were transformed from bacteria to mice. He used a series of systematic enzyme assays to
degrade each of the macromolecules one at a time. They discovered that it was only through the
use of DNAse (which degrades DNA) did the transformation cease.
Hershey & Chase:
Phage experiments
1
2
Experiment 1, on the top line, shows the results of when DN radioactively labelled, with radioactivity being detected in the cell.
Experiment 2, shows the results when protein was radioactively labelled, with radioactivity being detected in the solution which
contained the ‘phage ghosts’. The results revealed that DNA was the genetic material.
Erwin Chargaff - Chargaff’s Rules and the base composition of DNA
Chargaff analysis showed:
1. Hydrolysed DNA from a number of different organisms and found that DNA always
contained 50% A & T bases and 50% G + T bases.
2. Number of adenine + thymine basis equal Number of guanine + cytosine.
3. The percentage of each base was species specific and responsible for variation within a species.
The bases were not arranged in the same pattern on DNA across all species, there was the possibility of
DNA holding the key to the diversity of life.
Example: What is the percentage of Cytosine in DNA if the percentage of Adenine is 20%?
Percentage of A = Percentage of T
Thus, % T = 20%
Percentage A+ T = Percentage G + C
Thus, % G + C = 80%
Percentage of G = Percentage of C
Thus, % G = 40%
Rosalind Franklin & Maurice Wilkins–DNA is helical & has measured regularities
in its structure
Using a technique called x-ray diffraction, Franklin and Wilkins produced x-rays of molecular structure of
DNA. The technique involved sending beams of parallel x-rays at isolated strands of DNA. When the xrays collide with the atoms they diffract to an extent which is dependent on the molecular weight and spatial
arrangement of the atoms. These diffracted x-rays are then collected on a photographic plate and the
resulting pattern analysed.
James Watson & Francis Crick–Model for physical & chemical structure of DNA
Watson and Crick came to their conclusions from the experimental data of others, (Chargaff, Wilkins and
Franklin), and offered no fresh experimental data of their own.
The structure of DNA:
 DNA is a double helix formed from two polynucleotide
chains that are wound around in a clockwise direction.
 The two polynucleotide chains are antiparallel, meaning that
they are positioned head to tail (each chain has a 5’ end and
a 3’ end and so the 5’ end of one lies opposite the 3’ end of
the other)
 The sugar-phosphate backbone which forms from the
connection between the nucleotides is on the outside of the
double helix. The nucleotide bases are on the inside,
perpendicular to the sugar phosphate backbone.
 Each base is connected to a complementary base on the
parallel chain by weak hydrogen bonds. Adenine always pairs with thymine by two hydrogen bonds
and guanine to cytosine by three hydrogen bonds. No other base pairings would work to give rise to
this DNA structure.
 Structurally, the base pairs are 0.34 nm apart and each
3600 degree turn of the helix is 3.4 nm (10 base pairs).
Also, as the nucleotides are unequally spaced between the
two polynucleotide strands because they are antiparallel,
there are unequal grooves in the helical twist.
1(a)(ii) Organisation of DNA in prokaryotes and eukaryotes
In both prokaryote cells and eukaryote cells DNA is organised into structures called chromosomes.
CELL TYPES
Examples of cells:
Prokaryotic cells
1. Bacteria and fungal cells
Eukaryotic cells
1. Animal and Plant cells
Nucleus present:
2. No nucleus
2. Contain a nucleus
Chromosome number:
3. One
3. Numerous
Chromosome shape:
4. Circular
4. Linear
DNA folding type
5. Supercoiled DNA
5. DNA coiled with proteins
Additional DNA:
6. In plasmids
6. In mitochondria and/or chloroplasts
Prokaryotic chromosomes
PROKARYOTE CHROMOSOME:
Prokaryotes have a single double-stranded and circular chromosome, which carries the
organism’s genetic material. In bacteria, DNA is packaged tightly, into a given area of the cell
called the nucleoid.
PROKARYOTE PLASMID:
If the prokaryote has a second circular chromosome carrying a DNA sequence that is superfluous
to the existence of the organism then it is called a plasmid. Some prokaryotes, have more than
plasmid, which can be either a copy of the first or be composed of a different DNA sequence and
which can contain essential or non-essential genes.
(A) Circular chromosomal DNA and plasmids in bacteria.
SUPERCOILING
Supercoiling is the key way in which prokaryotes package
the huge length of DNA that makes up their genome into a
small area in the cell.
Imagine an elastic band being twisted, it first makes twists
which then produce an ever-tighter wound band. The
elastic band will finally begin to supercoil, producing bends
of twisted elastic, making the elastic band ever more
compact. This happens when DNA supercoils.
(B) Circular plasmids in yeast.
Not super coiled
Super coiled
Further information about chromosomes in prokaryotes can be found at the Nature Scitable site:
http://www.nature.com/scitable/topicpage/genome-packaging-in-prokaryotes-the-circular-chromosome-9113
Eukaryotic chromosomes
In contrast to prokaryote chromosomes:
1. Eukaryotes have several linear chromosomes contained within a membrane-bound nucleus.
2. The number of eukaryotic chromosomes is consistent in a species but can vary across species.
e.g.Humans have a haploid set of 23 chromosomes; wheat has a haploid set of 7 chromosomes.
DNA in eukaryotes:
Eukaryotes use different methods from Prokaryotes to compact their DNA into chromosomes.
Linear chromosomes in the nucleus.
Circular chromosomes in mitochondria/chloroplasts
Eukaryotic cells also contain extra packages of DNA out with the nucleus: Mitochondrial DNA
mtDNA is found in both plants and animals, whereas chloroplast DNA (cpDNA) is only found in
green plants. These genomes are not inherited in a medallion fashion like chromosomes in the
nucleus, but instead are inherited solely from the mother with the other cytoplasmic organelles.
MITOCHONDRIAL DNA (mtDNA)
MtDNA is often circular, double-stranded and lacking in the structural proteins of the nuclear
chromosomes, much like the chromosomes found in prokaryotes. Their size varies enormously
between species. In the main, the mitochondrial genome codes for transfer RNAs (tRNAs),
ribosomal RNAs (rRNAs) and some subunits of proteins found in mitochondria.
CHLOROPLAST DNA (cpDNA)
CpDNA is structured similarly to mtDNA: it is circular, double-stranded and lacks structural
proteins. Chloroplasts can contain many copies of cpDNA, with the copy number variable between
species. The size of the cpDNA genome varies between species and can be anywhere between
80 and 600 kb. Amongst the genes on the cpDNA lie those that code for the rRNAs, tRNAs and
some proteins required for translation, transcription and
photosynthesis.
(The origin of mitochondria and chloroplasts is debated
scientifically. The endosymbiont theory, proposes both
mitochondria and chloroplasts were originally free-living
bacteria that invaded primitive eukaryotic cells and
through the course of evolution the bacteria and the
original host became dependent to the point where one
could not live without the other. This emphasises the
interconnectivity of living things).
Packaging of DNA in eukaryotic chromosomes
The organisation of DNA in a eukaryotic cell
depends on the stage of mitosis they are in.
The level of organisation in the packaging of DNA
is truly amazing.
The length of a DNA molecule, if held taut, end-toend, in just one human chromosome would
measure 4 cm. Given that cells are not nearly that
big, our cells are capable of packaging this amount
of DNA into chromosomes 1.2–2 µm in length. (This
means that end-to-end you could fit 10,000
chromosomes along the length of a fingernail).
If you take this figure and the fact that we have 46
chromosomes in each cell we can calculate a total
length of DNA in one human cell to be 1.84 m (the
height of a 6-foot person). Considering the number
of cells we have, we have enough DNA that if put
end to end it would reach the moon and back!
Figure 4: Overview of the levels of packaging seen in a
metaphase chromosome
Nucleosomes
DNA double helix is wrapped around histone
proteins forming nucleosomes (beads on a string)
The pieces of DNA between the nucleosomes is
known as linker DNA and is a constant length.
The combination of DNA and protein is called
chromatin.
This level of organisation is seen throughout the cell
cycle and mitosis.
DNA in the linear chromosomes in the nucleus of eukaryotes is tightly coiled and packaged with
associated proteins.
There are 4 levels of packaging in cells, the highest of which is only seen during metaphase.
Level 1: Nucleosomes
DNA in the form of a double helix is wound around
histone proteins, forming nucleosomes.
Histones are positively charged and so bind tightly to
the negatively charged DNA.
The lengths of DNA between the nucleosomes are
called linker DNA.
This level of organisation is seen throughout the cell
cycle, with only transient separation during replication.
When several nucleosomes form this is commonly
called ‘beads on a string’.
The combination of proteins and DNA is called
chromatin, so the beads on a string structure shown
here is a chromatin fibre.
Level 2: Thick chromatin fibre
The length of nucleosomes then coils to form a thicker
chromatin fibre, about 30 nm thick, due to interactions
between the nucleosomes and linker DNA. This level
of packaging can be seen during interphase.
Level 3: Looped fibres
The thick chromatin fibre then folds along a nonhistone protein scaffold, producing fibres that are now
300 nm thick. This level of packaging can be seen
during prophase.
Level 4: More folds to make the most compacted chromosome
The chromatin (DNA + protein)
folded along the protein scaffold
then folds further to produce the
compacted chromosomes that are
seen during metaphase. This is
DNA in its most compacted form.
Note that this image shows a
metaphase chromosome, which
consists of two chromatids following
replication.
Arrangement of DNA in a Prokaryote and Eukaryote cell
DNA is packaged in a different way in eukaryotes and prokaryotes.
Prokaryote
Eukaryote
Both
DNA usually found as a
double-stranded
circular molecule
DNA packaged into a
set of linear
chromosomes
DNA is packaged into
chromosomes
DNA not found within a
nucleus
Mitrochondrial DNA
located within the
cytoplasm
Plasmids can be present
Chloroplast DNA in
some species
Genetic material
contained within the
nucleus
The DNA is doublestranded
Organisms have a
different sequence of
bases along the DNA
DNA is the genetic
material
Student activity 9: Prokaryote or eukaryote?
Students cut out the statements on the sheets and place them into one of three groups:
prokaryotes, eukaryotes or both, depending on which they are true for.
(b) DNA can direct its own replication
(i) Replication of DNA
Prior to cell division, DNA polymerase replicates a DNA strand precisely using DNA nucleotides.
DNA REPLICATION
AIM: DNA replication in the nucleus prior to cell division (INTERPHASE)
EQUIPMENT:
1. DNA template
2. Supply of each type of DNA nucleotide (Bases A,T,G,C)
3. Energy supplied by triosphosphate molecules such as ATP.
4. Appropriate enzymes-DNA polymerase (enzyme to join new nucleotides to the DNA strand)
5. Forward and reverse primers to start replication.
1. Template DNA unzips: Hydrogen bonds between base pairs break.
The 2 anti-parallel strands are
COMPLIMENTARY as nucleotides
on one strand can be used as a
template for the other.
Template – Nucleotide binding is as follows:
Adenine----Thymine
Cytosine---Guanine
2. PRIMERS: bind to the origin of replication to permit the DNA polymerase to bind to the DNA.
Free nucleotides position themselves so that their bases can HYDROGEN BOND with the
complimentary bases on each of the nucleotide strands [A-T] [C-G]. ATP supplies the energy for
bond formation.
3. Free DNA nucleotides now in position, link up through sugar phosphate groups by forming
DEOXIRIBOSE SUGAR PHOSPHARE BONDS. DNA polymerase catalyses addition of
complementary nucleotides to the deoxyribose (3') end of the leading DNA strand. This occurs at
several locations on a DNA molecule to speed up the process.
4. Problem:
DNA polymerase only adds nucleotides in one direction 3’ to 5’
Solution: One strand (leading strand) is replicated continuously.
The other strand (lagging strand) winds round twice in the DNA
polymerase so that a short section can be read in the correct 3’ to
5’ direction. This is repeated so that the lagging strand is
replicated in Okasaki fragments.
5. Fragments of DNA are joined together by ligase.
6. Once the whole length of the DNA has
been replicated 2 DNA molecules are formed,
which recoil into double helices identical to
each other and the original.
This is the semi-conservative model
of DNA replication.
Only DNA has all the requirements for genetic material essential to the continuation of life.
1. Very stable: Coded instructions remain intact.from one generation to the next.
2. Replicate: Can provide new copies of the genetic instructions for each new cell.
3. Controls cells activities by controlling protein synthesis: DNA is aided by another nucleic acid
called RNA.
QUESTIONS
1. What shape is the DNA molecule?
2. What type of bonding holds two DNA strands together?
3. Which two components make up a DNA molecule?
4. Name the nitrogenous base that pairs with cytosine.
5. Name the nitrogenous base that pairs with thymine.
6. Which is the stronger bond: one between complementary bases A and T, or one between G
and C?
Semi-conservative replication
The mechanism of DNA replication is said to be semi-conservative.
That is, after replication, each of the two resulting DNA molecules is composed of one original (or
conserved) strand and one new strand (middle diagram below).
This hypothesis, put forward by Watson and Crick, was proved experimentally by Meselson and
Stahl in the late 1950s.
METHOD:
1. Their experiment involved growing a culture of the bacterium Escherichia coli in a growth
medium containing heavy nitrogen (15N).
2. As the bacteria grew, they incorporated the heavy nitrogen into their nitrogenous bases.
3. The bacteria were subsequently inoculated into growth media containing light nitrogen
(14N) and 3 DNA classes were subsequently extracted after changing to the light medium.
4. The three classes of DNA were:
a. parental DNA. b._ first replication DNA; c. second replication DNA.
RESULTS:
The results of the experiment showed that parental DNA grown in heavy medium was ’heavier’
than when grown in light medium. First generation growth showed that the DNA was all of medium
density. Lastly, the second generation showed DNA of both medium and light intensities. Second
generation growth supported the semi-conservative model of DNA replication since there were two
bands of growth (one with both conserved and new DNA, and a band of light DNA).
Essay question
Give an account of the structure and replication of DNA.
REMEMBER:
_ DNA is found on chromosomes inside the nucleus of the cell.
_ Chromosomal DNA is divided up into regions containing genes.
_ DNA consists of two strands twisted into a double helix.
_ DNA strands are made of nucleotides joined together. There are four types of nucleotides.
_ Each nucleotide consists of deoxyribose sugar, a phosphate group and one of four types of
…organic base (adenine, guanine, cytosine or thymine).
_ Base pairing rules - A always pairs with T and G always pairs with C.
Polymerase Chain Reaction: The technique to produce DNA in vitro
PCR is a technique that enables specific sections of DNA to be amplified (replicated) in vitro,
producing millions of copies from a DNA template.
PCR was developed by Kary Mullis in the mid 1980s, revolutionising molecular biology. He
received the Nobel Prize for chemistry for its conception in 1993. Mullis developed the technique
manually, and it can still be carried out using water baths. However, the technique is now fully
automated in laboratories, using thermal cyclers no bigger than a bread machine.
The technique manipulates the cell’s natural mechanism for replication
by using DNA polymerase and the following steps:
High energy bond like ATP
Preparation of PCR mix which contains:
 Dideoxynucleotides:
(This is each base type A, T, G, C with their own
phosphates added using high energy bonds. Like
ATP this enables formation of the new DNA strand
as energy for attachment of nucleotides is released
when phosphates are removed)
 Mg2+, which is a polymerase cofactor.
 Buffer to keep the pH stable.
 Template DNA (Blood, hair root, bacterial colony)
 Forward and reverse primers
 Taq DNA polymerase
The sample is placed in a thermocycler
where the temperature cycles through
3 settings to replicate DNA.
1. Sample DNA is denatured by heating to
give two polynucleotide chains.
2. Sequence-specific primers, which are small
sequences of single-stranded DNA, typically
of 8–15 base pairs in length, anneal to the
DNA flanking the section of interest. One
primer anneals to one strand (forward primer),
another to the other DNA strand (reverse primer).
3. Polymerase begins to replicate the DNA section
of interest using the primers as a starter sequence.
4. The mixture now contains the original template
plus the newly amplified sections.
5. The cycle begins again using original & copied
DNA as templates. As the reaction is exponential,
millions of copies are produced in about 3 hours.
Figure 6: The polymerase chain reaction.
Applications of PCR
PCR is used widely, for example:
1.
DNA profiling/fingerprinting:
PCR is used to rapidly identify individuals. Specific regions of DNA known to vary between
individuals are amplified using fluorescently labelled primers and then analysed using
capillary gel electrophoresis. Profiling is not only used in forensics but also in plant variety
identification, paternity testing and evolutionary biology.
2.
Disease diagnosis: DNA sequences that are known to indicate certain genetic disorders or
diseases are amplified using PCR for the purposes of diagnosis.
3.
Archaeological analysis: Ancient DNA, degraded over the years, can be amplified and
used in archaeological, paleontological and evolutionary research.
4.
Population studies: Analysis of human or other species’ population genetics can be rapidly
performed using PCR analysis.
5.
Sequencing: DNA sequence analysis previously took place following lengthy cloning
experiments, which have now been replaced by PCR.
QUESTIONS:
Q1: DNA is present in which part of the cell?
a) Cytoplasm
b) Nucleus
c) Cytoplasm and nucleus
Q2: DNA is made of which of the following?
a) Nucleotides
b) Amino acids
c) Fatty acids
d) Glucose molecules
Q3: What is the name of the monomers that make proteins?
a) Nucleotides
b) Amino acids
c) Fatty acids
d) Glucose molecules
For further information about PCR refer to the following website:
http://www.dnalc.org/resources/animations/pcr.html
A song about PCR can be seen here:
http://www.youtube.com/watch?v=x5yPkxCLads
And there is a PCR rap here:
http://www.youtube.com/watch?v=oCRJ4r0RDC4&feature=related
RNA Structure and Protein Synthesis
Gene
 Chromosomes

mRNA 
(sequence of 3 bases)
This Topic explores how information flows from gene to protein.
Polypeptide(s)
 Protein
RNA structure
Ribose Nucleic Acid (RNA) consists of nucleotides with the generalised structure:
RNA is a type of nucleic acid called ribonucleic acid:


The RNA nucleotides are joined to form a single strand.
RNA nucleotides are joined by a bond between the sugar and the phosphate of the next molecule.
Comparison of DNA and RNA
Nucleic acid DNA
Sugar
Deoxyribose
Bases
A (adenine), G (guanine),
T (Thymine), C (cytosine)
_
Structure
Location
Double stranded
Nucleus
RNA
.
Ribose.
A (adenine), G (guanine),
C (cytosine), U (uracil).
RNA has nitrogenous base uracil rather than thymine.
Single stranded.
Nucleus and cytoplasm
FUNCTION OF RNA: Ribonucleic acid (RNA) provides a bridge between DNA and protein synthesis.
1. messenger RNA, or mRNA.
Formed: In the nucleus.
Function: It rewrites the sequence of bases
………………of a section of DNA in a process
……………..called transcription.
mRNA carries the code for building a specific
protein from the nucleus to the ribosomes
in the cytoplasm. It acts as a messenger.
2. transfer RNA, or tRNA.
Found: In the cytoplasm.
Function: The tRNA picks up specific amino acids from
cytoplasm and brings them into position on
the surface of a ribosome where they can be
joined together in specific order to make a specific
protein. This process is called TRANSLATION
Questions
1. Name the three components of an RNA nucleotide.
2. Which base is found in RNA but not DNA?
3. Is RNA single-stranded or double-stranded?
Protein synthesis
Process whereby DNA encodes for the production of amino acids and proteins.
This process can be divided into two parts:
1. Transcription (Takes place in the nucleus)






the gene coding for the protein required untwists
then unzips, the H-bonds between the strands
break
free RNA nucleotides form complementary base
pairs with one strand of DNA bases
weak hydrogen bonds form between base pairs
sugar phosphate bonds form between RNA
nucleotides
mRNA strand is synthesized
mRNA peels off the DNA and moves out of the
nucleus into the cytoplasm
2. Translation (Takes place in the cytoplasm)






the ribosomes are the sites of protein
synthesis
the mRNA strand attaches to a ribosome
tRNA molecules transport specific amino
acids to the ribosome
each mRNA codon codes for a specific
amino acid
the anti-codons and codons match up and
form complementary base pairs
peptide bonds form between the adjacent
amino acids to form the polypeptide
(protein)
tRNA is reused and collects another specific amino acid. Once the protein has been synthesised mRNA may move
to another ribosome to make a further protein or it can be broken down into free nucleotides to be reused.
Aim: To copy part of one strand of DNA into a single stranded mRNA molecule.
Apparatus:
DNA template
RNA nucleotides
ATP
RNA polymerase
Transcription of DNA into mRNA
Transcription is the first step in protein synthesis.
1. . Before protein synthesis begins, the
corresponding RNA molecule is produced by
RNA transcription.
2. The
2. DNA double helix unwinds and
Unzips in a short section,
exposing a single template strand of DNA.
…
3. One strand of the DNA double helix is used as a
template by the RNA polymerase to synthesize a
….messenger RNA (mRNA).
Free RNA nucleotides in the nucleus
bind to complementary DNA nucleotides
…using the base pair rules
DNA nucleotide RNA nucleotide
A pairs with U T pairs with A
G pairs with C C pairs with G
4. The RNA molecule produced during transcription of DNA is
called PRE-messenger RNA
(pre-mRNA) and is a faithful transcript of the DNA template.
5. Pre-mRNA migrates from the nucleus to the
cytoplasm.
RNA SPLICING
During this step, mRNA goes through different types of
maturation including one called splicing when the
non-coding sequences (introns) are eliminated.
6. The coding regions (exons) are ligated together to
form mRNA. The coding mRNA sequence can be
described as a unit of three nucleotides called a codon.
Introns: Intervening sequences
which are not part of the protein
being produced.
Introns may be:
1.Promoters for RNA transcription
2.They may be part of another
protein
3.
Pre-mRNA with introns removed is
called mRNA.
The mRNA molecules pass through
the nuclear pores to the cytoplasm
the site protein synthesis and the
processes of:
1. Translation
2. Post-translational
modification
Translation of mRNA into protein
Once the DNA in a gene has been transcribed into mRNA, translation can take place.
Aim: To complete translation of the codons on mRNA into amino acids linked by peptide bonds (protein)
Translation of mRNA into protein.
Location: On ribosomes in the cytoplasm
Apparatus:
Transfer RNA (tRNA)
Messenger RNA (mRNA)
tRNA folds due to base pairing to form
a triplet anticodon site and an
attachment site for a specific amino acid.
Ribosomal RNA (rRNA)
TRANSLATION-Translation of mRNA into a polypeptide by tRNA at the ribosome.
tRNA folds due to base pairing to form a triplet anticodon site and an attachment site for a specific amino
acid. Triplet codons on mRNA and anticodons translate the genetic code into a sequence of amino acids.
Start and stop codons exist. Codon recognition of incoming tRNA, peptide bond formation and exit of tRNA
from the ribosome as polypeptide is formed.
Translation of mRNA by the ribosome occurs in three stages: initiation, elongation, and termination.
Initiation
1. The small ribosomal subunit binds to the start of the mRNA sequence.
2. Then a transfer RNA (tRNA) molecule carrying the amino acid methionine binds to what is called the
start codon of the mRNA sequence.
3. The start codon in all mRNA molecules has the sequence AUG and codes for methionine.
4. the large ribosomal subunit binds to form the complete initiation complex.
Elongation stage
1. The ribosome continues to translate each mRNA codon in turn.
2. The tRNA molecule carrying the complementary anticodon binds briefly to the mRNA codon.
3. The amino acid attached to the tRNA is then added to the polypeptide chain being synthesised.
4. Each corresponding amino acid is added to the growing chain and linked via a bond called a
peptide bond. Elongation continues until all of the mRNA codons are read.
Termination,
1. When the ribosome reaches a stop codon (UAA, UAG, and UGA).
2. Since there are no tRNA molecules that can recognize these codons, the ribosome recognizes that
translation is complete. The new protein is then released, and the translation complex comes apart.
3. After the amino acid has been added to a polypeptide chain during translation, the tRNA is free to
pick up another amino acid in the cytoplasm.
As a mRNA molecule passes through a
………..ribosome each codon is translated into an
an amino acid.
One specific amino acid can correspond to
…more than one codon.
The genetic code is said to be.degenerate.
The table shows how the genetic code indicates which amino acid corresponds to
each mRNA codon.
Notice that more than one mRNA codon codes for each amino acid. Some tRNA molecules have
anticodons that recognise two or more different codons. This relaxation of the base pairing rules is called
wobble. This explains why the mRNA codons GUU, GUC, GUA and GUG, for example, all code for the
same amino acid, valine. tRNA molecules pick up the appropriate amino acids in the cytoplasm of the cell.
SUMMARY OF TRANSCRIPTION AND TRANSLATION
RNA and protein synthesis exam skills
Questions on this topic often require you to demonstrate an ability to deal with the complementary base
pairings between DNA, mRNA and tRNA. You need to understand the progression working forward from
DNA to mRNA then to tRNA and to the associated amino acid may be provided in a table. Other questions
may reverse this order of events. To make the task more manageable draw a diagram showing the base
pairings to allow you to work forward or backwards as required.
Example 1
Part of a DNA strand has the base order A T C G T T C A G. You are asked to identify the anti-codons
associated with this strand. Remember the sequence of events in the stages of RNA protein synthesis:
 transcription of mRNA from DNA
 tRNA matches the mRNA (anti-codons match the codons)
You should then work forward identifying the triplet codes as follows (make sure you substitute uracil (U) for
thymine (T) when dealing with the RNA molecules):
Triplet codes in DNA, mRNA, and tRNA
DNA strand:ATC GTT CAG
mRNA
:UAGCAA GUC
tRNA
:AUC GUUCAG
Processing and secretion of proteins
Proteins made in ribosomes that are attached to the endoplasmic reticulum are secreted
out of the cell. This process is illustrated in an on-line example that also gives a
description of the stages involved in protein processing and secretion.
After translation, the protein passes into the channels of the rough endoplasmic reticulum (ER) for
transportation. The protein is then passed from the rough ER to the Golgi apparatus inside tiny
fluid-filled sacs, called vesicles. The Golgi apparatus is a system of membranes, which are
responsible for the modification, processing, and packaging of the proteins. The protein may have
a carbohydrate added, to form a glycoprotein. The Golgi apparatus packages the protein in a
secretory vesicle, which fuses with the cell membrane and releases the protein from the cell.
Questions:
1: Where are proteins initially processed?
a) Golgi apparatus
b) Ribosomes
c) Mitochondria
d) Endoplasmic reticulum
2: What name is given to proteins that contain a carbohydrate component?
a) Amino acids
b) Insulin
c) Glycoproteins
d) Polypeptides
3: What name is given to the process of secretion of intracellular products by the cell?
a) Endocytosis
b) Exocytosis
c) Lysis
d) Phagocytosis
Essay: protein synthesis
Give an account of protein synthesis under the following headings:
1. transcription; (4)
2. translation. (6)
Functional Variety of Proteins
Proteins are essential in all biological systems.
Protein functions:
1. Structure
2. Metabolism
3. Energy (only in starvation)
The structure of proteins are related to their function:
Structural proteins are fibrous
Metabolic proteins are globular
Proteins are made of long chains of amino acids.
There are 20 different amino acids.
They are joined together by peptide bonds.
Proteins:
are polymers, made up of amino acids joined together;
the type and order of amino acids determines protein structure;
interactions between amino acids in polypeptide chains defines the structure and function of the protein.
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MAKING PROTEINS FROM POLYPEPTIDES
The same gene can be used to make several different proteins by:
1. Alternative RNA splicing
2. Post-translational modification
1. Alternative RNA splicing (AS BEFORE)
The primary transcript is separated into exons and introns and
the exons are spliced together to make the mature transcript.
Under certain conditions alternative segments of RNA may
be treated as exons and introns.
In other words one gene can produce several different mature
mRNA transcripts and therefore, several different proteins.
2. Post-translational modification
Once translation is completed, proteins can be modified by:
(a) Cleavage
(b) Addition of other molecules
(a) Cleavage
A single poly-peptide chain can be cleaved (cut) by enzymes
to make it active.
Insulin is an example of the protein modified in this way.
A central section of the “pro-insulin” molecule is removed to
make insulin.
(b) Addition of other molecules
Carbohydrates and phosphate groups can be added to proteins.
Mucus is a glycoprotein made by the addition of a protein and a carbohydrate.
Some regulatory proteins need phosphate groups added to them to make them active.
e.g. p53 is a regulator involved in DNA repair. Normally it is inactive. When phosphate is added it
becomes active.
Proteins are organised at four different structural levels:
Primary (sequence of amino acids linked by PEPTIDE
BONDS);
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Secondary (weak HYDROGEN bonds between amino acids cause the polypeptide chain to fold);
Result: alpha-Helices
or
Beta-barrels
_
Tertiary (strong bonds form between amino acids causing more folding to take place);
Sulphur atoms, which are found in some amino acids, can also lead to the
formation of links within a polypeptide, or between different polypeptides.
_
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Fibrous proteins,
e.g. collagen,
are formed from polypeptide
chains linked in parallel
_
Globular proteins,
e.g. enzymes,
are highly folded,
coiled structure
Conjugated proteins
e.g. Glycoproteins
chemically modified or
contain a non-protein part
Quaternary (two or more polypeptide chains often
associate together to form the final protein structure).
_
Haemoglobin is an example of a protein with a quaternary
structure. It is found in red blood cells and is responsible
for carrying oxygen around the body. It is composed of
four chains of the protein globin, with two each of alphaand beta-globin.
.
Protein structure is affected by various factors including: 1. pH;
2. temperature
_
Any shift from optimal conditions reduces the ability of a protein to function properly.
A major shift causes it to denaturation and all function is lost.
Globular proteins include the following:
enzymes;
many membrane proteins
some hormones;
antibodies.
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Structural (fibrous) proteins include the following:
Collagen
Elastin
QUESTIONS
Q1: Which of the following statements describes antibodies?
a) They are part of the cell membrane.
b) They cut, assemble or digest other molecules.
c) They make holes in the cell membrane.
d) They recognise molecules of invading organisms.
Q2: Proteins are composed of which of the following?
a) Nucleotides
b) Glucose molecules
c) Glycerol molecules
d) Amino acids
Q3: A polypeptide chain is held together by which of the following?
a) Weak hydrogen bonds
b) Weak peptide bonds
c) Strong hydrogen bonds
d) Strong peptide bonds
Q4: The description "The peptide is coiled around an imaginary cylinder and stabilised
by hydrogen bonds" is true for which of the following?
a) Alpha helix
b) Fibrous protein
c) Globular protein
d) Structural protein
Q5: Glycoproteins are composed of proteins containing which of the following?
a) Carbohydrate
b) Nucleotides
c) A non-protein chemical
d) Fatty acids