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Lecture notes Biomedical Sciences (BSc) Lecture Notes BB1705 The Biology of the Cell
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Lecture Notes BB1705 The Biology of the Cell at Brunel University
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Past 10 years of Exam (SOLVED) BMI2604 - Molecular Biology of the Cell
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Biology of the Cell – Chapter 4: DNA, chromosomes and genomes- Universal features of cells
o Cells are the things of life. All living things are made of cells
Chemical factors that take matter from their surroundings to generate
copies of themselves
o Organisms can be single-celled or multicellular (this is generated by cell divisions
from an original single cell)
o All cells store their heredity information in the form of double-stranded molecules of
DNA (deoxyribonucleic acid).
o All cells transcribe portions of their hereditary information into the same
intermediary form (RNA, ribonucleic acid)
Transcription:
Segments of DNA are used as template to synthesise RNA
mRNA to make protein
catalytic or structural RNA
o All cells translate RNA into protein in the same way
Translation:
mRNA directs polypeptides to ultimately form proteins
tRNA and rRNA are also involved
o Genes are information-containing elements that determine the characteristics of a
species as a whole and of the individuals within it.
o All of the DNA in a cell (coding and non-coding) is called the genome
- Heredity: the concept by which an organism reproduces itself faithfully
o It is passed on to daughter cells by cell division
o It is passed on from one generation to the next through the organism’ s gametes
- The unit of heredity is the gene
- Cells produce by two processes:
o Asexual
Division of the cell to form two daughter cells containing identical genetic
information as the parent cell
o Sexual
Fusion of two gametes to form a zygote
- Single celled organisms can reproduce both sexually and asexually
- Multicellular organisms only reproduce sexually, however most human cells (e.g. in skin,
brain, heart etc.) reproduce asexually
- Gregor Mendel studied inheritance by performing breeding experiments with peas. The
results were published in 1866.
- An allele is a possible alternative of a gene
- Homozygous – a diploid in which the two alleles of a gene are identical (AA or aa)
- Heterozygous – a diploid in which the two alleles of a gene are different (Aa)
- If the heterozygote Aa resembles the homozygote AA, allele A is dominant and allele a is
recessive.
- If the heterozygote Aa resembles an intermediary between AA and aa, then there is no
dominance. The alleles are partially dominant or incompletely dominant
,Discovery of DNA
- The breakthrough in our understanding of cells came
from studies of inheritance in bacteria. These
experiments showed that adding purified DNA to a
bacterium changes its properties and that this change
was passed on to subsequent generations. There are
two strains of bacterium. One strain is smooth and
causes death and the other is rough and nonlethal.
o In the first experiment – The R strain cells grow
in presence of heat-killed S strain cell but a
substance present in the S strain can transform
the R strain into the S strain and this change is
inherited by subsequent generations of
bacteria
o In the subsequent experiment – the R strain has been incubated with various
biological molecules from the S strain purified from the S strain, identifies the
substance as DNA
- The mechanism of copying and transmitting DNA is still unknown. In 1953 the structure of
DNA was correctly predicted by James Watson and Francis Crick.
Structure and function of DNA
- A DNA (deoxyribonucleic acid) molecule consists of two long polynucleotide chains
composed of four types of nucleotide subunits.
- Each of these chains in knows as a DNA chain or DNA strand
- Hydrogen bonds between the base portions of the nucleotides hold the two chains together.
- Nucleotides:
o Five-carbon sugar
o Phosphate group
o Base (adenine, thymine, guanine and cytosine)
- Base + ribose = nucleoside. Base + ribose + phosphate = nucleotide
- The DNA strands are antiparallel. The 5’ end of one strand forms hydrogen bonds to the 3’
end of the partner strand.
- Types of double helical structures:
o R-handed helices
A-DNA (11bp per turn)
B-DNA (10bp per turn)
o L-handed helices
Z-DNA (12bp per turn)
- The 5’ end ends with a phosphate group and the 3’ end ends with a hydroxyl group
- Bases: Purines – double ring structures
o Adenine and guanine
- Bases: Pyrimidines – single ring structures
o Cytosine and thymine
- A consequence of these base-pairing requirements is that each strand of a DNA molecule
contains a sequence of nucleotides that is exactly complementary to the nucleotide
sequence of its partner strand
- DNA is described by writing the sequence of bases of one strand in the 5’ to 3’ direction.
- 5’ to 3’ is the direction of synthesis of new DNA strands during replication and it is also the
direction of RNA transcription.
,DNA packaging
- In eukaryotes, the DNA in the nucleus is divided between a set of different chromosomes.
- The maternal and paternal chromosomes of a pair are called homologous chromosomes.
The only nonhomologous chromosome pairs are the sex chromosomes in males.
- Each chromosome consists of a single long linear DNA molecule associated with proteins
that fold and pack the fine DNA thread into a more compact structure. The complex of DNA
and protein is called chromatin.
- The proteins that bind to the DNA to form eukaryotic chromosomes are traditionally divided
into two general classes: the histones and the nonhistone chromosomal proteins. The
complex of both classes of proteins with the nuclear DNA of eukaryotic cells is known as
chromatin.
- Histones are responsible for the first and most basic level of chromosome packaging, the
nucleosome, a protein-DNA complex discovered in 1974.
o Each individual nucleosome core particle consists of a complex of eight histone
proteins – two molecules of each of histones H2A, H2B, H3 and H4 – and double
stranded DNA that is 147bp long
o The histone octamer forms a protein core around which the double-stranded DNA is
wound
o Each nucleosome core particle is separated from the next by a region of linker DNA,
which can vary in length from a few nucleotide pairs up to 80
o The formation of nucleosomes converts a DNA molecules into a chromatin thread
about one-third of its initial length
- Adjacent nucleosomes connect via spacer DNA. Most of the chromatin is in the form of a
fibre with a diameter of 30nm. H1, also called the linker DNA, is what links one nucleosome
to another.
- The nucleosomes are now packed on top of one another, so the DNA is even more highly
condensed.
- Lampbrush chromosomes are clearly visible even in the light microscope, where they are
soon to be organised into a series of large chromatin loops. Lampbrush chromosomes are
unusual visible paired chromosomes from amphibian oocytes during meiotic cell division.
The chromatin fibre loops are attached to a central scaffold.
- During the ‘prometaphase’ stage of cell division, the loop-scaffold complex (lampbrush) is
compacted by further coiling to form two visible sister chromatids of the chromosome.
- Most chromosomes in interphase cells are too fine and tangled to be clearly visualised.
There are two types of chromatin:
o Heterochromatin
Highly condensed chromatin visible by light microscopy in interphase
eukaryotes
Resistant to gene expression
Found at ends of chromosomes (telomeres) and centre of chromosomes
(centromere)
o Euchromatin
Less condensed
Active gene expression
, Chapter 5: – DNA replication, repair and recombination
DNA replication
- This process entails the recognition of each nucleotide in the DNA template strand by a free
complementary nucleotide, and it required the separation of the two strands of the DNA
helix.
- DNA replication is semiconservative, i.e. each daughter DNA duplex contains one parental
DNA stand and one new DNA strand
- DNA synthesis is carried out (5’ to 3’) by a nucleotide polymerizing enzyme: DNA
polymerase. Each deoxynucleoside triphosphate comes and attaches itself to the 3’ end of
the primer strand, which is paired to a template strand. Once attached the pyrophosphate
dissociated from the deoxynucleoside triphosphate.
- The accuracy of copying the new strand is achieved due to complementary base-pairing
- Replication fork: the y-shaped structure of the DNA when it splits up. This shape is
asymmetrical. At this site, a multi enzyme complex that contains DNA polymerase
synthesizes the DNA of both new daughter strands.
- Due to the replication fork, one daughter strand (leading strand) polymerises in the 5’-to-3’
direction and the other (lagging strand) in the 3’-to-5’ direction. But thanks to Okazaki
fragments, short DNA molecules (1000-2000 nucleotides), the lagging strand can synthesise
in the 5’-to-3’ direction as well.
Proofreading
- If the DNA polymerase did nothing special when a mispairing occurs then the wrong
nucleotide would often be incorporated into the new DNA chain, producing frequent
mutations. This fidelity of DNA replication depends on several ‘proofreading’ mechanisms.
1. DNA polymerase: the correct nucleotide has a higher affinity for the moving
polymerase than does the incorrect nucleotide, because the correct pairing is
more energetically favourable. Then the enzyme undergoes conformational
change where its ‘fingers’ tighten around the active site. This change occurs
more readily with correct than incorrect base-pairing, it allows the polymerase
to ‘double-check’ the exact base-pair geometry before it catalyses the addition
of the nucleotide.
2. Exonucleolytic proofreading: this takes place when an incorrect nucleotide is
covalently added to the growing chain. It clips off any unpaired residues until
enough nucleotides have been removed to regenerate a correctly base-paired
3’-OH terminus that can prime DNA synthesis. DNA polymerase functions as a
‘self-correcting’ enzyme that removes its own polymerization errors as it moves
along the DNA.
3. Strand-directed mismatch repair: detects the potential for distortion in the DNA
helix from the misfit between noncomplementary base pairs.
Okazaki fragments
- For the leading strand, a s5r6+pecial primer is needed only at the start of replication. For the
lagging strand, every time the DNA polymerase completes an Okazaki fragment it must start
synthesizing a completely new fragment at a site further along the template strand.
- DNA primase is an enzyme that uses ribonucleoside triphosphate to synthesise short RNA
primers on the lagging strand. These primers are about 10 nucleotides long
1. New RNA primer synthesis by DNA primase
2. DNA polymerase add to new RNA primer to start new Okazaki fragment
3. DNA polymerase finishes fragment
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