Introduction 1/2/2020
Assessments: 2 short essays out of 5, 1 hour 15 min. Essays submitted to turnitin. No need to
have the questions on the answer sheet; <20% similarity. Coursework: 20-25 MCQs MCQ test
(based on labs, case studies, and workshops) in week 13 at 2pm for 1 hour and 15 minutes (10
May). All exams online! Come in for labs, not exams.
Chromosomes, DNA, Genes: Structures and Functions REVIEW
Timeline: “1944-DNA, not protein, was shown to be the genetic material. 1953-Structure of
DNA: the double helix. 1966-Elucidation of the genetic code. 1970-Birth of recombinant DNA
technology. 1984-Polymerase Chain Reaction (PCR). 1991-Human genome mapping project
initiated. 2001-Draft sequence of the Human genome. 2003-Sequence of the Human genome
mostly completed. Present-Comparative genomics & individual genomes (with next generation
sequencing).”
The Book of Life: Nucleotides come together to form codons which form genes which make up
chromosomes which make up the entire genome.
DNA to Genomes: “Each cell nucleus contains an identical complement of
chromosomes in two copies; each copy is a genome. One specific
chromosome pair. Each chromosome is one long DNA molecule, and genes
are functional regions of this DNA. DNA is a double helix.” So, genetics can be
transformed tho molecular biology through molecular genetics.
Chromosomes: “Genome is the organism’s hereditary information. Coded in
nucleic acid (usually DNA). Organised in chromosomes. A circular archaea
chromosome is pictured (the circular map of the single chromosome of
Picrophilus torridus, a thermoacidophile).” Nucleus: Nuclear envelope + 3000-4000 nuclear
pores. Nucleolus > rRNA + ribosomes. DNA is retained in the nucleus. Pore activity: Imports
about 10^6 histone molecules every 3 min. Exports 3 new ribosomes/min/pore. mRNA as
ribonucleoproteins (RNP).
Chromosome Types: “Viral chromosomes: Not complete (need host DNA). Retroviruses have
RNA xsomes.” “Prokaryotes (bacteria & archaea): No nucleus (xsome in cytoplasm as
‘nucleoid’). Usually a single circular dsDNA xsome. Some genes found on plasmids – extra
chromosomal circular DNA molecules.” “Eukaryotes: Cell nucleus. Chromatin: DNA-Protein
complex. Multiple xsomes possible.”
Human Chromosomes: “Double stranded DNA molecules. A chromosome contains 50 x 106 to
250 x 106 nucleotide base pairs. Molecules this big are 1.7 to 8.5cm long when unpacked. 46
chromosomes (23 pairs inc. X/Y in males). 46 x ca 4cm = 2 m length in a nucleus of 5 microns
(0.005 mm). A set of 23 chromosomes contains about 25000 genes.” “Genome &
Chromosomes: A chromosome contains 50 x 106 to 250 x 106 base pairs. Molecules
this big are 1.7 to 8.5cm long when unpacked. 46 chromosomes (23 pairs inc. X/Y in
males). A set of 23 chromosomes contains about 34000 genes.”
Packing DNA: “Protein complexed with DNA in an ordered structure = chromatin.”
How many chromosomes: “Different species have different & characteristic
numbers of chromosomes known as a karyotype. Table-number of pairs of
chromosomes in different species of plants and animals.”
Human Female Karyotype: “46XX. Females have 2 X chromosomes; Males have an
X and a Y xsome.”
, Coding and Non-coding DNA: “Coding DNA carries code for assembly of
polypeptide chains. Non-coding doesn’t. Coding DNA makes up part of a gene.
Non-coding DNA can be within genes or between genes.”
Nucleotides: “In DNA and RNA the phosphate group is on the 5' position of the ribose
ring. Strictly dAMP should be written 5‘dAMP. Nucleotides are the building blocks of
nucleic acids DNA and RNA.” There is the base (A), beta glycosidic linkage (anti), and
sugar (ribose).
Pentose Sugars: “Nucleotides always use pentose sugars. DNA and RNA
use the furan sugars ribose or deoxyribose. In RNA the sugar is always ribose.
In DNA, the sugar is deoxyribose. Deoxyribonucleotides are written as dAMP,
etc. Left-Ribose 5’ phosphate (in RNA). Right-Deoxyribose 5’ phosphate (in
DNA).”
General structures of the bases: purine, pyrimidine. Purines: adenine;
guanine. Pyrimidines: cytosine; thymine, 5-methyl uracil (DNA; uracil (RNA).
Attachment of the bases in nucleotides: the attachment sites: N-9 in
purines (in purines it is the adenosine), and N-1 in pyrimidines
(pyrimidine-cytidine).
Sugar Phosphate Backbone: “At neutral pH, each phosphate group has a
single negative charge. Thus NAs are anions of acids, they are highly
charged polymers. All nucleic acid chains have a free 3' end, usually an OH and a free 5' end,
which may have an attached phosphate group.” There is a 3’ to 5’ phosphodiester bond.
DNA Base Pairing: “Watson-Crick. Occurs between complimentary bases by hydrogen
bonding. Amount of purine equals amount of pyrimidine. Ratios of A to T and G to C always 1:1
in dsDNA. GC rich regions more stable than AT regions. Order of bases determines the
information content of genes.”
Structure of DNA: “Double helix structure discovered by Watson & Crick in 1953. Can see the
bases stacking on top of each other. Stability of helix comes NOT from H-bonding between
complementary bases but dipole forces which excludes water from between the bases. Base
stacking angle produces two grooves in double helix.” M is a major groove and m is a minor
groove.
,Non-coding DNA (98.5%): introns. tRNA, r-RNA + snRNA genes. pseudogenes (non-functional
copies). control sequences. “Repeated sequences (note: some genes are repeated): long
interspersed elements (LINEs), 6000 bp long; short interspersed elements (SINEs), 130-500 bp
long, thousands of copies per genome; satellite DNA. Simple sequences, 5-200 bp long,
tandem arrays, localised in centromere [LINEs & SINEs are extinct transposons]”. Transposons:
segments of DNA that can move around to different positions in the genome of a single cell. In
the process, they may cause mutations and increase (or decrease) the amount of DNA in the
genome. These mobile segments of DNA are sometimes called ‘jumping genes’.
“Molecules of DNA store genetic information. The order of nucleotides determines the
information. Synthesis of proteins has a specific code – the Universal genetic code to unlock the
genetic information. ‘Universal’ same code applies to virtually all organisms. Some exceptions in
eg mitochondrial genomes and a few protozoans. Sometimes bacteria use GUG rather than
AUG as the start codon.”
The Genetic Code: “Written in a linear sequence of nucleotides- ACGT. We ‘read’ the code
from the gene’s coding strand not the template strand of DNA. Transcribed to RNA: ACGT ;
ACGU. Sequence of 3 nucleotides is a codon that specifies a given amino acid (AA). Collinear:
order of codons same as AA order, 3 nts – a triplet code. Triplet code is most efficient way of
coding 20 AAs from 4 letters. In 18 of 20 AAs, more than one codon specifies a given AA
(degenerate).”
The Central Dogma of Molecular Biology: DNA to DNA through replication. DNA to
RNA through transcription. DNA to Protein through translation.
Biological Gene Definition: “Genes are functional regions of the genome. Factors of
inheritance. Genes were first identified biologically: Inheritance of a particular trait and
Observed effect on an organism. Genes can now be identified in molecular terms.”
This is the biological definition. Recombination tests can identify linked genes &
positions. These measure the occurrence of an observable heritable trait.
Complementation tests (crosses)-Rely more on gene function. This allows the
recognition of cistrons – code for polypeptide chains or protein subunits.
Complementation test: A (bacterial) mating test to determine whether two different
recessive mutations (a1;a2) on opposite chromosomes (trans, a1+/+a2) of a diploid or
partial diploid will not complement (ie have a mutant phenotype) each other; but the same two
recessive mutations on the same chromosome (cis, a1a2/++) in a diploid or partial diploid show
a wild-type phenotype; A test for allelism. A test to determine whether two mutant sites are in
the same functional unit or gene.
“One Gene = One Protein? <25000 genes in the genome. >100000 proteins in the proteome.
How? We need to consider genes at the molecular level.”
Molecular Gene Definition: “Control Regions-Essential for function but are not transcribed.
Considered part of the gene but may be distant from the mRNA coding region, e.g. enhancers.”
Introns and Splicing: “Genes have Exons-coding regions-interspersed with Introns non-coding
regions. Introns are removed from mRNA after transcription. A gene may generate several
RNA’s/proteins, e.g. by splicing pre mRNA.” “Transcription units may generate several
mRNA’s/proteins, e.g. by splicing hnRNA. Mutations in region A affect TWO proteins, but this
cannot be shown from complementation tests. Mutations in region B & in region C, etc. can be
located from complementation tests, but regions A, B, etc. are not cistrons.”
, “Genes within genes -> in introns of other genes. The alternative DNA strand is transcribed.
Genes for tRNA’s and rRNA’s, ie a gene does not necessarily carry the ‘genetic code’. These
genes are not translated into proteins.”
Final Gene Definition: “The entire nucleic acid sequence that is necessary for the synthesis of
functional polypeptide/s or RNA sequence.”
A typical protein coding gene looks as pictured.
A gene transcribed to mRNA looks a different way.
Genes: “Genes are functional regions of the genome. Genes occur at a specific position or
locus on the genome. Gene locus is a gene address, eg beta-globin is found at 11p15.5 (short
arm of xsome 11).”
Allele Definition: “Genes can exist in different forms at the same locus – alleles. Beta-globin
exists both in a normal form and sickle cell anaemia-causing form and as
β-thalassaemia-causing form. Different forms of same gene NOT different genes. Multiple
alleles of a gene are possible. Allele has same basic DNA sequence with changes from one bp
to many base pairs. Only one allele will be present at that
gene’s locus on one xsome. Different alleles can lead to
