Transcript Biology 3.3 - Describe the role of DNA in relation to gene

Biology 3.3 Describe the role of DNA in
relation to gene expression
Dr Hayley Ridgway
Ms Dalin Dore
Things to know
1.
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The role of DNA includes DNA structure and replication, the control of gene
expression, protein synthesis, and the determination of phenotype.
The structure of DNA includes the molecular components and their role in
carrying the genetic code. The replication of DNA includes the processes
involved in replication and the role that enzymes have in producing accurate
copies.
Control of gene expression is limited to factors that operate at transcription
level:
1.
feedback in prokaryotes (repressors, inducers)
2. enhancers and transcription factors in eukaryotes.
Protein synthesis includes the role of DNA in determining the structure of a
protein and how that protein is produced (transcription and translation).
The determination of phenotype includes:
–
allele interactions: dominance, incomplete dominance, co-dominance,
multiple alleles, lethal alleles
–
linkage and sex linkage
–
gene-gene interactions: epistasis, collaboration, polygenes
–
pleiotropy
–
mutations: gene mutations, chromosomal mutations
–
control of metabolic pathways by gene expression.
Previous questions
2005 - Munchkin cat
Key concepts to know:
• Dominance
• Expected progeny from
crosses
• Selective breeding (genome)
• Transgenics
• Cloning (genome)
2006 - A1 and A2 Milk
Key concepts to know:
• Codominance
• Alleles
• Mutation (single nucleotide
polymorphism)
• Frequency and what affects it
eg.
– founder, linkage, selective
breeding, selective advantage
2007 - Huntington’s disease
Key concepts to know:
• Mutation
• Dominance
• Autosomal - therefore how is it
passed on?
• Factors affecting disease expression
– what is disease expression?
– number of repeats
– heterozygous vs homozygous, any
difference?
– female vs male
• Needed to carefully read the material
provided
The neuron in the center
(yellow) contains an
abnormal accumulation of
huntingtin (orange).
Studies demonstrated
that neurons with
huntingtin survive longer
than those that do not.
Key Concepts
Dominance & Co-dominance
• How can you tell the
difference?
Frequency
• What is it
• What could affect
frequency?
What is an allele?
Mutation
• How can it arise?
• What are the
consequences?
Linkage
Breeding systems
• Selective
• Cloning
• Transgenics
“Superbugs”
MRSA or Methicillin Resistant
Staphyloccocus aureus
What is MRSA?
A common bacterium that can causes infections in different parts
of the body. Usually no problem but it has become resistant to
some commonly used antibiotics.
Staphylococcus aureus - a short history
• Bacteria have very good adaptive capabilities
• 1940s: Penicillin was introduced - a strong selective
pressure, induces mutation
• Bacteria can transfer traits by mobile DNA such as
heavy metal tolerance etc
• Penicillin was virtually useless as an antibiotic within a
decade because a plasmid spread the penicillinase (ßlactamase ) gene through the entire species of S.
aureus
• New antibiotics such as methicillin which were not
degraded by the product of the ß-lactamase gene
were used
• By 1960 methicillin resistant S. aureus (MRSA)
strains were identified
• By the 1980s, epidemic clones of MRSA acquired
multidrug resistant traits and spread worldwide to
become one of the most important causes of hospital
acquired infections
• In the early 2000s, MRSA strains carrying the
additional Tn1546 transposon-based vancomycin
resistant mechanism were identified, bringing the
possibility of a totally resistant bacterial pathogen
closer to reality
How did this happen?
• Selection pressure applied
• S. aureus acquired and mutated a gene from another species of
Staphylococcus (S. sciuri)
– the penicillinase gene (via a plasmid)
– then the methicillin resistance gene mec
Mec:
• Originated in S. scuiri another species of Staphylococcus
• Located in a mobile piece of DNA that contains its own enzymes
for moving it around the genome
• This piece of DNA is called the Staphylococcal cassette
chromosome mec (SCCmec)
• Has about 100 ORF on this element – so also contains other
genes
Mobile DNA
• Common in bacteria
• Two general types:
1. Plasmids
– extrachromosomal circular or linear DNA
molecules which are not part of the bacterial
genome
– carry functions advantageous to the host such as
eg antibiotics or heavy metal resistance
2. Transposons
– jumping genes, mobile genetic elements
– composed of a gene coding for a special enzyme
and two short flanking segments of DNA called
inverted repeats
Transposition
•
Transpositions duplicate genes by inserting
copies of DNA segments into new positions in
the genome
•
Result from a biological process not a random
chemical or physical one
•
The result of "jumping genes", mobile genetic
elements called transposons
– composed of a gene coding for a special
enzyme and two short flanking segments
of DNA called inverted repeats
•
transposon
gene
Gene for transposon
enzyme
transposon enzyme
The gene product of the transposon is an
enzyme called transposase and it can insert a
copy of the transposon anywhere in the
genome
transposon in new
location
How do antibiotics work?
Penicillin (β-lactam)
• Inhibits formation of peptidoglycan cross-links
(major part of bacterial cell wall) in the cell wall
• Normally crosslinking is done by PBPs (penicillin
binding proteins or transpeptidases )
• The β-lactam moiety (functional group) of penicillin
binds to the enzyme (PBPs)
• Weakens the cell wall of the bacterium and causes
lysis
Resistance to Penicillin
• Bacteria evolved Penicillinases which hydrolysing
penicillin
Methicillin (also β-lactam)
• Acts the same way as Penicillin
• BUT insensitive to penicillinases
Resistance to Methicillin
• Expresses a different PBP, called PBP2a, that is
resistant to methicillin
• Often resistant S. aureus are resistant to other
classes of antibiotics (through different mechanisms)
• Accessory factors (genes) influence the level and
nature of methicillin resistance
Selection pressures
• Selection pressure – killing bacterium
• One mechanism of action – only need to find a away
around one thing
• Bacteria multiply rapidly
• Over prescription of antibiotics,
• People not finishing the course of antibiotics
• And others……
Added info….
• Mutation
• Genes
Evolution depends on accidents and mistakes!
• In general cells do not have mechanisms for creating changes in
their genomes
– Normally replication, recombination and repair are high
fidelity processes
– 1/1000 bp randomly changed every 200,000 years
– So if n = 10,000, every SNP tried out 50 x over 1 million
years – relatively short time evolutionarily speaking
• Most changes result from mistakes in normal copy and repair
mechanisms
• Transposable elements play a role
• Can vary from SNPs to large scale rearrangements such as
deletions, duplications, inversions and translocations
•
Genome differences have accumulated over 3 billion years
•
Comparisons of genomes allow reconstruction of evolutionary
process
•
Balanced process – genome stabilty and evolutionary change
•
Mutation/variation are rare because DNA is a very stable molecule
for several reasons:
1. DNA is made of complementary
strands and repairs can be made
when one side is damaged
2. The nucleotides are protected
inside the sugar-phosphate backbone
and secured by hydrogen bonds.
3. DNA structure (nucleosomes etc)
provide a tight structure which
restricts access.
Point mutations
•
Once a nucleotide or nucleotides have been altered the genetic code
will be subject to one of the following mutations.
– Base substitution
• Single base pair changes or deletions in DNA
• Diallelic
• Approx 2,000,000-3,000,000 in every chromosome (1
evry 1000 bp)
• silent mutation - the new base pair codes for
the same amino acid
• neutral mutation - the new base pair codes for a
different amino acid but the shape of the
resulting protein is unchanged
• MUTATION - most are disastrous, but some
can benefit the organism
Normal Protein
DNA
………..agg gta ggg cta tta tag
Protein ………Arg – Val – Gly – Leu – Leu – STOP
SNPs:
Silent (third base in codon no aa change)
DNA
………..agg gtc ggg cta tta tag
Protein
……Arg – Val – Gly – Leu – Leu – STOP
Protein change (polar to nonpolar)
DNA
………..tgg gta ggg cta tta tag
Protein
……… Trp – Val – Gly – Leu – Leu – STOP
Insertion/Deletion – Frameshift change
DNA
………..agg ggt agg gct att ata ………..
Protein
………Arg – Gly – Arg – Ala – Ile – Ile …………….
Deleterious effects:
– Chain termination - Produce a stop codon,
premature chain termination = non-functional
proteins
– Additions and Deletions - When the number of
nucleotides added or removed is not equal to
three, causes a frameshift
– Point Mutations may also occur in non-coding regions - introns
or regulatory regions, severity of the mutation depends upon
the region it occurs in, mutations in introns have little or no
effect.
Genes – regions of DNA that encode a protein
Prokaryotes
– Intronless DNA,
characterised by open
reading frames (ORFs)
– Start with a ATG and
stop with TAA, TAG or
TGA
– Have conserved upstream
regions in the promoter
Eukaryotes
– Harder to identify
– Have ATG with ORF after
it
– Have conserved upstream
sequences - TATA , CAAT
But….
– May contain introns that
do not encode amino acids
– Introns may not start and
end as a triplet codon
– Introns start with GT and
end with AG
•
Prokaryote
– No introns, genes next to each other, ORF
ATG & promoter
•
ORF
STOP
Eukaryotes
– Introns, genes at a distance from each other, complex promoters
(controls)
Promoter can lie many bases upstream
ATG
Introns – can be
larger than ORF
ORF
STOP