Genetics Lecture Notes
Lecture 1 = Introduction of DNA and Chromosomes
(deoxyribonucleic acid) needs to be:
1. Stable over time
2. Able to be faithfully replicated (semi-conservative replication)
3. Accessible by the cell (H-bonds between 2 strands are easily broken)
4. Able to be changed in a controlled way
5. Replicated in mitochondria + the nucleus
- DNA was discovered in 1868 by Friedrich Miescher by isolating “nuclein’ from pus
- He recognised the molecule has high mol. weight, high levels of P and was acidic
- Avery, McLeod and McCarty = pathogenic bacteria can transfer info non-pathogenic
bacteria and make it pathogenic
- Hershey + Chase = used bacteriophage (protein coat + DNA that infect bacteria) w/
labelled DNA (using isotopes) and tracked DNA transfer
- Rosalind Franklin = used X-ray crystallography to see double helix w/
phosphate group on the outside
- Watson + Crick + Wilkins = proposed double helix model we use today
Nucleotide = sugar + phosphate + base
Nucleoside = sugar + base
1. Deoxyadenosine = deoxyribose + adenine
2. Deoxyguanosine = deoxyribose + guanine
3. Deoxycytidine = deoxyribose + cytosine
4. Deoxythymidine = deoxyribose + thymine
Each DNA strand has directionality
- 5’ end = phosphate group
- 3’ end = hydroxyl group
In the double helix, the two strands are anti-parallel
- Hydrogen bonds form + hold complimentary base pairs (AT + CG)
Large bases (purines) bond with small bases (pyrimidine)
- Adenine + thymine = 2 H bonds
- Guanine + cytosine = 3 H bonds
The birds eye view of DNA shows it is not symmetrical
- You have a minor and major groove
Genetic information is a digital, quaternary code
- This means it can be stored and analysed on a computer
, Lecture 2 = RNA, Transcription, RNA Processing, Introns, Exportation
Central dogma = DNA to RNA to protein
- Done through transcription and translation
Different types of RNA have different functions
1. mRNAs (messenger) = used to code for proteins
2. rRNAs (ribosomal) = from ribosomes
3. tRNAs (transfer) = used in protein synthesis
Transcriptome = set of all RNA molecules
- This varies with the cell or cell type (genome never changes)
- This produces an RNA molecule complementary to one strand of DNA
How does RNA differ from DNA?
1. The sugar is different (ribose)
2. Uracil replaces thymine
This means:
1. The two -OH groups make a more reactive molecule/less stable
2. Uracil is energetically less expensive to make (RNA came before DNA)
3. If uracil was used in DNA, cytosine deamination (mutation that turns cytosine to
uracil) would be difficult to detect + repair
4. RNA is single stranded but can form base pairs e.g.
between the same strand
5. Can form base pairs w/ other nucleic acids for catalytic
functions
6. Overall RNA is transient + less stable
RNA is synthesised for a DNA template using RNA polymerase
1. DNA locally unwinds to expose the template
2. DNA bases are transcribed left to right
3. RNA nucleotides enter the molecule + pair w/ template in
the groove, phosphodiester bonds form w/ RNA polymerase as catalyst
4. Transcript= 5’ to 3’, template read 3’ to 5’
5. Pyrophosphate (2 phosphates) are lost + provide energy for phosphodiester bond
formation
- Eukaryotic cells have organelles including nucleus (membrane bound) therefore
require processing before translation in the cytoplasm
- Prokaryotic cells have free falling DNA therefore transcription and translation occur
in the cytoplasm
- mRNAs are processed before leaving the nucleus
This occurs on 3’ and 5’ ends to add stability:
1. 5’ end = capping process, adds atypical nucleotide (usually guanine w/ atypical bond)
, a. This protects the molecules end from exonuclease degradation
2. 3’ end = addition of a tail of adenine not encoded by DNA
3. Introns (non-coding sequences) need to be removed/spliced
Eukaryotic genes have non-coding sequences that need to be removed, prokaryotic cells
don’t, these are called introns (discovered in 70s)
- Introns spliced out by spliceosomes (found in 5’ UTR, coding region + 3’ UTR
o These are a mixture of RNAs and proteins
o They form bonds w/ splice site
This is when more than 1 protein (isoform) is expressed from 1 gene
- One pre-mRNA can be spliced into different molecules
In humans up to 95% of genes exhibit alternative splicing therefore there are multiple mRNA
variants
Variations include:
1. Exon skipping
2. Alternative poly(A) tail site (cut off exons)
3. Intron retention
These all produce different protein isoforms
- These are selectively exported from the nucleus through nucleur pores
- Nuclear transport receptors are bound to mRNA + mediate export + mark a mature
RNA
- mRNAs are degraded by a cell
o Stability determines how many times mRNA is translated, more times = more
stable (can be 10 hours or 30 mins)
Lecture 3: Translation
How is information translate into proteins? 4 bases to code for 20 different amino acids?
- This is what Crick + Brenner wanted to research
-
1. 1 nucleotide = 1 amino acid = 4 amino acids
2. 2 nucleotides = 1 amino acid = 42 = 16 amino acids
3. 3 nucleotides = 1 amino acid = 43 = 64 amino acids
Therefore, we can tell that there must be at least 3 nucleotides per amino acid
- If all combos are used, the code is degenerate (i.e. more than 1 combo per aa)
, No, because single base mutations only affect 1 amino acid
They used bacteriophage T4 which infects E. coli by lysis (breaking down membrane),
generated mutants in the rII gene which gave distinctive large plaque in E. coli strain B
- They used proflavine to generate these mutants, which insets itself b/w base pairs
- They found that triple mutations were special
- Genetic code = similar to a language (needed to read it in 3s)
Example = the big red fox ate the egg
Insertion (FCO+) = the xbi gre dfo xat eth egg g.
- Affects all codons after
Deletion (FCI-) = the big rdf oxa tet hee gg
- Affects all codons after
Bit of both (pseudo wildtype) = the xbi grd fox ate the egg
- Codons are restored
Double insertion = the xbi gyr edf oxa tet hee gg
Triple insertion (wild type) = the xbi gyr edz fox at the egg
- Can see 3 insertions = new codon, codons restored
Therefore, we can see genetic code of mRNA is read is 3s
1. Degenerate = some amino acids have more than one codon/tRNA
2. Some amino acids tolerate mismatches on 3 rd codon position
3. There are 3 stop codons, these don’t code for amino acids
4. Amino acids can be 3 letter (Ala) or 1 letter (A)
a. One letter allows for digital analysis
5. Genetic code is universal (except for some variations in mitochondria)
1. mRNA (messenger) = carries genetic information
2. rRNA (ribosomal) = makes up ribosome where translation occurs
3. tRNA (transfer) = adapter b/w mRNA codons + amino acids
a. Step 1 = enzyme, tRNA synthetases, couple tRNAs to correct amino acids
b. Step 2 = charged tRNA pairs w/ codon on mRNA + delivers amino acid
- This makes up ribosomes w/ proteins
- Ribosomes are where translation occurs
- Ribosomes has 2 sub units
o Has E-site (exit), P-side (peptidyl-tRNA-site), A-site (aminoacyl-tRNA site)
Lecture 1 = Introduction of DNA and Chromosomes
(deoxyribonucleic acid) needs to be:
1. Stable over time
2. Able to be faithfully replicated (semi-conservative replication)
3. Accessible by the cell (H-bonds between 2 strands are easily broken)
4. Able to be changed in a controlled way
5. Replicated in mitochondria + the nucleus
- DNA was discovered in 1868 by Friedrich Miescher by isolating “nuclein’ from pus
- He recognised the molecule has high mol. weight, high levels of P and was acidic
- Avery, McLeod and McCarty = pathogenic bacteria can transfer info non-pathogenic
bacteria and make it pathogenic
- Hershey + Chase = used bacteriophage (protein coat + DNA that infect bacteria) w/
labelled DNA (using isotopes) and tracked DNA transfer
- Rosalind Franklin = used X-ray crystallography to see double helix w/
phosphate group on the outside
- Watson + Crick + Wilkins = proposed double helix model we use today
Nucleotide = sugar + phosphate + base
Nucleoside = sugar + base
1. Deoxyadenosine = deoxyribose + adenine
2. Deoxyguanosine = deoxyribose + guanine
3. Deoxycytidine = deoxyribose + cytosine
4. Deoxythymidine = deoxyribose + thymine
Each DNA strand has directionality
- 5’ end = phosphate group
- 3’ end = hydroxyl group
In the double helix, the two strands are anti-parallel
- Hydrogen bonds form + hold complimentary base pairs (AT + CG)
Large bases (purines) bond with small bases (pyrimidine)
- Adenine + thymine = 2 H bonds
- Guanine + cytosine = 3 H bonds
The birds eye view of DNA shows it is not symmetrical
- You have a minor and major groove
Genetic information is a digital, quaternary code
- This means it can be stored and analysed on a computer
, Lecture 2 = RNA, Transcription, RNA Processing, Introns, Exportation
Central dogma = DNA to RNA to protein
- Done through transcription and translation
Different types of RNA have different functions
1. mRNAs (messenger) = used to code for proteins
2. rRNAs (ribosomal) = from ribosomes
3. tRNAs (transfer) = used in protein synthesis
Transcriptome = set of all RNA molecules
- This varies with the cell or cell type (genome never changes)
- This produces an RNA molecule complementary to one strand of DNA
How does RNA differ from DNA?
1. The sugar is different (ribose)
2. Uracil replaces thymine
This means:
1. The two -OH groups make a more reactive molecule/less stable
2. Uracil is energetically less expensive to make (RNA came before DNA)
3. If uracil was used in DNA, cytosine deamination (mutation that turns cytosine to
uracil) would be difficult to detect + repair
4. RNA is single stranded but can form base pairs e.g.
between the same strand
5. Can form base pairs w/ other nucleic acids for catalytic
functions
6. Overall RNA is transient + less stable
RNA is synthesised for a DNA template using RNA polymerase
1. DNA locally unwinds to expose the template
2. DNA bases are transcribed left to right
3. RNA nucleotides enter the molecule + pair w/ template in
the groove, phosphodiester bonds form w/ RNA polymerase as catalyst
4. Transcript= 5’ to 3’, template read 3’ to 5’
5. Pyrophosphate (2 phosphates) are lost + provide energy for phosphodiester bond
formation
- Eukaryotic cells have organelles including nucleus (membrane bound) therefore
require processing before translation in the cytoplasm
- Prokaryotic cells have free falling DNA therefore transcription and translation occur
in the cytoplasm
- mRNAs are processed before leaving the nucleus
This occurs on 3’ and 5’ ends to add stability:
1. 5’ end = capping process, adds atypical nucleotide (usually guanine w/ atypical bond)
, a. This protects the molecules end from exonuclease degradation
2. 3’ end = addition of a tail of adenine not encoded by DNA
3. Introns (non-coding sequences) need to be removed/spliced
Eukaryotic genes have non-coding sequences that need to be removed, prokaryotic cells
don’t, these are called introns (discovered in 70s)
- Introns spliced out by spliceosomes (found in 5’ UTR, coding region + 3’ UTR
o These are a mixture of RNAs and proteins
o They form bonds w/ splice site
This is when more than 1 protein (isoform) is expressed from 1 gene
- One pre-mRNA can be spliced into different molecules
In humans up to 95% of genes exhibit alternative splicing therefore there are multiple mRNA
variants
Variations include:
1. Exon skipping
2. Alternative poly(A) tail site (cut off exons)
3. Intron retention
These all produce different protein isoforms
- These are selectively exported from the nucleus through nucleur pores
- Nuclear transport receptors are bound to mRNA + mediate export + mark a mature
RNA
- mRNAs are degraded by a cell
o Stability determines how many times mRNA is translated, more times = more
stable (can be 10 hours or 30 mins)
Lecture 3: Translation
How is information translate into proteins? 4 bases to code for 20 different amino acids?
- This is what Crick + Brenner wanted to research
-
1. 1 nucleotide = 1 amino acid = 4 amino acids
2. 2 nucleotides = 1 amino acid = 42 = 16 amino acids
3. 3 nucleotides = 1 amino acid = 43 = 64 amino acids
Therefore, we can tell that there must be at least 3 nucleotides per amino acid
- If all combos are used, the code is degenerate (i.e. more than 1 combo per aa)
, No, because single base mutations only affect 1 amino acid
They used bacteriophage T4 which infects E. coli by lysis (breaking down membrane),
generated mutants in the rII gene which gave distinctive large plaque in E. coli strain B
- They used proflavine to generate these mutants, which insets itself b/w base pairs
- They found that triple mutations were special
- Genetic code = similar to a language (needed to read it in 3s)
Example = the big red fox ate the egg
Insertion (FCO+) = the xbi gre dfo xat eth egg g.
- Affects all codons after
Deletion (FCI-) = the big rdf oxa tet hee gg
- Affects all codons after
Bit of both (pseudo wildtype) = the xbi grd fox ate the egg
- Codons are restored
Double insertion = the xbi gyr edf oxa tet hee gg
Triple insertion (wild type) = the xbi gyr edz fox at the egg
- Can see 3 insertions = new codon, codons restored
Therefore, we can see genetic code of mRNA is read is 3s
1. Degenerate = some amino acids have more than one codon/tRNA
2. Some amino acids tolerate mismatches on 3 rd codon position
3. There are 3 stop codons, these don’t code for amino acids
4. Amino acids can be 3 letter (Ala) or 1 letter (A)
a. One letter allows for digital analysis
5. Genetic code is universal (except for some variations in mitochondria)
1. mRNA (messenger) = carries genetic information
2. rRNA (ribosomal) = makes up ribosome where translation occurs
3. tRNA (transfer) = adapter b/w mRNA codons + amino acids
a. Step 1 = enzyme, tRNA synthetases, couple tRNAs to correct amino acids
b. Step 2 = charged tRNA pairs w/ codon on mRNA + delivers amino acid
- This makes up ribosomes w/ proteins
- Ribosomes are where translation occurs
- Ribosomes has 2 sub units
o Has E-site (exit), P-side (peptidyl-tRNA-site), A-site (aminoacyl-tRNA site)
