BIOL1007 Lecture Notes - Lecture 1: Microorganism, Digestion, Reading Frame
8 May 2018
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BIOL7
Lecture 2 – 2.8.17
• Information must be:
o Stored (stable, corruption-free, protected, backed up) - DNA
o Accessed (easily) – DNA and RNA
o Retrieved (quickly) - DNA
o Transferred 9copied accurately) – DNA and RNA
o Read (de-coded easily and selectively) - RNA
o Used – RNA and protein
• Our brain is long term memory, all the information contained in your brain is a stable
copy. And a short term memory, a transient copy of some of the information about
the events of the day etc. The brain controls the organs etc.
• Information is the opposite of entropy. Whereas entropy is disorder, information is
very much about order
• Translation needs an adaptor
• Once in a lifetime of DNA, it replicates itself – template of the cell and making a copy
for the next generation. This process needs to be a lot more accurate than
transcription/translation
• The genome (DNA), transcriptome (RNA) and the proteome (protein)
• Transcriptome (RNA) can be messenger RNA, transfer RNA, ribosomal RNA, micro
RNA and small nuclear RNA
• The DNA is the hard drive or long term memory
• RNA is the short term memory
• Central dogma: flow of genetic information in the cell
• The DNA in almost every cell in your body contains the same information
• There is usually only one copy of each gene yet each cell will need a few proteins in
large numbers and many at low copy numbers
• Many sequences are not represented at all
• General biopolymer properties:
o All linear biopolymers have a defined beginning and end
o Biopolymer synthesis is an anabolic process (requires energy input)
o All biopolymers are synthesized in one direction only
o Some of the monomer is lost in polymerization, leaving a residue
incorporated in the growing chain
• Elements of life: they all come from the first 2 to 3 rows of the periodic table; H C N
O P S
• Carbon compounds are relatively inert or kinetically stable to hydrolysis and
oxidation. Organic reactions tend to be under kinetic control rather than
thermodynamic control.
Lecture 3
• RNA
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o Sugar – called ribose, 5 carbons, the base A, G, C or U attaches to Cao
with an N-glosidi od jois ase to akoe, Cao ed of pole
at hdol ad Cao has hdoide attahed, phosphate is added to
Cao stat of the pole
o Sugar phosphate backbone: negative charge, hydrophilic, used for
electrophoresis and ethanol precipitation
o The phosphodiester bond: joins monomers together, when broken it releases
a lot of energy
o Purine Bases: Adenine and Guanine
o The aromatic character of the 4 bases gives the DNA and RNA its UV
absorbance (pi electron clouds above and below the flat rings)
o Pyrimidine bases: Cytosine and Uracil
o DNA: polymer linked by phosphodiester bonds
o Nucleotides: are a base + sugar + phosphate
o Base: heterocyclic ring either purine or pyrimidine
o DNA vs RNA:
▪ DNA has Methyl added to ao ad o hdol at
▪ The RNA sugar phosphate backbone is vulnerable to base attack – the
back bone is snapped because there is an OH
▪ DNA is double stranded
▪ Cytosine is deamenated to Uracil (corruption in the code)
▪ The double helix: major and minor grooves (gives proteins access to
base pairs)
o Forces that maintain the double helix
▪ “tog ods: uleotides joied a phosphodieste od P jois
to the –OH)
▪ Weak forces: hydrophobic interactions, electronic interactions (base
stacking), H-bonding, Ionic interactions, Van der Waals forces
▪ To promote base pairing: lower temp, increase ionic strength, pH 7
▪ To disrupt base pairing: increase temp, reduce ionic strength, pH >9
▪ Increase melting Temp of DNA: increasing GC content, increasing ionic
strength, increasing length
▪ Weak interactions: electrostatic forces give the DNA its twist, bases
like each other but phosphates want to be away from each other
(repulsion)
Lecture 4
• Proteins:
o Some are hydrophobic
o Some are polar but uncharged (hydrophilic)
o Some are positively charged at pH 7
o The alpha amino acid
o Two amino acids combine by condensation polymerization to form a
dipeptide (peptide bond)
o This reaction is thermodynamically unfavourable due to the large amount of
water around
o Peptide bond formation in cells: happens in translation
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o Peptide bond resonance – peptide bond has a partial double bond character
od at otate ad it has patial hage
o Amino acid side chains: hydrophobic aliphatic (chains of –CH2-), aromatic
(rings with double bonds), polar non-ionic (side chains with –OH, -SH or
amides – dissole i ate ut dot dissoiate), acidic (side chains with -
COO-), basic (side chains with -N+ , positive at pH 7)
o The start of a peptide is the N-terminal, the end of the peptide is the C-
terminal
o At pH 7 the overall charge is ~ 0
o Weak forces that maintain 3-D protein conformation: hydrogen bonding
(peptide bonds and polar side chains), electrostatic or ionic interactions
haged side hais, a de Waals iteatios all lose iteactions),
hydrophobic interaction (hydrophobic side chains), disulphide bonds (-SH of
cysteine)
o Hierarchy of protein folding
▪ Primary: amino acid sequence
▪ Secondary: local structures, alpha helix and beta sheet
▪ Tertiary: overall DQ arrangement of a polypeptide chain
▪ Quaternary: organisation of subunits
o Alpha helix:
▪ ‘igid stutue ith a sigle polpeptide hai, its the akoe
forming the shape
▪ Right handed (due to L-amino acids)
▪ Side chains face outwards
▪ Structure is maintained by H-bond to an amide N-H
o Protein folding: dictated by amino acid sequence of the polypeptide and the
environment
Lecture 5
• Free energy: the change in free energy (G) is a combination of enthalpy (H) and
entropy (S):
G = H - TS
o G = available energy to do useful work
o H = total energy
o S = energy utilised in wiggling and jiggling (the nervous energy), decreases
when temperature is lowered
• The cell exists in a steady state that is NOT at equilibrium
• Thermodynamics:
o The negative G makes the reaction thermodynamically favourable
o Standard conditions: when both substrate and product are at 1M
o We denote standard conditions by the
o At equilibrium, the total free energy difference, G, is zero
o The equilibrium favours product formation – this is called the equilibrium
constant
▪ Keq is the [product]/[substrate]
• Kinetics
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Document Summary
And a short term memory, a transient copy of some of the information about the events of the day etc. Whereas entropy is disorder, information is very much about order: translation needs an adaptor, once in a lifetime of dna, it replicates itself template of the cell and making a copy for the next generation. This process needs to be a lot more accurate than transcription/translation: the genome (dna), transcriptome (rna) and the proteome (protein, transcriptome (rna) can be messenger rna, transfer rna, ribosomal rna, micro. O p s: carbon compounds are relatively inert or kinetically stable to hydrolysis and oxidation. Organic reactions tend to be under kinetic control rather than thermodynamic control. Increase melting temp of dna: increasing gc content, increasing ionic strength, increasing length: weak interactions: electrostatic forces give the dna its twist, bases like each other but phosphates want to be away from each other (repulsion)
