Delve into the intricacies of Biochemistry and Molecular Biology through these meticulous notes tailored for Year 1 students at University College London, focusing specifically on the cell and molecular biology chapter. Explore the diverse world of cells, distinguishing between prokaryotic and euka...
Structure of DNA
DNA molecule – deoxyribonucleic acid
o Double helix – two complementary chains of nucleotides (polynucleotide chains)
Each chain – composed of 4 types of nucleotide subunits = polymer
A molecular structure formed from a large number of monomers
linked together
o Polymerisation – chemical process by which 2 or more
monomers are linked to form a polymer
Two strands – held together by hydrogen bonds between nuncleotides
Run antiparallel to each other
o Oritened with opposite polarities (3’ and 5’ – 5’ and 3’)
o Twist around eachother to form a doble helix (contains 10
base pairs per helical turn)
o Nucleotides (monomer)
Composed of cyclic nitrogen containing base + pentose sugar + one or more
phosphate groups
DNA nucleotide = base + deoxyribose sugar + phosphate groups
o Base = adenine, cytosine, guanine, thymine, uracil (RNA)
Covalently linked together in a chain through sugars and phosphates
Nucleoside – nitrogenous base + pentose sugar
Ribose nucleosides
o Adenosine = adenine + ribose sugar
o Guanosine = guanine + ribose sugar
o Cytidine = cytosine + ribose sugar
o Uridine = uracil + ribose
Deoxyribose nucleosides
o Deoxyadenosine = adenine + deoxyribose sugar
o Deoxyguanosine = guanine + deoxyribose sugar
o Deoxycytidine = cytosine + deoxyribose sugar
o Deoxythymidine = thymine + deoxyribose
Nucleotide
2’-deoxyadenosine 5’-monophosphate (dAMP) – adenine +
deoxyribose sugar + 1 phosphate
2’-deoxyguanosine 5’-monophosphate (dGMP) – guanine +
deoxyribose sugar + 1 phosphate
2’-deoxycytidine 5’-monophosphate (dCMP) – cytosine +
deoxyribose sugar + 1 phosphate
2’- deoxythymidine 5’-monophosphate (dTMP) – thymine +
deoxyribose sugar + 1 phosphate
Nucleases
Cleave phosphodiester bonds
o Exonuclease = cleaves DNA sequences in a polynucleotide
chain from either 5’ or 3’ end at one time
o Endonuclease = cleaves phosphodiester bond present within
a polynucleotide chain – cleave the nucleotide sequence
from the middle
,DNA and Chromosomes
o DNA strand has chemical polarity
Each strand is formed through bonds between sugars and phosphates
3’ hydroxyl and 5’ phosphate
o Bonding between 3’ of one sugar and 5’ of a phosphate
group
3’-5’ phosphodiester linkage
Left chain – has free 5’ end
Right chain – has free 3’ end
o Base pairs
Purine-pyramidine pair – Chargaff’s rule – ratio of purines to pyramidines = 1
Purine = adenine + guanine = 2 ring base
Pyramidine = cytosine + thymine = 1 ring base
Complementary base pairing – maintains geometry
Purine + pyramidine
o Adenine + thymine
o Cytosine + guanine
Most favourable arrangement
o Each base pair has a similar width = sugar phosphate
backbone is held an equal distance apart
o Double helix twist contributes to enegentically favourable
arrangement
The DNA Helix
o A-DNA
Right handed helix
75% humidity condition
o B-DNA – normal form of DNA
Right handed helix – helix turns right
92% humidity condition
Number of base pairs per turn = 10.4
Average rise per base pair = 0.34 nm
Helical diameter = 2.4 nm
Pitch = 3.5 nm
o Z-DNA
Left handed helix
High salt condition
DNA packaging – proteins and scaffolds
o Chromosomes
Specialised proteins (histones) bind to and fold the DNA = more compact
structure
DNA + histone = chromatin
Cells contain 2 copies of each chromosome – one from mother and one from
father
Homologous chromosomes (homologs)
o Maternal and paternal chromosomes of a pair
Nonhomologous chromosomes = sex chromosomes
o Y chromosome = sex chromosome from father
o X chromosome = sex chromosome from mother
, Control of Gene Expression
Gene expression
o Gene expression – process by which the instructions in DNA are converted into a protein
Allows cells to respond to changes in environment
Acts as an on/off switch – controls when and the amount of proteins are made
Protein synthesis
o Transcription
Promoter – sequence of DNA needed to turn a gene on or off
Downstream region from promoter = transcribed
o Contains introns and exons
Introns = regions of non-coding DNA
Exons = regions of coding DNA
Prokaryotic gene structure – promoters
o Promoter = 2 short sequences at -10 and -35 positions upstream from the
transcription start site
o Polycistronic – multiple genes are expressed in the promoter region
Eukaryotic gene structure – promoters
o Promoter – TATA box = 25-35 base pairs upstream from the transcription
start site
o Monocistronic – only one gene is expressed from a promoter region
RNA polymerase binds to promoter sequence = initiating transcription
Uses RNA nucleotides to bind to the template strand (antisense strand = non-coding
strand) – complementary to coding strand = forming mRNA strand
Works from 5’ to 3’
Does not require a primer
After mRNA strand is transcribed = processed – removes introns regions from strand + exons
are joined together
o Translation
mRNA strand leaves nucleus to ribosome
tRNA in ribosomes read mRNA
mRNA is read a codon at a time (3 bases)
o Each codon specifies a particular amino acid
Multiple codons can code for the same amino acid
tRNA molecule delivers an amino acid to the ribosome = binds to the codon on the mRNA
Adjacent amino acids join = forming a polypeptide
Operon
o Operon – multiple genes are in a promoter region + regulated by a common operator
Transcribed as a single large mRNA – which contains multiple genes
o Structure (4 components)
Promoter
RNA polymerase binds to the promoter = initiates transcription of the structural
genes
Operator
Region of DNA that partially lies within the promoter
Interacts with a regulatory protein that controls the transcription of the structural
genes
Regulator
Codes for a repressor protein that binds to the operator = blocking the promoter –
stopping transcription of the structural genes
Structural genes
Genes that are regulated by the operon
o E.g E coli – lac operon
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