Biochemistry And Molecular Biology (BIOC0001) Notes - Cell and Molecular Biology

DNA and Chromosomes

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