IMAT Biology · Free notes

Molecular Biology: DNA, RNA and Protein Synthesis

Molecular Biology and Gene Expression has 38 past questions since 2011, and the ministry papers from 2023 on have asked 13 of them. The ministry papers mostly ask for definitions and structure facts: what translation or an anticodon is, what an operon is, what DNA and mRNA are made of. The older papers added base-pairing arithmetic: Chargaff percentages, counts of hydrogen and phosphodiester bonds, and turning a DNA strand into mRNA, anticodons or a mutant protein. The difficulty sits in direction and naming: which end is 5′, which strand is the template, and keeping DNA letters apart from RNA letters.

The handout has every subtopic, worked example, formula and trap with answers shown. The formula sheet is the chapter’s formulas and traps alone, on one page.

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Subtopic notes

Formula & revision sheet

6 formulas · 16 reference tables · 27 gotchas across all subtopics — the exam-eve cheat-sheet

Nucleotides, the Double Helix and Base Pairing

Formulas (2)

Chargaff's rule: base percentages in double-stranded DNA · Chargaff's rule $\%A = \%T, \quad \%G = \%C, \quad \%A + \%G = 50\%$
Counting nucleotides, hydrogen bonds and phosphodiester bonds · Bonds in a linear double-stranded fragment $n_{\text{H}} = 2\,n_{AT} + 3\,n_{GC}, \qquad n_{\text{PDE}} = 2(N - 1)$

Reference tables (2)

Nucleotides: the building blocks of DNA and RNA5 rows

Part	In DNA	In RNA
Sugar	deoxyribose (no -OH on carbon 2′)	ribose (-OH on carbon 2′)
Purine bases (two rings)	adenine, guanine	adenine, guanine
Pyrimidine bases (one ring)	cytosine, thymine	cytosine, uracil
Phosphate	one per nucleotide	one per nucleotide
Number of strands	usually two, as a double helix	usually one, which can fold back on itself

Thymine is found only in DNA and uracil only in RNA. Everything else in the first four rows is shared.

The DNA double helix: backbone outside, paired bases inside6 rows

Feature	Fact
Outside of the helix	the sugar-phosphate backbones, with negatively charged phosphates
Inside of the helix	the bases, stacked on each other and paired across the strands
A-T pair	2 hydrogen bonds
G-C pair	3 hydrogen bonds, so G-C rich DNA is harder to separate
Direction of the strands	antiparallel: 5′→3′ beside 3′→5′
Dimensions	about 2 nm wide, 0.34 nm per base pair, about 10 base pairs per turn

Watch out for (8)

DNA has no uracil, but DNA bases can still pair with uracil
→ Nucleotides: the building blocks of DNA and RNA
Hydrogen bonds join the strands; phosphodiester bonds build each strand
→ The DNA double helix: backbone outside, paired bases inside
Complement AND reverse to write the partner 5′→3′
→ Writing the complementary strand and reading 5′ to 3′
A start codon does not mark the 5′ end
→ Writing the complementary strand and reading 5′ to 3′
Pair the right partners: G with C, A with T
→ Chargaff's rule: base percentages in double-stranded DNA
Chargaff's rule needs two strands
→ Chargaff's rule: base percentages in double-stranded DNA
Count pairs, not nucleotides, before multiplying
→ Counting nucleotides, hydrogen bonds and phosphodiester bonds
Phosphates are not phosphodiester bonds
→ Counting nucleotides, hydrogen bonds and phosphodiester bonds

DNA Replication: Semi-conservative Copying

Formulas (1)

Semi-conservative replication and counting labelled strands · Molecules after n rounds $\text{molecules} = 2^n, \qquad \text{fraction holding an original strand} = \frac{2}{2^n}$

Reference tables (3)

The enzymes of DNA replication and what each one does7 rows

Enzyme or protein	Job	Bond made or broken
Helicase	unwinds the helix at the fork and separates the strands	breaks hydrogen bonds between bases
Topoisomerase (DNA gyrase in bacteria)	relieves the over-twisting ahead of the fork	cuts and rejoins phosphodiester bonds
Single-strand binding proteins	keep the separated strands apart	makes or breaks none; they only bind
Primase	lays down a short RNA primer	makes phosphodiester bonds in RNA
DNA polymerase III (bacteria)	extends the primer 5′→3′, pairing each new base with the template, and proofreads	makes phosphodiester bonds
DNA polymerase I (bacteria)	removes the RNA primers and fills the gaps with DNA	breaks and makes phosphodiester bonds
DNA ligase	seals the last gap in the backbone between neighbouring fragments	makes one phosphodiester bond

Leading and lagging strands and Okazaki fragments4 rows

Feature	Leading strand	Lagging strand
Direction of growth	5′→3′, towards the fork	5′→3′, away from the fork
How it is made	continuously, in one piece	in short Okazaki fragments
RNA primers needed	one, at the origin	one for every fragment
Work for DNA ligase	very little	joins every pair of neighbouring fragments

Key experiments: DNA as the genetic material and its structure7 rows

Who and when	What they did	What it showed
Griffith (1928)	mixed heat-killed virulent pneumococci with live harmless ones; the mice died	a 'transforming principle' can pass between bacteria
Avery, MacLeod and McCarty (1944)	destroyed each type of molecule in the extract in turn	the transforming principle is DNA
Chargaff (about 1950)	measured the bases in DNA from many species	A = T and G = C
Hershey and Chase (1952)	labelled phage protein with ³⁵S and phage DNA with ³²P	only DNA enters the bacterium: genes are DNA
Franklin and Wilkins (1951 to 1953)	X-ray crystallography of DNA fibres	a regular helix with the backbone on the outside
Watson and Crick (1953)	built the double-helix model	base pairing suggests how DNA is copied
Meselson and Stahl (1958)	grew bacteria in ¹⁵N then ¹⁴N and separated DNA by density	replication is semi-conservative

Watch out for (4)

Molecules and strands give different fractions
→ Semi-conservative replication and counting labelled strands
DNA polymerase needs a primer; RNA polymerase does not
→ The enzymes of DNA replication and what each one does
The lagging strand is not built 3′→5′
→ Leading and lagging strands and Okazaki fragments
X-ray crystallography, not electron microscopy, revealed the helix
→ Key experiments: DNA as the genetic material and its structure

Transcription: From DNA to mRNA

Formulas (1)

Template strand, coding strand and the mRNA sequence · mRNA from the two DNA strands $\text{mRNA} = \text{coding strand with } T \rightarrow U = \text{complement of the template strand}$

Reference tables (3)

The stages of transcription and where it happens5 rows

Stage or feature	What happens
Initiation	RNA polymerase binds the promoter (in eukaryotes helped by transcription factors, often at a TATA box) and opens a short stretch of the helix
Elongation	RNA polymerase moves along the template, adding ribonucleotides to the 3′ end of the growing RNA; the DNA closes again behind it
Termination	at a terminator sequence (bacteria) or after a polyadenylation signal (eukaryotes) the RNA and the enzyme are released
Where	eukaryotes: in the nucleus, and in mitochondria and chloroplasts, which have their own DNA; prokaryotes: in the cytoplasm
Enzymes	bacteria: one RNA polymerase; eukaryotes: three (I makes most rRNA, II makes mRNA, III makes tRNA)

Replication compared with transcription6 rows

Feature	Replication	Transcription
Template	both strands of the whole molecule	one strand of one gene at a time
Main enzyme	DNA polymerase (with helicase, primase, ligase)	RNA polymerase
Primer	needed (RNA primer)	not needed
Sugar and bases added	deoxyribose; A, T, G, C	ribose; A, U, G, C
Product	two double-stranded DNA molecules	one single-stranded RNA
When	once per cell cycle, in S phase	continually, gene by gene, as the cell needs

Processing eukaryotic mRNA: cap, poly-A tail and splicing4 rows

Step	What is added or removed	Why
5′ cap	a modified guanine (7-methylguanosine) added to the 5′ end	protects the 5′ end and helps the ribosome bind
Poly-A tail	about 100 to 250 adenine nucleotides added to the 3′ end, without a template	protects the mRNA from breakdown and helps export
Splicing	introns cut out and exons joined by the spliceosome (small nuclear RNAs and proteins)	leaves one continuous coding sequence
Alternative splicing	different combinations of exons kept in different cells	one gene can give several different proteins

Watch out for (4)

Transcription makes RNA, not protein
→ The stages of transcription and where it happens
The mRNA matches the coding strand, not the template
→ Template strand, coding strand and the mRNA sequence
The same three bond events happen in both processes
→ Replication compared with transcription
Exons are expressed; introns are removed
→ Processing eukaryotic mRNA: cap, poly-A tail and splicing

The Genetic Code and Protein Synthesis

Formulas (2)

Codons: why the code uses triplets, and the start and stop codons · Number of possible codons $\text{codons} = 4^{\,n}, \qquad 4^3 = 64 = 61 \text{ (amino acids)} + 3 \text{ (stop)}$
From DNA to mRNA codons to tRNA anticodons · Anticodons and the template strand $\text{anticodon} = \text{complement of the codon} = \text{template strand with } T \rightarrow U$

Reference tables (3)

Properties of the genetic code: degenerate, unambiguous, universal5 rows

Property	Meaning	Example
Triplet	three bases make one codon	AUG is one codon
Degenerate	most amino acids have more than one codon	glycine: GGU, GGC, GGA and GGG
Unambiguous	each codon has only one meaning	GGU always means glycine
Non-overlapping	each base belongs to one codon, read codon after codon with no gaps	AUGGCC is read AUG, then GCC
Nearly universal	the same codons mean the same in almost all organisms	bacteria can make human insulin from the human gene

mRNA, tRNA and rRNA: structure and job of each3 rows

RNA	Structure	Job
mRNA (messenger)	one linear strand of codons; in eukaryotes with a cap and a poly-A tail	carries the gene's message from DNA to the ribosome
tRNA (transfer)	one strand of about 75 to 90 nucleotides folded into a cloverleaf, with an anticodon loop; the amino acid binds the 3′ end	brings one kind of amino acid and pairs its anticodon with the codon
rRNA (ribosomal)	long strands folded and combined with proteins into the two ribosome subunits	forms the ribosome; the rRNA of the large subunit makes the peptide bonds

Translation on the ribosome: initiation, elongation, termination4 rows

Stage	What happens
Initiation	the small subunit binds the mRNA and finds AUG; the initiator tRNA carrying methionine pairs with it in the P site; the large subunit joins
Elongation	a charged tRNA enters the A site; the rRNA forms a peptide bond, passing the chain onto the new amino acid; the ribosome moves one codon along and the empty tRNA leaves from the E site
Termination	a stop codon reaches the A site; a release factor (a protein) binds; the polypeptide is freed and the subunits separate
After translation	the chain folds; proteins for secretion, made on the rough ER, are modified in the Golgi apparatus

Watch out for (5)

Stop codons code for no amino acid and have no tRNA
→ Codons: why the code uses triplets, and the start and stop codons
Degenerate is not the same as ambiguous
→ Properties of the genetic code: degenerate, unambiguous, universal
Codons are on mRNA; anticodons are on tRNA
→ mRNA, tRNA and rRNA: structure and job of each
Anticodons match the template strand, not the coding strand
→ From DNA to mRNA codons to tRNA anticodons
Translation is in the cytoplasm, in every kind of cell
→ Translation on the ribosome: initiation, elongation, termination

Mutations at the Level of DNA

Reference tables (2)

Point mutations: silent, missense, nonsense and frameshift5 rows

Type	Change in the DNA	Effect on the protein
Silent	substitution giving a codon for the same amino acid	no change
Missense	substitution giving a codon for a different amino acid	one amino acid replaced; the protein may fold differently
Nonsense	substitution giving a stop codon	a shorter protein, usually not functional
Frameshift	insertion or deletion of 1, 2, 4 ... bases (not a multiple of 3)	every codon after it read wrongly, often reaching an early stop
In-frame insertion or deletion	3 bases (or a multiple of 3) added or lost	one amino acid gained or lost; the rest unchanged

Causes of mutation, repair and inheritance of mutations5 rows

Source or system	What it does to DNA
Copying errors	a wrong base slips past DNA polymerase; after proofreading and repair about 1 base in $10^9$ to $10^{10}$ copied stays wrong
Ultraviolet light	joins neighbouring thymines into thymine dimers, which distort the helix
Ionising radiation (X-rays, gamma rays)	breaks one or both strands of the backbone
Chemical mutagens	alter bases or slip between them (intercalating agents cause frameshifts); tobacco smoke contains several
Repair systems	proofreading by DNA polymerase, mismatch repair, and excision repair of damaged bases

Watch out for (3)

A single-base change can have any of several effects
→ Point mutations: silent, missense, nonsense and frameshift
Equal length does not rule out insertion or deletion
→ Reading two sequences to name the mutation
Mutations are random, not directed by need
→ Causes of mutation, repair and inheritance of mutations

The Genome, Chromatin and the Control of Genes

Reference tables (3)

Chromatin packing and the organisation of the genome5 rows

Level	What it is	Approximate size
Histone	one small protein; eight (two each of H2A, H2B, H3, H4) form a core	a few nanometres
Nucleosome	about 147 base pairs of DNA wound nearly twice round a histone core	about 10 nm across ('beads on a string')
Chromatin fibre	nucleosomes packed together, helped by histone H1	about 30 nm thick
Looped domains	the fibre folded in loops on a protein scaffold	a few hundred nanometres
Metaphase chromosome	the most condensed form: two sister chromatids	about 1 µm wide and several µm long

The lac operon: switching bacterial genes on with lactose3 rows

Lactose	Glucose	Repressor	Transcription of lacZ, lacY, lacA
absent	present or absent	bound to the operator	off
present	present	released (allolactose bound)	low (no help from CAP)
present	absent	released (allolactose bound)	high (cAMP and CAP help RNA polymerase bind)

Control of gene expression in eukaryotes, in outline5 rows

Level	How expression is controlled
Chromatin	acetylating histones loosens chromatin and allows transcription; methylating DNA silences genes
Transcription	transcription factors bind promoters, enhancers and silencers to switch genes on or off
RNA processing	alternative splicing chooses which exons enter the mRNA
mRNA lifetime and translation	microRNAs and the length of the poly-A tail decide how long an mRNA lasts and how often it is read
Protein	proteins are activated by modification (for example phosphorylation) or destroyed by the proteasome

Watch out for (3)

Rank the packing levels by what contains what
→ Chromatin packing and the organisation of the genome
The repressor gene is outside the operon and always active
→ The lac operon: switching bacterial genes on with lactose
Transcription factors regulate genes; RNA polymerase only transcribes them
→ Control of gene expression in eukaryotes, in outline

PYQ weightage by concept

24 concepts · 0 PYQs — where the marks actually sit, so you know what to drill first

Nucleotides, the Double Helix and Base Pairing0 PYQs · 0%

Concept	PYQs	Share
Nucleotides: the building blocks of DNA and RNAfoundation	—	—
The DNA double helix: backbone outside, paired bases insidefoundation	—	—
Writing the complementary strand and reading 5′ to 3′foundation	—	—
Chargaff's rule: base percentages in double-stranded DNAfoundation	—	—
Counting nucleotides, hydrogen bonds and phosphodiester bondsfoundation	—	—

DNA Replication: Semi-conservative Copying0 PYQs · 0%

Concept	PYQs	Share
Semi-conservative replication and counting labelled strandsfoundation	—	—
The enzymes of DNA replication and what each one doesfoundation	—	—
Leading and lagging strands and Okazaki fragmentsfoundation	—	—
Key experiments: DNA as the genetic material and its structurefoundation	—	—

Transcription: From DNA to mRNA0 PYQs · 0%

Concept	PYQs	Share
The stages of transcription and where it happensfoundation	—	—
Template strand, coding strand and the mRNA sequencefoundation	—	—
Replication compared with transcriptionfoundation	—	—
Processing eukaryotic mRNA: cap, poly-A tail and splicingfoundation	—	—

The Genetic Code and Protein Synthesis0 PYQs · 0%

Concept	PYQs	Share
Codons: why the code uses triplets, and the start and stop codonsfoundation	—	—
Properties of the genetic code: degenerate, unambiguous, universalfoundation	—	—
mRNA, tRNA and rRNA: structure and job of eachfoundation	—	—
From DNA to mRNA codons to tRNA anticodonsfoundation	—	—
Translation on the ribosome: initiation, elongation, terminationfoundation	—	—

Mutations at the Level of DNA0 PYQs · 0%

Concept	PYQs	Share
Point mutations: silent, missense, nonsense and frameshiftfoundation	—	—
Reading two sequences to name the mutationfoundation	—	—
Causes of mutation, repair and inheritance of mutationsfoundation	—	—

The Genome, Chromatin and the Control of Genes0 PYQs · 0%

Concept	PYQs	Share
Chromatin packing and the organisation of the genomefoundation	—	—
The lac operon: switching bacterial genes on with lactosefoundation	—	—
Control of gene expression in eukaryotes, in outlinefoundation	—	—