IMAT Biology · Formula sheet
Molecular Biology and Gene Expression formulas
6 formulas, 16 reference tables and 27 common traps for IMAT Biology Molecular Biology and Gene Expression, grouped by subtopic.
Nucleotides, the Double Helix and Base Pairing
Learn this subtopic in the notesChargaff's rule: base percentages in double-stranded DNA
Chargaff's rule
- percentage of all bases that are adenine (and so on for T, G, C)
Counting nucleotides, hydrogen bonds and phosphodiester bonds
Bonds in a linear double-stranded fragment
- numbers of A-T and G-C base pairs
- total base pairs,
- phosphodiester bonds in both strands together
Nucleotides: the building blocks of DNA and RNA
| 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 inside
| 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 |
Common traps
DNA has no uracil, but DNA bases can still pair with uracil
Uracil is never part of DNA. But during transcription an adenine in the DNA template pairs with uracil in the new RNA. So 'DNA bases may form hydrogen bonds with uracil' is true, while 'DNA contains uracil' is false.
Hydrogen bonds join the strands; phosphodiester bonds build each strand
Options often swap the two bonds. The bases of opposite strands are held by hydrogen bonds, which are weak and easy to break for copying. Each strand's own nucleotides are linked by covalent phosphodiester bonds, which stay intact when the helix opens.
Complement AND reverse to write the partner 5′→3′
Swapping the bases gives the partner strand running 3′→5′. Many options print those letters with 5′ and 3′ labels in the usual order, which is a different molecule. Reverse the complement before you compare it with options written 5′→3′.
A start codon does not mark the 5′ end
The 5′ end is a chemical feature (the free phosphate on carbon 5′). A sequence beginning with AUG or ATG tells you nothing about direction unless the ends are labelled or the 5′→3′ convention is stated.
Pair the right partners: G with C, A with T
Given guanine, the matching share belongs to cytosine, not thymine. To find thymine from guanine, double the guanine figure, subtract from 100%, then halve. Copying the guanine number as the answer is the commonest wrong option.
Chargaff's rule needs two strands
A single strand of DNA, or any RNA, can have any base ratio. The rule is a consequence of pairing, so it applies only to double-stranded DNA taken as a whole.
Count pairs, not nucleotides, before multiplying
If a fragment has 9 cytosines, it has 9 G-C pairs (9 C plus 9 G), not 18. Multiplying the nucleotide count by 3 double-counts every pair.
Phosphates are not phosphodiester bonds
Every nucleotide carries one phosphate, so phosphates = nucleotides. But a linear strand of n nucleotides has only n − 1 phosphodiester bonds, because the end nucleotide has no neighbour on one side.
DNA Replication: Semi-conservative Copying
Learn this subtopic in the notesSemi-conservative replication and counting labelled strands
Molecules after n rounds
- number of rounds of replication
The enzymes of DNA replication and what each one does
| 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 fragments
| 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 structure
| 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 |
Common traps
Molecules and strands give different fractions
After n rounds there are molecules but strands. The 2 original strands are of the molecules but only of the strands. Check which one the question asks for.
DNA polymerase needs a primer; RNA polymerase does not
DNA polymerase can only add to an existing 3′ end, so every new DNA strand starts on a short RNA primer. RNA polymerase in transcription starts a chain on its own. An option saying DNA polymerase begins a new strand from nothing is wrong.
The lagging strand is not built 3′→5′
No strand is ever built 3′→5′. The lagging strand is built 5′→3′ like the leading strand, but in pieces, each pointing away from the fork. An option saying one strand grows 3′→5′ is wrong.
X-ray crystallography, not electron microscopy, revealed the helix
Franklin's evidence came from the pattern X-rays make after passing through DNA fibres. Electron microscopes, chromatography and electrophoresis played no part in finding the double helix.
Transcription: From DNA to mRNA
Learn this subtopic in the notesTemplate strand, coding strand and the mRNA sequence
mRNA from the two DNA strands
The stages of transcription and where it happens
| 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 transcription
| 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 splicing
| 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 |
Common traps
Transcription makes RNA, not protein
The direct product of transcribing any gene, even the insulin gene, is an RNA molecule. The protein is made later, by translation. Options naming a protein as the product of transcription are wrong.
The mRNA matches the coding strand, not the template
The template strand is the one read, so the mRNA is its complement. Writing the template's own letters with U for T gives the wrong mRNA, and that error is usually among the options.
The same three bond events happen in both processes
Breaking hydrogen bonds, forming hydrogen bonds and forming phosphodiester bonds all occur in replication and in transcription. A statement using one of these to tell them apart is wrong; the real differences are the sugar, the base U or T, the enzyme and the product.
Exons are expressed; introns are removed
The names help: EXons are EXpressed, INtrons stay IN the nucleus. So a mature mRNA is shorter than its gene, and protein length cannot be predicted from the length of the whole gene.
The Genetic Code and Protein Synthesis
Learn this subtopic in the notesCodons: why the code uses triplets, and the start and stop codons
Number of possible codons
- number of bases per codon
- number of different bases in mRNA (A, U, G, C)
From DNA to mRNA codons to tRNA anticodons
Anticodons and the template strand
Properties of the genetic code: degenerate, unambiguous, universal
| 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 each
| 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, termination
| 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 |
Common traps
Stop codons code for no amino acid and have no tRNA
At a stop codon a protein release factor, not a tRNA, binds the ribosome. So count stop codons when finding mRNA length, but not when counting amino acids.
Degenerate is not the same as ambiguous
Degenerate means one amino acid has several codons. Ambiguous would mean one codon has several amino acids, which never happens. The code is degenerate but unambiguous.
Codons are on mRNA; anticodons are on tRNA
rRNA has no anticodons, and mRNA has no anticodons. A codon is a triplet of the message; an anticodon is the complementary triplet on the tRNA that reads it.
Anticodons match the template strand, not the coding strand
Two complements cancel out: template → mRNA → anticodon brings you back to the template sequence, with U for T. An option that matches the coding strand describes the mRNA, not the anticodons.
Translation is in the cytoplasm, in every kind of cell
Capping, splicing and transcription happen in the eukaryotic nucleus, but translation happens on ribosomes in the cytoplasm. It is not special to eukaryotes: bacteria translate on their own 70S ribosomes.
Mutations at the Level of DNA
Learn this subtopic in the notesPoint mutations: silent, missense, nonsense and frameshift
| 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 mutations
| 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 to 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 |
Common traps
A single-base change can have any of several effects
Do not assume a point mutation always changes the protein, or always ruins it. The same kind of event can be silent, change one amino acid, shorten the protein or shift the frame. A 'which effects are possible' question usually wants all of them.
Equal length does not rule out insertion or deletion
If one base is inserted and another deleted a few bases later, the length is unchanged but the codons between them are read in the wrong frame. When two sequences of equal length differ in a run of bases, consider substitution, insertion and deletion together.
Mutations are random, not directed by need
A mutagen raises the rate of mutation everywhere in the genome. It does not produce the change an organism needs; natural selection later acts on whatever variation arises.
The Genome, Chromatin and the Control of Genes
Learn this subtopic in the notesChromatin packing and the organisation of the genome
| 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 lactose
| 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 outline
| 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 |
Common traps
Rank the packing levels by what contains what
A chromosome contains many nucleosomes, and each nucleosome contains eight histones, so chromosome > nucleosome > histone. Options that put a histone above a nucleosome reverse the nesting.
The repressor gene is outside the operon and always active
lacI has its own promoter and makes the repressor all the time. Lactose does not stop its production; it binds the repressor and changes its shape so that it falls off the operator.
Transcription factors regulate genes; RNA polymerase only transcribes them
RNA polymerase is needed for every gene and does not choose which genes are used. Gene expression is regulated by transcription factors (and by chromatin, splicing and the other levels), not by replication factors or by organelles such as the rough ER.