BIOC Molecular Biology

What is the most basic unit of life?

The cell

What is the organisational hierarchy of life from smallest to largest?

Cell → tissues → organs → systems → organism

What are the three domains of life?

Bacteria, Archaea, Eukarya

What is haem and what is its biological role?

A prosthetic group containing a porphyrin ring with a central Fe²⁺ ion — found in haemoglobin and cytochromes where it is involved in oxygen binding and electron transfer

What is chlorophyll and what is its biological role?

A porphyrin-based molecule containing a central Mg²⁺ ion — found in photosynthetic organisms where it absorbs light for energy conversion

What key structural feature do haem and chlorophyll share?

They both contain a porphyrin ring

What is a porphyrin ring?

A large flat ring structure made of four pyrrole rings linked by methine (-CH-) bridges

What is a pyrrole ring?

A five-membered heterocyclic ring containing four carbon atoms and one nitrogen atom

What is a methine group?

A -CH- group that links pyrrole rings together in a porphyrin structure

How do haem and chlorophyll differ chemically?

They coordinate different central metal ions — Fe²⁺ in haem and Mg²⁺ in chlorophyll

Why does the central metal ion matter in haem vs chlorophyll?

The metal determines the molecule's function — Fe²⁺ enables oxygen binding in haem while Mg²⁺ enables light absorption in chlorophyll

What is a prosthetic group?

A non-peptide component permanently or tightly associated with a protein that is essential for its function

Can prosthetic groups bind covalently or non-covalently?

Yes — they can bind either covalently or non-covalently

What types of molecules can prosthetic groups be?

Organic molecules or metal ions

What are the functions of prosthetic groups?

Support protein structure; enable biochemical activity; act as electron carriers in redox reactions

Is haem a prosthetic group?

Yes — haem is a prosthetic group found in proteins such as haemoglobin and cytochromes

What does it mean that key biological motifs are evolutionarily conserved?

Their structure and function have been preserved across species because they are essential for life

What is a motif?

A recurring pattern of amino acids or nucleotides at a sequential or structural level

What is the globin protein?

A protein that binds haem and is involved in oxygen transport and storage

What does a gene tree represent?

The evolutionary history of a specific gene across different organisms

How does a gene tree differ from a species tree?

A gene tree tracks the evolution of a gene while a species tree tracks the evolution of organisms — they can differ due to gene duplication, loss, or horizontal gene transfer

What are the key differences between prokaryotic and eukaryotic cells?

Prokaryotes have naked DNA in a nucleoid region, no membrane-bound organelles, 70S ribosomes, no introns, and are usually haploid. Eukaryotes have DNA packaged with histones into chromosomes enclosed in a nucleus, membrane-bound organelles, 80S ribosomes, introns, and are diploid or polyploid

What are the three major classes of membrane lipids?

Phosphoglycerides, sphingolipids, and sterols

What is a phosphoglyceride?

A membrane lipid composed of glycerol, two fatty acid tails, and a phosphate-containing head group

Which part of a phosphoglyceride is hydrophobic and which is hydrophilic?

The fatty acid tails are hydrophobic; the phosphate-containing head group is hydrophilic

Name the four common phosphoglyceride head groups.

Phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylinositol (PI)

What is phosphatidylcholine (PC)?

A phosphoglyceride with a choline head group — cylindrical in shape and commonly found in the outer leaflet of membranes

What is phosphatidylethanolamine (PE)?

A phosphoglyceride with an ethanolamine head group — cone-shaped due to its small head and promotes membrane curvature

What is phosphatidylserine (PS)?

A negatively charged phospholipid with a serine head group important for cell signalling and apoptosis

What is phosphatidylinositol (PI)?

A phospholipid with an initosol head group involved in signalling pathways via phosphorylation of its head group

What are sphingolipids?

Membrane lipids built on a sphingosine backbone rather than glycerol

What is sphingomyelin (SM)?

A sphingolipid with a phosphocholine head group — abundant in animal cell membranes and found in lipid rafts

How do sphingolipids differ structurally from phosphoglycerides?

They use a sphingosine backbone instead of glycerol and tend to have longer more saturated fatty acid tails

What are sterols?

Rigid ring-shaped lipids that regulate membrane fluidity — examples include cholesterol (animals), ergosterol (fungi), and stigmasterol (plants)

What is the function of cholesterol in membranes?

Regulates membrane fluidity — increases rigidity at high temperatures, prevents crystallisation at low temperatures, and increases membrane thickness by ordering lipid tails

Which lipid combinations produce the thickest membranes?

Sphingomyelin and cholesterol combinations

What is the approximate thickness of a PC bilayer?

~3.5 nm

How does adding cholesterol to a PC bilayer affect its thickness?

Increases thickness to approximately 4.0 nm

What is the thickness range of sphingomyelin bilayers?

~4.6-5.6 nm

Why does membrane thickness matter biologically?

It influences protein localisation and membrane domain formation

What are lipid rafts?

Cholesterol- and sphingolipid-rich microdomains within membranes that organise and concentrate signalling proteins

How does lipid shape influence membrane structure?

Cylindrical lipids like PC form flat bilayers; cone-shaped lipids like PE promote curvature and membrane bending

What is cis configuration in a fatty acid tail?

Hydrogens on the same side of a double bond — creates a kink in the tail preventing tight packing and increasing membrane fluidity

How does an unsaturated fatty acid tail differ from a saturated one in terms of membrane fluidity?

Unsaturated tails are kinked and more fluid; saturated tails are straight and pack tightly reducing fluidity

What is the fluid mosaic model?

Membrane proteins float within a fluid phospholipid bilayer — proteins are not fixed but can move laterally

What are the three types of light microscopy covered and what can each visualise?

Light microscopy (whole cells and tissues); phase contrast (living unstained cells and internal structures); confocal (fluorescently labelled structures with sharp 3D optical sections)

What is phase contrast microscopy?

A technique that converts phase differences in light passing through and around a specimen into brightness differences — produces contrast without staining and can image living cells

What is confocal microscopy?

Uses a laser to scan point by point with a pinhole blocking out-of-focus light — a computer reconstructs sharp optical sections and 3D images of fluorescently labelled structures

What are the three types of electron microscopy and which has the highest resolution?

Transmission EM (internal ultrastructure), scanning EM (3D surface images), cryogenic EM (near-native high-resolution 3D macromolecular structures) — cryo-EM has the highest resolution

What is transmission EM?

Electrons pass through an ultra-thin specimen — dense regions scatter electrons and appear darker; used to visualise internal organelles and viruses

What is scanning EM?

An electron beam scans the surface of a specimen and reflected electrons are detected — produces detailed 3D surface images

What is cryogenic EM?

Specimens are rapidly frozen and imaged at cryogenic temperatures — produces near-native high-resolution 3D structures of macromolecules

What are mitochondria?

Double-membrane organelles responsible for aerobic respiration and ATP production — contain cristae, their own DNA, and ribosomes

What are lysosomes?

Acidic enzyme-filled organelles that digest macromolecules and recycle cellular components

What is the nuclear envelope?

A double membrane surrounding the nucleus — contains nuclear pores and is continuous with the ER

What is the nucleolus?

A non-membrane-bound nuclear region where rRNA is synthesised and ribosomal subunits are assembled

What is the smooth ER?

Synthesises lipids and steroids; detoxifies drugs; stores Ca²⁺

What is the rough ER?

Studded with ribosomes — synthesises secreted and membrane proteins; performs protein folding and initial glycosylation

What is the Golgi complex?

Modifies, sorts, and packages proteins and lipids — forms lysosomes and secretory vesicles

What are peroxisomes?

Organelles containing oxidative enzymes that break down fatty acids and toxins and convert hydrogen peroxide to water

What are the three types of cytoskeletal fibres?

Microfilaments (actin), microtubules, and intermediate filaments

What are microvilli?

Actin-supported membrane projections that increase surface area for absorption

What is the cell wall composition in plants

fungi, and bacteria?,Cellulose in plants; chitin in fungi; peptidoglycan in bacteria

Is DNA mostly coiled or uncoiled in the cell?

Mostly uncoiled

What is the hierarchy of DNA packaging?

DNA double helix → nucleosomes → chromatin fibres → looped domains → chromosomes

What is a nucleosome?

147 bp of DNA wrapped around a histone octamer — appears as beads on a string

What is a chromatosome?

A nucleosome plus the linker histone H1

What is the role of histone H1?

Stabilises DNA entry and exit from the nucleosome and promotes higher-order chromatin folding

What are histone proteins?

Positively charged proteins that package DNA into chromatin

What is euchromatin?

Loosely packed chromatin that is transcriptionally active and accessible to transcription machinery

What is heterochromatin?

Highly condensed chromatin that is transcriptionally inactive — structural and protective

What are looped domains?

DNA loops anchored to scaffold proteins that compact and organise chromatin into higher-order structures

What is the structure of a nucleotide?

A pentose sugar + a phosphate group + a nitrogenous base

What is a pyrimidine?

A single-ring nitrogenous base — cytosine, thymine (DNA), and uracil (RNA)

Nitrogen at position 1 and 3

Double bonds alternate around the ring

Everything else (cytosine, thymine, uracil) = this + extra groups

What is a purine?

A double-ring nitrogenous base — adenine and guanine

2 fused rings:

one 6-membered ring

one 5-membered ring

Total 9 atoms in the rings

4 nitrogens

5 carbons

Which carbon of the ribose attaches to the nitrogenous base?

The 1′ carbon

Which carbon of the ribose is linked to the phosphate group?

The 5′ carbon

Which carbon provides the hydroxyl group for phosphodiester bond formation?

The 3′ carbon

What is the structural difference between ribose and deoxyribose?

Ribose has an -OH at the 2′ carbon; deoxyribose has an -H at the 2′ carbon

Why is DNA more chemically stable than RNA?

Because deoxyribose lacks the reactive 2′ hydroxyl group that makes RNA susceptible to hydrolysis

What is a furanose ring?

A five-membered monosaccharide ring made of four carbons and one oxygen — the ribose sugar in nucleotides forms this ring

What is a nucleoside?

A nitrogenous base + a pentose sugar with no phosphate group attached

What is a phosphodiester bond?

A covalent bond linking the 3′ carbon of one nucleotide to the 5′ carbon of the next via a phosphate group — forms the backbone of DNA and RNA

What is the charge of DNA and why?

Negatively charged — due to the phosphate groups in the sugar-phosphate backbone

In which direction is DNA synthesised?

Always 5′ → 3′ — new nucleotides are added to the free 3′-OH end

What are the three major forms of the DNA helix?

A-DNA (right-handed, dehydrated), B-DNA (right-handed, physiological), Z-DNA (left-handed, high salt)

What conditions favour A-DNA formation?

~75% relative humidity — dehydrated conditions

What conditions favour B-DNA formation?

~92% relative humidity — physiological conditions

What conditions favour Z-DNA formation?

High salt concentrations

How many base pairs per turn in B-DNA?

~10-10.4 bp per turn

What is the vertical rise per base pair in B-DNA?

~3.4 Å (0.34 nm)

What is the pitch of B-DNA?

~3.4-3.5 nm per turn

How long would the human genome be if fully extended?

Approximately 1 metre — calculated from ~3 × 10⁹ bp × 0.34 nm per bp

What stabilises the DNA double helix?

Hydrogen bonds between complementary base pairs and hydrophobic base stacking interactions between adjacent bases

What is DNA denaturation?

Separation of the two DNA strands by breaking hydrogen bonds — caused by heat or alkaline conditions

What is DNA reannealing?

Reformation of the double helix when complementary single strands reassociate under appropriate conditions

What are endonucleases?

Enzymes that cut within a nucleic acid strand (in the middle of the strand)

What are exonucleases?

Enzymes that remove nucleotides from the ends of a nucleic acid strand by cleaving the phosphodiester bond

can be cutting from 3'--5' or 5'--3'

What are restriction enzymes?

Sequence-specific bacterial endonucleases that recognise short palindromic DNA sequences and cut them — used in bacteria as defence against foreign DNA

What are sticky ends?

Single-stranded overhangs produced by restriction enzyme cleavage that can base-pair with complementary ends to facilitate DNA ligation during cloning