Biochemistry Week 1 – Atoms, Water, Carbon & Macromolecules

A comprehensive set of flashcards covering key concepts from atoms and elements through water chemistry, carbon-based molecules, functional groups, and the four classes of biological macromolecules as presented in Week 1 Biochemistry lecture notes.

What is matter?

Anything that takes up space and has mass.

How do elements differ from compounds?

Elements are pure substances that cannot be broken down chemically, whereas compounds are substances composed of two or more elements in fixed ratios.

Which four elements make up about 96% of living matter?

Carbon (C), Hydrogen (H), Oxygen (O) and Nitrogen (N).

What are trace elements?

Elements required by organisms in minute quantities, e.g., Fe, Zn, I.

Define atomic number.

The number of protons in an atom’s nucleus.

Define atomic mass.

The sum of protons and neutrons in an atom.

What are isotopes?

Atoms of the same element with the same number of protons but different numbers of neutrons.

Give one biological use of radioactive isotopes.

Dating fossils (e.g., 14C) or medical tracers (e.g., 131I).

Name the three main types of chemical bonds.

Covalent, ionic, and hydrogen bonds (with van der Waals as weak interactions).

What characterises a covalent bond?

Sharing of at least one pair of valence electrons between atoms.

Define electronegativity.

The attraction of an atom for the electrons in a covalent bond.

When is a covalent bond non-polar?

When the bonded atoms have similar electronegativities and share electrons equally.

Why is water considered a polar molecule?

Oxygen is more electronegative than hydrogen, creating partial charges (δ− on O, δ+ on H).

What is an ionic bond?

Electrostatic attraction between oppositely charged ions formed after electron transfer.

Describe a hydrogen bond.

Attraction between a δ+ hydrogen in one molecule and a highly electronegative atom (O, N, F) in another.

What causes van der Waals interactions?

Transient positive and negative regions in molecules causing weak attractions.

List the four emergent properties of water critical for life.

Cohesive behavior, moderation of temperature, expansion upon freezing, and versatility as a solvent. (CTFS)

Define cohesion.

Attraction between water molecules via hydrogen bonding.

What is surface tension?

The difficulty of stretching or breaking the surface of a liquid due to cohesive forces.

Explain water’s high specific heat.

Hydrogen bonds absorb heat when breaking and release heat when forming, so water resists temperature change (1 cal/g °C).

What is heat of vaporization?

Energy required to convert 1 g of liquid to gas; high in water due to hydrogen bonds.

Why does ice float on water?

Hydrogen bonds form a lattice making solid water (Ice) less dense than liquid water.

Differentiate hydrophilic and hydrophobic substances.

Hydrophilic substances are ionic or polar and dissolve in water; hydrophobic substances are non-polar and do not dissolve in water or covalent.

State the pH equation.

pH = –log [H⁺].

What is a buffer?

A substance that minimizes pH changes by accepting or donating H⁺ ions (e.g., carbonic acid/bicarbonate).

What element forms the backbone of biological molecules?

Carbon.

How many covalent bonds can a carbon atom form?

Four.

Define hydrocarbon.

A molecule consisting solely of carbon and hydrogen.

What are isomers?

Compounds with the same molecular formula but different structures and physical properties.

Name the three types of isomers.

Structural, geometric (cis-trans), and enantiomers.

Why are enantiomers pharmacologically important?

Different enantiomers of a drug can have different biological activities (e.g., S-ibuprofen active, R-ibuprofen inactive).

What is a functional group?

A chemically reactive group of atoms that gives distinctive chemical properties to an organic molecule.

Identify the functional group: –OH.

Hydroxyl group; found in alcohols, polar, forms H-bonds.

Identify the functional group: C=O.

Carbonyl group; forms ketones or aldehydes depending on position.

Identify the functional group: –COOH.

Carboxyl group; acts as an acid.

Identify the functional group: –NH₂.

Amino group; acts as a base.

Identify the functional group: –SH.

Sulfhydryl group; can form disulfide bridges in proteins.

Identify the functional group: –OPO₃²⁻.

Phosphate group; contributes negative charge and energy transfer (ATP). Confers(grant) a molecule tha ability to react with water, releasing energy.

Identify the functional group: –CH₃.

Methyl group; affects genes expression and the shape and functions of sex hormone.

Define polymer.

A large molecule that forms by polymerization, where monomer subunits form covalent bonds to make a polymer

What reaction links monomers into polymers?

Dehydration synthesis (removal of water).

What reaction breaks polymers into monomers?

Hydrolysis (addition of water).

Give the general formula for a monosaccharide.

(CH₂O)ₙ where n = 3–8.

Name three common monosaccharides.

Glucose, fructose, galactose.

What bond joins two monosaccharides?

Glycosidic linkage.

Give the formula for disaccharides.

C₁₂H₂₂O₁₁ (due to loss of water during linkage).

Match each disaccharide with its monomers: maltose, lactose, sucrose.

Maltose = glucose + glucose; lactose = glucose + galactose; sucrose = glucose + fructose.

What is starch?

A storage polysaccharide of plants composed of α-glucose units.

Contrast cellulose and starch.

Cellulose is a structural β-glucose polymer; starch is a storage α-glucose polymer.

What is glycogen?

An extensively branched α-glucose storage polysaccharide in animals.

Where is chitin found?

Fungal cell walls and arthropod exoskeletons; polymer of β-glucose with nitrogen group.

What are the components of a triglyceride?

Three fatty acids attached to a glycerol molecule.

Differentiate saturated and unsaturated fatty acids.

Saturated have only single covalent bond between each carbon (C–C) bonds (straight chains, solid at room temp); unsaturated have one or more C=C double bonds (kinked, liquid at room temp) and each of the two carbon have only one hydrogen bonded to it.

Describe a phospholipid.

A lipid with two fatty acids and a phosphate group containing hydrophilic head attached to glycerol; forms cell membranes., instead of a third fatty acid

What is a steroid?

A lipid with four fused carbon rings (e.g., cholesterol, hormones).

List five functions of proteins.

Structural support, storage, transport, defense (antibodies), and enzymatic catalysis.

What two functional groups are present in every amino acid?

Amino (–NH₂) and carboxyl (–COOH) groups.

What type of bond links amino acids?

Peptide bond.

Define primary protein structure.

The linear sequence of amino acids in a polypeptide.

What stabilises secondary protein structure?

Hydrogen bonds between backbone atoms forming α-helices or β-pleated sheets.

Name four interactions that stabilise tertiary structure.

Hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges.

What is quaternary structure?

The association of two or more polypeptide subunits into a functional protein.

Give two causes of protein denaturation.

Extreme pH, high temperature, or changes in salt concentration.

What are the three components of a nucleotide?

Nitrogenous base, five-carbon sugar, and phosphate group.

Differentiate purines and pyrimidines.

Purines (adenine, guanine) have double rings; pyrimidines (cytosine, thymine, uracil) have single rings.

What sugars are found in DNA and RNA?

DNA contains deoxyribose; RNA contains ribose.

State the base-pairing rules in DNA.

A pairs with T; G pairs with C via hydrogen bonds.

What does antiparallel mean in DNA structure?

The two strands run in opposite 5′→3′ directions.

List two structural differences between DNA and RNA.

DNA is double-stranded, contains thymine; RNA is single-stranded, contains uracil.

What is the role of mRNA?

To carry genetic information from DNA to ribosomes for protein synthesis.

Summarise the four classes of macromolecules.

Carbohydrates (fuel/structure), lipids (energy storage/membranes), proteins (diverse functions), nucleic acids (genetic information).