1.1 Chemistry of life — EST 2 Biology Revision Notes & Topical Questions

Section 1 of 30Water and hydrogen bonding

Hydrogen bonding explains water’s solvent, thermal and cohesive properties.

Polar molecule

Water is a polar molecule: oxygen carries a partial negative charge and the hydrogen atoms carry partial positive charges. Attraction between these regions creates hydrogen bonds between water molecules.

Hydrogen bonding gives water a high specific heat and heat of vaporisation. Water therefore resists rapid temperature change, and evaporation of sweat removes thermal energy from the body.

Section 2 of 30Cohesion, adhesion and solvent action

Cohesion

Cohesion is attraction between water molecules and contributes to surface tension and continuous columns of water in plants. Adhesion is attraction to other surfaces and helps capillary movement.

Water dissolves many ionic and polar substances, making it an effective medium for reactions and transport. Ice is less dense than liquid water, so floating ice insulates the water beneath it.

Section 3 of 30pH and buffers

Tenfold

pH measures hydrogen-ion concentration. A lower pH means a higher H⁺ concentration; each change of one pH unit represents a tenfold change in H⁺ concentration.

Buffers

Cells function within a limited pH range. Buffers resist sudden pH changes by accepting excess H⁺ or donating H⁺ when its concentration falls; the bicarbonate system helps buffer human blood.

Section 4 of 30Build and break polymers

Dehydration synthesis

Dehydration synthesis joins monomers by removing water. Hydrolysis adds water to break a larger molecule into smaller units; digestion uses hydrolysis.

Carbohydrates provide quick energy and include starch, glycogen and cellulose. Lipids store concentrated energy and form membranes. Proteins are amino-acid polymers, while nucleic acids store and transmit genetic information.

Section 5 of 30Protein structure and enzymes

Protein structure and enzymes

Denature

A protein's amino-acid sequence determines how it folds, and its three-dimensional shape determines its function. High temperature or unsuitable pH can disrupt this shape and denature the protein.

Enzymes are biological catalysts. A substrate binds at an active site, the enzyme lowers activation energy, and products are released. Enzymes are specific and can be reused after the reaction.

Section 6 of 30Nucleotides and the 5′ and 3′ ends

DNA and RNA are polynucleotides: many nucleotide monomers linked in a chain. Each nucleotide has three components: a pentose (five-carbon) sugar, a phosphate group and a nitrogenous base. DNA bases are adenine, guanine, cytosine and thymine; RNA bases are adenine, guanine, cytosine and uracil.

A polynucleotide has two distinct ends.

5′ (five prime) end

The 5′ (five prime) end has a terminal phosphate group on carbon 5 of a sugar.

3′ (three prime) end

The 3′ (three prime) end has a terminal hydroxyl (–OH) group on carbon 3 of a sugar.

During nucleic acid synthesis, new nucleotides are always added to the 3′ end of the growing strand,

forming strong covalent bonds between the nucleotides.

Section 7 of 30DNA versus RNA

DNA is an antiparallel double helix: the two strands of nucleotides run in opposite 5′ → 3′ orientations. Hydrogen bonds join complementary bases between the strands. RNA is usually single-stranded, but it can fold, and the folds are held together by base pairing, with adenine pairing with uracil (not thymine) and cytosine pairing with guanine as in DNA.

Feature	DNA	RNA
Pentose sugar	Deoxyribose	Ribose
Nitrogenous bases	A, T, C, G	A, U, C, G
Base pairing	A–T, C–G	A–U, C–G
Strands	Double helix	Usually single-stranded

Section 8 of 30Amino acids and peptide bonds

Proteins are made of linear chains of monomers called amino acids.

Amino acids and peptide bonds

R group

Each amino acid has an amine group (–NH₂), a carboxyl group (–COOH), a hydrogen atom and a variable R group attached to a central carbon.

The 20 R groups fall into three categories based on the properties of the side chains: non-polar (hydrophobic), polar (uncharged) and charged (acidic or basic).

Amino acids are joined by peptide bonds, which are covalent bonds formed at the carboxyl end of the growing peptide chain: a hydroxyl group (–OH) is lost from the carboxyl group of one amino acid and a hydrogen atom is lost from the amino group of the neighbouring amino acid.

Amino acids and peptide bonds

The R group is not involved in forming the peptide bond.

To find a peptide bond in a diagram, look for nitrogen bonded to a carbon that has a double bond to oxygen.

The sequence, type and number of amino acids determine the shape and therefore the function of the protein.

Section 9 of 30Primary and secondary structure

DNA determines the primary structure of a protein by instructing the cell to add particular amino acids in a specific sequence.

Primary and secondary structure

One alteration in the sequence can alter the function of the protein.

Secondary structure

The secondary structure is formed by hydrogen bonds between peptide bonds: an α-helix forms when hydrogen bonds form between every fourth peptide bond,

and a β-pleated sheet forms when the chain folds so that two parts lie parallel and hydrogen bonds form between the folded layers.

Hydrogen bonds are weak, so they are broken easily by high temperatures and pH changes.

Remember that the four common macromolecule classes are carbohydrates, lipids, proteins and nucleic acids, and that nucleic acids and proteins are information-carrying polymers: the order of bases in DNA codes for the order of amino acids in a protein, which determines its shape and function.

Section 10 of 30Worked examples

State two differences between DNA and RNA. [2]2 marks
Explain what antiparallel means in DNA. [2]2 marks
Describe how a peptide bond forms. [3]3 marks
Why does a change in one amino acid in the sequence sometimes alter a protein's function? [2]2 marks

Section 11 of 30Tertiary and quaternary structure of proteins

The tertiary structure is the overall three-dimensional folding of one polypeptide, held by interactions between R groups: hydrogen bonds, disulphide bonds between cysteine amino acids, ionic bonds between charged R groups and weak hydrophobic interactions between non-polar R groups. The quaternary structure is the arrangement of two or more polypeptide subunits working together; haemoglobin, for example, has four subunits that carry oxygen.

Section 12 of 30Carbohydrates

Carbohydrates are biological molecules made of monosaccharide monomers, such as glucose. Two monosaccharides join by dehydration synthesis to form a disaccharide, and many join to form a polysaccharide by covalent glycosidic bonds. Complex carbohydrates can be linear or branched.

Polysaccharide	Found in	Structure and function
Cellulose	Plant cell walls	Long chains of β-glucose joined by 1,4 glycosidic bonds; alternate glucose molecules are rotated through 180°. Many hydrogen bonds between chains give great strength
Starch	Plants (storage)	α-glucose; amylose is unbranched and amylopectin is a branched form
Glycogen	Animals and fungi (storage)	Always branched, so large quantities can be stored in a small space

Storage polysaccharides do not dissolve in the cytoplasm, so they have no effect on the water potential of cells.

Section 13 of 30Lipids

Lipids are energy-dense molecules that provide energy storage and support cell function.

A triglyceride is made of glycerol and three fatty acids.

Saturated

Fatty acids can be saturated (no double bonds, saturated with hydrogen atoms so they cannot hold any more) or unsaturated (one or more double bonds),

which affects structure and function.

Subcutaneous fat gives thermal insulation, as in whale blubber.

Phospholipids have a hydrophilic head and hydrophobic tails and form bilayers in plasma and cell membranes. Steroids are a class of lipids; steroid hormones support growth and development, energy metabolism and homeostasis.

Section 14 of 30Polymers, hydrolysis and dehydration synthesis

A polymer is a large molecule made of many repeated monomers; the term macromolecule is often used for biological polymers.

Monomer	Polymer
Monosaccharide (glucose)	Polysaccharide (starch, glycogen, cellulose)
Amino acid	Polypeptide / protein
Nucleotide	Polynucleotide (DNA, RNA)

Dehydration synthesis (a condensation reaction) joins two smaller molecules through covalent bonding and removes a molecule of water. Hydrolysis (hydro = water, lysis = splitting) breaks covalent bonds by adding water, splitting large molecules into smaller ones.

Section 15 of 30Linking structure to function

Each molecule's properties arise from its bonding.

Linking structure to function

Cellulose is strong because of hydrogen bonds between parallel chains; glycogen is compact because it is highly branched, with many ends from which glucose can be released quickly; phospholipids form bilayers because their heads are attracted to water and their tails avoid it; proteins fold because of R group interactions.

When asked to explain a function, name the structural feature, the bond or property, and the benefit.

Section 16 of 30Identifying molecules in diagrams

Recognise carbohydrates by their rings of carbon, hydrogen and oxygen in the ratio near 1 : 2 : 1; amino acids by the amine and carboxyl groups; triglycerides by glycerol joined to three fatty acid chains; and nucleotides by a sugar bonded to a phosphate and a base. Check for double bonds in the fatty acid tails to decide if a lipid is saturated or unsaturated.

Finish by checking that you can state, for every molecule type, its monomer, its bond, the reaction that forms it and the reaction that breaks it down.

Section 17 of 30Worked examples

Name the bonds that hold the tertiary structure of a protein. [3]3 marks
Explain why cellulose is strong. [2]2 marks
Give two reasons why glycogen is a good storage molecule. [2]2 marks
Define hydrolysis. [1]1 mark

Section 18 of 30Nucleotides and polynucleotide polarity

DNA and RNA are polynucleotides: many nucleotide monomers linked in a chain. Each nucleotide has three components: a pentose (five-carbon) sugar, a phosphate group and a nitrogenous base. DNA bases are adenine, guanine, cytosine and thymine; RNA bases are adenine, guanine, cytosine and uracil.

A polynucleotide has two distinct ends.

5′ (five prime) end

The 5′ (five prime) end has a terminal phosphate group on carbon 5 of a sugar.

3′ (three prime) end

The 3′ (three prime) end has a terminal hydroxyl (–OH) group on carbon 3 of a sugar.

During nucleic acid synthesis, new nucleotides are always added to the 3′ end of the growing strand,

forming strong covalent bonds between the nucleotides.

Section 19 of 30DNA and RNA compared

DNA is an antiparallel double helix: the two strands of nucleotides run in opposite 5′ → 3′ orientations. Hydrogen bonds join complementary bases between the strands. RNA is usually single-stranded, but it can fold, and the folds are held together by base pairing, with adenine pairing with uracil (not thymine) and cytosine pairing with guanine as in DNA.

Feature	DNA	RNA
Pentose sugar	Deoxyribose	Ribose
Nitrogenous bases	A, T, C, G	A, U, C, G
Base pairing	A–T, C–G	A–U, C–G
Strands	Double helix	Usually single-stranded

Section 20 of 30Amino acids and peptide bonds

Proteins are made of linear chains of monomers called amino acids.

Amino acids and peptide bonds

R group

Each amino acid has an amine group (–NH₂), a carboxyl group (–COOH), a hydrogen atom and a variable R group attached to a central carbon.

The 20 R groups fall into three categories based on the properties of the side chains: non-polar (hydrophobic), polar (uncharged) and charged (acidic or basic).

Amino acids are joined by peptide bonds, which are covalent bonds formed at the carboxyl end of the growing peptide chain: a hydroxyl group (–OH) is lost from the carboxyl group of one amino acid and a hydrogen atom is lost from the amino group of the neighbouring amino acid.

Amino acids and peptide bonds

The R group is not involved in forming the peptide bond.

To find a peptide bond in a diagram, look for nitrogen bonded to a carbon that has a double bond to oxygen.

The sequence, type and number of amino acids determine the shape and therefore the function of the protein.

Section 21 of 30How DNA determines primary structure

DNA determines the primary structure of a protein by instructing the cell to add particular amino acids in a specific sequence.

How DNA determines primary structure

One alteration in the sequence can alter the function of the protein.

Secondary structure

The secondary structure is formed by hydrogen bonds between peptide bonds: an α-helix forms when hydrogen bonds form between every fourth peptide bond,

and a β-pleated sheet forms when the chain folds so that two parts lie parallel and hydrogen bonds form between the folded layers.

Hydrogen bonds are weak, so they are broken easily by high temperatures and pH changes.

Practise by writing a complementary strand

given the DNA sequence 5′-ATGC-3′, the complementary strand is 3′-TACG-5′ and the corresponding RNA is 5′-AUGC-3′ when transcribed from the complementary template.
This links base pairing rules, antiparallel orientation and the difference between DNA and RNA bases.

Check that you can state the five key contrasts: sugar (deoxyribose or ribose), bases (T or U), strands (two or one), pairing (A–T or A–U) and ends (5′ phosphate and 3′ hydroxyl).

Section 22 of 30Worked examples

Name the three components of a nucleotide. [3]3 marks
How does the sequence of DNA affect a protein? [3]3 marks
Identify the peptide bond in a diagram. [1]1 mark
State which bases pair in RNA folds. [2]2 marks

Section 23 of 30Secondary, tertiary and quaternary structure

DNA determines the primary structure of a protein by instructing the cell to add particular amino acids in a specific sequence.

Secondary, tertiary and quaternary structure

One alteration in the sequence can alter the function of the protein.

Secondary structure

The secondary structure is formed by hydrogen bonds between peptide bonds: an α-helix forms when hydrogen bonds form between every fourth peptide bond,

and a β-pleated sheet forms when the chain folds so that two parts lie parallel and hydrogen bonds form between the folded layers.

Hydrogen bonds are weak, so they are broken easily by high temperatures and pH changes.

The tertiary structure is the overall three-dimensional folding of one polypeptide, held by interactions between R groups: hydrogen bonds, disulphide bonds between cysteine amino acids, ionic bonds between charged R groups and weak hydrophobic interactions between non-polar R groups. The quaternary structure is the arrangement of two or more polypeptide subunits working together; haemoglobin, for example, has four subunits that carry oxygen.

Section 24 of 30Carbohydrate polymers

Carbohydrates are biological molecules made of monosaccharide monomers, such as glucose. Two monosaccharides join by dehydration synthesis to form a disaccharide, and many join to form a polysaccharide by covalent glycosidic bonds. Complex carbohydrates can be linear or branched.

Polysaccharide	Found in	Structure and function
Cellulose	Plant cell walls	Long chains of β-glucose joined by 1,4 glycosidic bonds; alternate glucose molecules are rotated through 180°. Many hydrogen bonds between chains give great strength
Starch	Plants (storage)	α-glucose; amylose is unbranched and amylopectin is a branched form
Glycogen	Animals and fungi (storage)	Always branched, so large quantities can be stored in a small space

Storage polysaccharides do not dissolve in the cytoplasm, so they have no effect on the water potential of cells.

Section 25 of 30Lipids and membranes

Lipids are energy-dense molecules that provide energy storage and support cell function.

A triglyceride is made of glycerol and three fatty acids.

Saturated

Fatty acids can be saturated (no double bonds, saturated with hydrogen atoms so they cannot hold any more) or unsaturated (one or more double bonds),

which affects structure and function.

Subcutaneous fat gives thermal insulation, as in whale blubber.

Phospholipids have a hydrophilic head and hydrophobic tails and form bilayers in plasma and cell membranes. Steroids are a class of lipids; steroid hormones support growth and development, energy metabolism and homeostasis.

Section 26 of 30Linking structure to function in macromolecules

Each class of biological macromolecule is built from monomers joined by dehydration synthesis and broken by hydrolysis.

Linking structure to function in macromolecules

The properties come from the bonds: weak hydrogen bonds allow proteins to fold and unfold reversibly, covalent peptide bonds hold the primary structure, hydrophobic interactions bury non-polar R groups,

and ionic and disulphide bonds lock the tertiary shape.

In carbohydrates, α-linked glucose forms compact, easily hydrolysed storage molecules, whereas β-linked glucose forms straight, strong fibres.

In lipids, the long non-polar hydrocarbon tails make them energy-dense and insoluble in water.

Section 27 of 30Exam technique

When asked to explain why a molecule suits its function, state the feature, the bond or property responsible, and the benefit.

Exam technique

For example: glycogen is highly branched, so it has many ends from which glucose can be removed quickly and can be packed compactly.

Heating a protein breaks hydrogen bonds, which changes its shape and so its function.

Always name the level of protein structure you mean.

Practise identifying unfamiliar diagramsfind the amine and carboxyl groups for amino acids, ring structures for sugars, long chains attached to glycerol for triglycerides.

Section 28 of 30Worked examples

Explain why a high temperature can make an enzyme stop working. [3]3 marks
Compare starch and cellulose. [3]3 marks
Why are lipids a good energy store? [2]2 marks
Describe how a phospholipid is arranged in a membrane. [2]2 marks

Section 29 of 30Key terms

Term	Meaning
Nucleotide	A monomer of nucleic acids made of sugar, phosphate and a base.
Antiparallel	Running in opposite directions.
Amino acid	The monomer of proteins.
Primary structure	The sequence of amino acids in a polypeptide.
R group	The variable side chain of an amino acid.
α-helix	A secondary structure with hydrogen bonds between every fourth peptide bond.

Term	Meaning
Polymer	A large molecule made of many repeating monomers.
Dehydration synthesis	A reaction that joins monomers and releases water.
Hydrolysis	A reaction that splits a molecule by adding water.
Peptide bond	The covalent bond between amino acids.
Quaternary structure	Arrangement of multiple polypeptide subunits.
Glycogen	Branched storage polysaccharide in animals and fungi.
Triglyceride	A lipid made of glycerol and three fatty acids.

Term	Meaning
Polymer	A large molecule made of many repeating monomers.
Dehydration synthesis	A reaction that joins monomers and releases water.
Hydrolysis	A reaction that splits a molecule by adding water.
Peptide bond	The covalent bond between amino acids.
Polynucleotide	A chain of many nucleotides.
Uracil	The base in RNA that pairs with adenine.
Deoxyribose	The sugar in DNA.

Term	Meaning
β-pleated sheet	A secondary structure where chain regions lie parallel, bonded by hydrogen bonds.
Tertiary structure	3D folding of a polypeptide held by R group interactions.
Amylopectin	A branched form of starch.
Cellulose	A structural polysaccharide of β-glucose.
Steroid	A class of lipids including some hormones.

Section 30 of 30Exam technique

1

Saying the 5′ end has a hydroxyl group — it has the phosphate; 3′ has the hydroxyl.

2

Saying the R group takes part in the peptide bond.

3

Saying RNA contains thymine.

4

Saying hydrogen bonds are strong covalent bonds.

1

Confusing dehydration synthesis (builds, releases water) with hydrolysis (splits, adds water).

2

Saying cellulose is made of α-glucose.

3

Saying saturated fats have double bonds.

4

Believing quaternary structure applies to every protein.

1

Saying uracil is found in DNA.

2

Saying new nucleotides are added at the 5′ end.

3

Saying proteins are polymers of nucleotides.

4

Believing amino acid structures need to be memorised for AP.

1

Confusing α-helix (hydrogen bonds along one chain) with β-pleated sheet (between parallel regions).

2

Saying tertiary structure is the sequence of amino acids.

3

Saying glycogen is stored in plants.

4

Saying unsaturated fats have no double bonds.

Section 1 of 30Water and hydrogen bonding

Section 2 of 30Cohesion, adhesion and solvent action

Section 3 of 30pH and buffers

Section 4 of 30Build and break polymers

Section 5 of 30Protein structure and enzymes

Section 6 of 30Nucleotides and the 5′ and 3′ ends

Section 7 of 30DNA versus RNA

Section 8 of 30Amino acids and peptide bonds

Section 9 of 30Primary and secondary structure

Section 10 of 30Worked examples

State two differences between DNA and RNA. [2]2 marks

Explain what antiparallel means in DNA. [2]2 marks

Describe how a peptide bond forms. [3]3 marks

Why does a change in one amino acid in the sequence sometimes alter a protein's function? [2]2 marks

Section 11 of 30Tertiary and quaternary structure of proteins

Section 12 of 30Carbohydrates

Section 13 of 30Lipids

Section 14 of 30Polymers, hydrolysis and dehydration synthesis

Section 15 of 30Linking structure to function

Section 16 of 30Identifying molecules in diagrams

Section 17 of 30Worked examples

Name the bonds that hold the tertiary structure of a protein. [3]3 marks

Explain why cellulose is strong. [2]2 marks

Give two reasons why glycogen is a good storage molecule. [2]2 marks

Define hydrolysis. [1]1 mark

Section 18 of 30Nucleotides and polynucleotide polarity

Section 19 of 30DNA and RNA compared

Section 20 of 30Amino acids and peptide bonds

Section 21 of 30How DNA determines primary structure

Section 22 of 30Worked examples

Name the three components of a nucleotide. [3]3 marks

How does the sequence of DNA affect a protein? [3]3 marks

Identify the peptide bond in a diagram. [1]1 mark

State which bases pair in RNA folds. [2]2 marks

Section 23 of 30Secondary, tertiary and quaternary structure

Section 24 of 30Carbohydrate polymers

Section 25 of 30Lipids and membranes

Section 26 of 30Linking structure to function in macromolecules

Section 27 of 30Exam technique

Section 28 of 30Worked examples

Explain why a high temperature can make an enzyme stop working. [3]3 marks

Compare starch and cellulose. [3]3 marks

Why are lipids a good energy store? [2]2 marks

Describe how a phospholipid is arranged in a membrane. [2]2 marks

Section 29 of 30Key terms

Section 30 of 30Exam technique

Marked practiceQuizzes for this lesson