Chemical composition of living tissue and metabolites
If you burn a piece of dry wood, ash is left behind. That ash is the minerals, and the smoke is mostly carbon, hydrogen and oxygen that were in the wood. Chemists analyse living tissue in a similar way.
Living tissues are made of the same elements as the earth's crust, but in very different proportions: carbon, hydrogen, oxygen and nitrogen are far more abundant in living things. Compounds are organic (carbon compounds) or inorganic (water, minerals). Primary metabolites are found in all living cells; secondary metabolites are found only in some organisms.
In the figure : Four kinds of building blocks of the cell.
Rule 1: Analysing chemical composition — A weighed piece of tissue is ground in trichloroacetic acid and filtered. The filtrate is the acid-soluble pool (small molecules) and the retentate is the acid-insoluble pool (macromolecules). Burning the tissue gives ash (inorganic part) and the carbon compounds are lost as gas. Water is the most abundant compound in a living cell.
- Easy : A little ash is left after burning dry leaves.
- Medium : Macromolecules such as proteins stay in the acid-insoluble fraction.
- Exam-type : Q: What is left behind after burning the tissue? A: Ash that has the inorganic elements.
Rule 2: Primary and secondary metabolites — Amino acids, simple sugars and nucleotides are primary metabolites, as they have a known role in normal growth. Secondary metabolites such as alkaloids (morphine, codeine), flavonoids, rubber, essential oils, antibiotics, coloured pigments, scents and gums have no direct role in basic growth but help the organism in other ways.
- Easy : Glucose is a primary metabolite.
- Medium : Morphine from the opium poppy is a secondary metabolite.
- Exam-type : Q: Give two examples of secondary metabolites. A: Alkaloids such as morphine and rubber (or antibiotics, essential oils).
Primary metabolites: needed for basic life. Secondary metabolites: have ecological and human uses.
Thinking that secondary metabolites are useless. They have important roles in defence, attraction and in medicines.
Memory clue: P-all, S-some — Primary in all, Secondary in some.
Spot the difference
| Point | Primary metabolites | Secondary metabolites |
|---|---|---|
| Occurrence | All organisms | Some organisms |
| Role | Growth and functions | Defence, attraction, human use |
| Example | Amino acids, sugars | Alkaloids, rubber, antibiotics |
Practice questions
- 1Which compound is the most abundant in a living cell?
- 2What is the acid-soluble pool?
- 3What remains after tissue is burnt?
- 4Give two examples of primary metabolites.
- 5Name two secondary metabolites.
- 6How do the elements of the living tissue compare with those of the earth's crust?
- 7What are macromolecules? Give two examples.
- 8Why are secondary metabolites called products of the cell and yet not part of normal growth?
Show answers (try them yourself first)
- 1Water.
- 2The filtrate containing small-molecular-weight compounds.
- 3Ash, which holds inorganic elements.
- 4Amino acids and simple sugars (nucleotides).
- 5Morphine and rubber (or other alkaloids, flavonoids).
- 6Carbon, hydrogen, oxygen and nitrogen are much more abundant in living tissue.
- 7Large molecules with high molecular weights, such as proteins and nucleic acids.
- 8They are made by the cell but have no known role in basic growth; they help the organism in defence or attraction instead.
Amino acids, fatty acids and nucleotides: the building blocks
A necklace is made by threading beads, and a wall by stacking bricks. The cell's large molecules are made by joining small units in the same way.
Amino acids have an amino group, a carboxyl group, a hydrogen and an R group on the same carbon. Fatty acids have a carboxyl group attached to a hydrocarbon chain. Nucleotides are made of a nitrogen base, a sugar and phosphate.
In the figure : Amino acids join by peptide bonds to form proteins.
Rule 1: Amino acids and lipids — The R group decides the type: glycine (H), alanine (methyl), serine (hydroxymethyl) are examples. Amino acids can be acidic, basic or neutral. In solution an amino acid is a zwitterion with both positive and negative charges. Lipids are esters of fatty acids with alcohols like glycerol. Fatty acids can be saturated or unsaturated; a triglyceride is a glycerol with three fatty acids. A phospholipid has a phosphate group and is found in cell membranes. Fats melt at a higher temperature than oils.
- Easy : Glycine is the simplest amino acid, with only H as R.
- Medium : Ghee (saturated fat) is solid at room temperature but groundnut oil (unsaturated) is liquid.
- Exam-type : Q: What is a zwitterion? A: An amino acid form with both a positive and a negative charge in the same molecule.
Rule 2: Nucleotides — A nucleotide has three parts: a nitrogenous base (adenine, guanine, cytosine, thymine or uracil), a pentose sugar (ribose or deoxyribose) and a phosphate group. A nucleoside has the base and the sugar only. Nucleotides join in a chain by phosphodiester bonds to form DNA and RNA.
- Easy : DNA uses deoxyribose; RNA uses ribose.
- Medium : Uracil is found in RNA in place of thymine.
- Exam-type : Q: Name the three parts of a nucleotide. A: A nitrogenous base, a pentose sugar and a phosphate group.
Twenty types of amino acids occur in proteins. Five nitrogen bases occur in nucleic acids (A, G, C, T, U).
Saying DNA has uracil. DNA has thymine, and RNA has uracil.
Memory clue: A-G-C-T/U — Adenine, Guanine, Cytosine, Thymine (DNA) or Uracil (RNA).
Spot the difference
| Unit | Parts | Forms |
|---|---|---|
| Amino acid | Amino, carboxyl, H, R group | Proteins |
| Fatty acid | COOH + hydrocarbon chain | Fats, oils, phospholipids |
| Nucleotide | Base + sugar + phosphate | DNA, RNA |
Practice questions
- 1Name the groups attached to the alpha carbon of an amino acid.
- 2How many types of amino acids are found in proteins?
- 3What is a triglyceride?
- 4Name the bases found in DNA.
- 5What is a nucleoside?
- 6What is a phospholipid and where is it found?
- 7How do saturated and unsaturated fatty acids differ?
- 8Why is an amino acid called amphoteric or a zwitterion?
Show answers (try them yourself first)
- 1An amino group, a carboxyl group, a hydrogen and an R group.
- 2Twenty.
- 3A glycerol molecule joined to three fatty acids.
- 4Adenine, guanine, cytosine and thymine.
- 5A nitrogenous base joined to a sugar.
- 6A lipid with a phosphate group; it is found in cell membranes.
- 7Saturated ones have no double bonds in the chain, while unsaturated ones have one or more double bonds.
- 8It has both an acidic carboxyl group and a basic amino group, so the molecule carries both charges.
Proteins: structure and importance
A long piece of string can be left straight, coiled like a spring, or crumpled into a ball. A protein chain does the same on three different scales, and its shape decides what it does.
Proteins are polymers of amino acids joined by peptide bonds. They have four levels of structure: primary (the sequence of amino acids), secondary (alpha helix or beta sheet), tertiary (3-D folding) and quaternary (more than one chain).
In the figure : The four levels of protein structure.
Rule 1: Four levels of structure — In the primary structure the first amino acid is the N-terminal and the last is the C-terminal. In the secondary structure the chain coils into a right-handed alpha helix. In the tertiary structure the chain folds like a ball and gives the molecule its 3-D shape; this is needed for most biological functions. In the quaternary structure two or more chains join, as the four subunits of adult haemoglobin (two alpha and two beta).
- Easy : The sequence of letters in a word is like the primary structure.
- Medium : Haemoglobin has four chains, so it has a quaternary structure.
- Exam-type : Q: How many chains does adult haemoglobin have? A: Four (two alpha and two beta).
Rule 2: Functions of proteins — Collagen is the most abundant protein in the animal world and RuBisCO is the most abundant protein in the whole biosphere. Proteins act as enzymes, hormones (insulin), antibodies, transport carriers, structural parts and receptors.
- Easy : Insulin is a protein hormone.
- Medium : RuBisCO catches carbon dioxide in photosynthesis.
- Exam-type : Q: Which is the most abundant protein in the animal world? A: Collagen.
Shape decides function. Heat or a strong acid unfolds the protein (denaturation) and changes its action.
Confusing primary with secondary structure. Primary is the amino acid sequence; secondary is the coiling.
Memory clue: 1-2-3-4 — Sequence, Coil, Fold, Combine.
Spot the difference
| Level | What it is | Example |
|---|---|---|
| Primary | Order of amino acids | N to C terminal chain |
| Secondary | Helix or sheet | Alpha helix |
| Tertiary | Overall fold | Myoglobin |
| Quaternary | More than one chain | Haemoglobin |
Practice questions
- 1What is a peptide bond?
- 2What is the primary structure of a protein?
- 3Which protein is the most abundant in the biosphere?
- 4What is the shape of the secondary structure called?
- 5Name a protein that has a quaternary structure.
- 6Give two functions of proteins.
- 7Why does the tertiary structure matter?
- 8What happens when a protein is denatured?
Show answers (try them yourself first)
- 1The bond joining two amino acids.
- 2The sequence of amino acids in the chain.
- 3RuBisCO.
- 4An alpha helix (or beta sheet).
- 5Haemoglobin.
- 6They act as enzymes and as hormones, antibodies, carriers or structural parts.
- 7The 3-D shape is needed for the protein to carry out its biological activity.
- 8Its higher-level structures unfold, and the protein loses its function.
Polysaccharides: starch, glycogen, cellulose and others
A potato stores energy as starch, a dog's liver stores it as glycogen, and the strong fibre in cotton is cellulose. All of them are long chains of glucose, but they are joined differently and serve different jobs.
Polysaccharides are long chains of monosaccharides joined by glycosidic bonds. Starch, glycogen and cellulose are polymers of glucose; inulin is a polymer of fructose; chitin is a polymer of an N-acetyl sugar.
In the figure : Three common polysaccharides.
Rule 1: Storage polysaccharides — Starch is the plant store of energy. It holds helical chains and gives a blue colour with iodine. Glycogen is the animal store, found in the liver and muscles; it is branched. Inulin is a polymer of fructose.
- Easy : A drop of iodine on a potato slice turns blue-black.
- Medium : Glycogen is released from the liver when the blood sugar falls.
- Exam-type : Q: Which polysaccharide stores energy in animals? A: Glycogen.
Rule 2: Structural polysaccharides — Cellulose is a polymer of glucose that makes plant cell walls; it has no branches and does not give a blue colour with iodine. Paper and cotton fibre are cellulose. Chitin is a complex polysaccharide with amino-sugar units found in the exoskeleton of arthropods and in fungal cell walls.
- Easy : Cotton is almost pure cellulose.
- Medium : The hard cover of a cockroach has chitin.
- Exam-type : Q: Name the polysaccharide of the arthropod exoskeleton. A: Chitin.
Starch → plants; glycogen → animals; cellulose → plant wall; chitin → arthropods and fungi.
Saying that cellulose gives a blue colour with iodine. Only starch does.
Memory clue: S-G-C-C — Starch (plants), Glycogen (animals), Cellulose (wall), Chitin (arthropods/fungi).
Spot the difference
| Polysaccharide | Monomer | Role |
|---|---|---|
| Starch | Glucose | Plant energy store |
| Glycogen | Glucose | Animal energy store |
| Cellulose | Glucose | Plant cell wall |
| Inulin | Fructose | Storage |
Practice questions
- 1Which polysaccharide is the plant store of energy?
- 2What is a glycosidic bond?
- 3What is cellulose made of?
- 4Which colour does starch give with iodine?
- 5Where is chitin found?
- 6Name the monomer of inulin.
- 7How do starch and cellulose differ?
- 8Why can humans digest starch but not cellulose?
Show answers (try them yourself first)
- 1Starch.
- 2The bond joining two monosaccharides.
- 3Glucose units.
- 4Blue (blue-black).
- 5In the exoskeleton of arthropods and the cell walls of fungi.
- 6Fructose.
- 7Starch is the plant's energy store and gives a blue colour with iodine; cellulose forms the cell wall and does not.
- 8Human digestive enzymes can break the bonds in starch, but they cannot break the glycosidic bonds of cellulose.
Nucleic acids: DNA and RNA
A recipe book holds instructions for every dish. DNA is the 'recipe book' of the cell: it stores the instructions to make proteins, and RNA is the photocopy that carries a recipe to the kitchen.
Nucleic acids are polymers of nucleotides. They are of two types: DNA (deoxyribonucleic acid) that stores genetic information and RNA (ribonucleic acid) that helps to express it.
In the figure : A nucleotide is built from a base, a sugar and a phosphate.
Rule 1: DNA and RNA — DNA has deoxyribose and the bases A, G, C and T; RNA has ribose and the bases A, G, C and U. DNA is usually a double strand, and RNA is single stranded. DNA is the genetic material, while the main types of RNA, mRNA, tRNA and rRNA, take part in protein synthesis.
- Easy : DNA is in the nucleus, and RNA is mostly in the cytoplasm.
- Medium : DNA has two strands, but a typical RNA has one.
- Exam-type : Q: What sugar does RNA have? A: Ribose.
Rule 2: Nucleotides in chains — Nucleotides are joined by phosphodiester bonds. The two DNA strands are held by hydrogen bonds between the bases: A pairs with T by two bonds and G with C by three bonds.
- Easy : In one strand, if the bases are A-T-G, the other strand has T-A-C.
- Medium : A DNA with more G-C pairs is more stable because of three bonds in each pair.
- Exam-type : Q: Which bases pair together in DNA? A: A with T, and G with C.
A–T has two hydrogen bonds; G–C has three.
Pairing A with C in DNA. A pairs with T, and G pairs with C.
Memory clue: AT-GC — A-T and G-C.
Spot the difference
| Point | DNA | RNA |
|---|---|---|
| Sugar | Deoxyribose | Ribose |
| Bases | A, G, C, T | A, G, C, U |
| Strands | Double | Single |
Practice questions
- 1What do DNA and RNA stand for?
- 2Which sugar is found in DNA?
- 3Which base is present in RNA instead of thymine?
- 4What type of bond joins nucleotides in a chain?
- 5What holds the two strands of DNA together?
- 6Name three types of RNA.
- 7How many hydrogen bonds join G and C?
- 8Write the complementary strand for A-A-G-C-T.
Show answers (try them yourself first)
- 1Deoxyribonucleic acid and ribonucleic acid.
- 2Deoxyribose.
- 3Uracil.
- 4Phosphodiester bond.
- 5Hydrogen bonds between the paired bases.
- 6mRNA, tRNA and rRNA.
- 7Three.
- 8T-T-C-G-A.
Enzymes: nature and mechanism of action
A match needs a little rub to light, and a few sparks start a big fire. Enzymes lower the 'rub' needed, so the reactions of life run quickly at body temperature.
Enzymes are biological catalysts, mostly proteins (some RNAs are catalytic: ribozymes). They speed up reactions by lowering the activation energy. The enzyme has an active site where the substrate binds to form an enzyme–substrate complex and then the product.
In the figure : An enzyme binds the substrate and releases the product unchanged.
Rule 1: Catalysis and activation energy — Without an enzyme, a reaction has to cross a high energy barrier called the activation energy. An enzyme lowers this barrier. The enzyme is not used up and can act again. For example, carbonic anhydrase speeds up the reaction of carbon dioxide and water about 10 million times.
- Easy : Digestion at body temperature is quick because of enzymes.
- Medium : The same enzyme molecule can work on many substrate molecules.
- Exam-type : Q: What do enzymes lower? A: The activation energy.
Rule 2: Nature of enzyme action — The active site is a crevice or pocket in the tertiary structure of the enzyme. The substrate fits into it, a bond-breaking or bond-forming change happens in the transition state, and the product is released. Enzymes are specific; the old lock-and-key idea is now refined by the induced-fit idea.
- Easy : A key fits one lock, as an enzyme fits one kind of substrate.
- Medium : The active site is formed by the folding of the protein chain.
- Exam-type : Q: Where does the substrate bind in an enzyme? A: At the active site.
Enzymes change the speed, not the direction or the end result, of a reaction.
Saying that an enzyme is used up in the reaction. It is released unchanged.
Memory clue: E+S → ES → E+P — Enzyme + Substrate, complex, then Enzyme + Product.
Spot the difference
| Term | Meaning | Example |
|---|---|---|
| Substrate | The reacting molecule | Starch for amylase |
| Active site | Pocket where the substrate binds | Part of enzyme protein |
| Activation energy | Energy barrier to reaction | Lowered by enzymes |
Practice questions
- 1What is an enzyme?
- 2What is meant by activation energy?
- 3What is an active site?
- 4Name a catalytic RNA.
- 5Is the enzyme consumed during the reaction?
- 6What is a substrate?
- 7How do enzymes speed up a reaction?
- 8Why is an enzyme specific to its substrate?
Show answers (try them yourself first)
- 1A biological catalyst, mostly a protein.
- 2The energy needed to start a reaction.
- 3The crevice in an enzyme where the substrate binds.
- 4A ribozyme.
- 5No, it is regenerated and can be used again.
- 6The molecule on which an enzyme acts.
- 7They lower the activation energy by forming an enzyme–substrate complex.
- 8The shape of its active site, which comes from the tertiary structure, fits only certain substrates.
Factors affecting enzymes; classification and cofactors
Boiling an egg turns it hard because heat changes its proteins. In the same way, too much heat, or a wrong acid level, makes an enzyme stop working.
Enzyme activity depends on temperature, pH, substrate concentration and inhibitors. Enzymes are classified into six classes. Some enzymes need a non-protein cofactor; the protein part is the apoenzyme, and with the cofactor it becomes the holoenzyme.
In the figure : Factors that affect the activity of an enzyme.
Rule 1: Factors and inhibition — Each enzyme has an optimum temperature and pH; low temperature keeps it inactive but safe, and high temperature denatures it. With more substrate the rate rises until the enzyme is saturated (Vmax). A competitive inhibitor looks like the substrate and competes for the active site, as malonate does for succinic dehydrogenase; sulpha drugs and many medicines work this way.
- Easy : Pepsin works best in acid, trypsin in a slightly alkaline medium.
- Medium : A high substrate level can overcome a competitive inhibitor.
- Exam-type : Q: Name a competitive inhibitor of succinic dehydrogenase. A: Malonate.
Rule 2: Classification and cofactors — Six classes: oxidoreductases (oxidation and reduction), transferases (transfer a group), hydrolases (break bonds with water), lyases (remove groups without water), isomerases (change the form) and ligases (join molecules, using ATP). Cofactors are of three kinds: prosthetic groups (tightly bound organic groups such as haem in catalase), coenzymes (loosely bound organic cofactors such as NAD and NADP, which contain the vitamin niacin) and metal ions (for example zinc for carboxypeptidase).
- Easy : Catalase has a haem prosthetic group.
- Medium : NAD is a coenzyme that has the vitamin niacin.
- Exam-type : Q: Which enzyme class joins two molecules? A: Ligases.
Six classes: Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, Ligases.
Thinking that low temperature destroys enzymes. It only slows them; high temperature denatures them.
Memory clue: OTHLIL — Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, Ligases.
Spot the difference
| Cofactor | Binding | Example |
|---|---|---|
| Prosthetic group | Tightly bound | Haem in catalase |
| Coenzyme | Loosely bound | NAD, NADP |
| Metal ion | Binds enzyme and substrate | Zinc in carboxypeptidase |
Practice questions
- 1Name two factors that affect enzyme activity.
- 2What is an apoenzyme?
- 3Name the six classes of enzymes.
- 4What is a coenzyme? Give an example.
- 5What is competitive inhibition?
- 6Which vitamin is a part of NAD and NADP?
- 7Why do enzymes stop working at high temperature?
- 8Why does the rate of an enzyme reaction stop rising when the substrate is very high?
Show answers (try them yourself first)
- 1Temperature and pH (or substrate concentration, inhibitors).
- 2The protein part of an enzyme that needs a cofactor.
- 3Oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases.
- 4A loosely bound organic cofactor, such as NAD.
- 5Inhibition by a molecule similar to the substrate that competes for the active site.
- 6Niacin.
- 7Heat denatures the protein, so the active site loses its shape.
- 8All the active sites are occupied, so the enzyme is saturated and the rate reaches its maximum (Vmax).