Biochemistry Revision Notes

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Water

  • High specific heat capacity
  • Polar molecule - oxygen slightly negative, both hydrogens slightly positive due to oxygen having larger charge in nucleus, so attracting electrons in bond more strongly.
  • Hydrogen bonds between molecule → dense and viscous liquid
  • Molecules stick together – cohesive forces
  • Surface tension – water molecules pull together
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Proteins 1

  • Proteins are made up of many amino acids joined together

  • Amino acids have a central C atom with COOH acid, NH2 group, R group and 1 Hydrogen atom attached.

  • In humans, approximately 20 amino acids

  • Amino acids are joined together on the ribosomes inside cells

  • At ribosomes the amino acids are brought close together and they form a peptide bond (CO – N) and water – condensation reaction.

  • Peptide bonds are very strong – they involve covalent bonds

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Proteins 2

  • Long chain of amino acids = polypeptide

  • Proteins contain ≥ 1 polypeptide chain

    • Haemoglobin = 4 chains coiled together

  • Polypeptides are broken down by adding H2O (hydrolysis reaction) to leave separate amino acids. Hydrolysis is used in digestion of proteins.

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Proteins: Primary and Secondary Structure

Primary Structure

  • 1ary structure of a protein is a linear arrangement of amino acids in a polypeptide chain. Very specific sequence, 1 amino acid difference changes whole protein

  • The primary structure determines all bonds. A change in one amino acid completely changes the shape of the protein. Enzymes are globular proteins with a specific shape in which substrates can fit to catalyse a reaction. The function of a protein is determined by its shape.

Secondary structure

  • 2ary structure is the regular folding into an α-helix or a β-pleated sheet.

  • Shape is maintained by hydrogen bonds

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Proteins: Tertiary and Quaternary Structure

Tertiary structure

  • 3ary structure is the irregular folding of an α-helix or a β-pleated sheet.

  • Held in position by H bonds, disulfide bridges, ionic bonds and hydrophobic interactions

  • Prosthetic groups are maintained in tertiary structure

    • Globular proteins have a ball like tertiary structure – e.g. haemoglobin

    • Fibrous proteins have a long, thin tertiary structure – e.g. collagen

Quaternary

  • 4ary structure is the shape produced when more than one polypeptide chains join together to create a protein, e.g. the four polypeptide chains which join together to make haemoglobin

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Protein: Collagen 1

  • Fibrous protein with a high tensile strength, that is insoluble in water and found in most animal's skin, tendons, teeth, cartilage, bones & walls of blood vessels

  • 3 polypeptide chains each in the shape of a helix, which wind around each other to form a linear rope shape.

  • Almost every third amino acid in each polypeptide is glycine (the smallest amino acid)

    • Strand can lie close together and form a tight coil

  • Each complete 3 stranded molecule of collagen interacts with other collagen molecules running parallel to it.

  • Bonds form between the R groups of lysines in molecules running parallel to each other

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Protein: Collagen 2

  • The cross links hold many collagen molecules side by side forming fibrils.

  • The ends are staggered to reduce weak spots

  • Fibrils associate to form bundles called fibres

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Protein: Haemoglobin

  • Globular protein

  • Soluble in water

  • Found dissolved in the cytoplasm of red blood cells

Consists of 4 polypeptide chains with 4 prosthetic haem groups

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Globular and Fibrous Proteins 1

Globular Proteins

Fibrous Proteins

Examples

Haemoglobin, enzymes, antibodies, transporters in membranes, some hormones (e.g. insulin)

Collage, keratin, elastin

Primary Structure

Very precise, usually made up of a non repeating sequence of amino acids forming a chain that is always the same length

Often made up of a repeating sequence of amino acids. Chain can be of a varying length

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Globular and Fibrous Proteins 2

Solubility

Often soluble in water

Insoluble in water

Functions

Usually metabolically active, taking part in chemical reactions in and around cells

Usually metabolically uncreative, with a structural role

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Carbohydrates

Carbohydrates are substances whose molecules are made of sugar units

  • General formula for a sugar unit is CnH2nOn

  • Carbohydrates involve sugars, starches and cellulose

    • Sugars are always soluble in water and taste sweet

    • Starches and cellulose (polysaccharides) are insoluble in water and do not taste sweet

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Monosaccharides

  • A carbohydrate whose molecules contain just one sugar unit
  • Glucose, fructose and galactose
    • Glucose is the main respiratory substrate in cells, providing energy when oxidised

    • Fructose is found in fruits and nectar where it attracts insects and animals which then inadvertently disperse the plant’s seeds or transfer pollen

  • Glucose is a sugar containing 6 carbon atoms, so it is said to be a hexose

  • Glucose molecules can exist as α-glucose and β-glucose. They have the same molecular formula, but are structural isomers

    • α-glucose: the OH group on Carbon 1 is below the chain

    • β-glucose: the OH group on Carbon 1 is above the chain

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Disaccharides

  • Two monosaccharide molecules link together to form a disaccharide.
    • E.g. 2 alpha glucose molecules can react to form maltose + water

  • Condensation reaction

  • Results in a glycosidic bond – very strong, involving covalent bonds

    • α 1—4 glycosidic bond

  • Soluble in water and taste sweet

  • When digested, glycosidic bonds are broken down by carbohydrase enzymes. The enzyme which breaks down maltose is called maltase. This is a hydrolysis reaction which adds water to the disaccharide.

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Polysaccharides: Starch

  • Linking together thousands of alpha glucose molecules with α1—4 glycosidic bonds produces the carbohydrate amylose, found in starch.
    • This is how plants store the carbohydrate hat they make in photosynthesis. Starch is insoluble and metabolically inactive so it does not interfere with the chemical reactions inside the cell or affect the water potential of the cell.

  • Amylose molecules coil to form a long spiral, which makes them very compact, so a lot of starch can be stored in a small area. The coil is held in shape by hydrogen bonds.

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Polysaccharides: Cellulose

  • Polysaccharide made of thousands of beta glucose molecules, linked with β 1—4 glycosidic bonds. Cellulose molecules do not coil, but lie straight.

  • They form hydrogen bonds with their neighbour producing bundles of molecules lying side by side, all held together by thousands of hydrogen bonds. These bundles are called fibrils. A group of fibrils is called a fibre.

  • Structurally very strong

  • Very few animals have an enzyme capable of breaking the β 1—4 glycosidic bonds.

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Polysaccharide: Glycogen

  • Plants contain amylose (starch) and cellulose; animal cells never contain either of these. Animals store carbohydrate as glycogen.
  • Glycogen is a polysac. of α-glucose joined together by α-1—4 glycosidic bonds, but it has branches (unlike amylose) where 1—6 glycosidic bonds are formed.
    • This makes it more difficult for glycogen to form helices so they are not as tightly coiled as starch molecules.

  • Stores found in the liver & muscles – little dark granules of glycogen can often be seen.
  • They are easily broken down to form glucose by an enzyme called glycogen phosphorylase which is activated by insulin when blood glucose levels are low.
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Lipids

  • Lipids are a group of substances that are made up of Carbon, Hydrogen, Nitrogen and Oxygen.
  • Much higher proportion of hydrogen than carbohydrate.
  • They are insoluble in water.
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Triglycerides (i)

  • Molecules made from 3 fatty acids attached to a glycerol molecule.
  • Acidic because they contain a carboxyl group (COOH)
  • Carboxyl groups can react with –OH (hydroxyl) groups of glycerol forming ester bonds. Ester bonds are very strong and involve covalent bonds.
  • Forming an ester bond is also a condensation reaction. The breakage of an ester bond is a hydrolysis reaction
  • Insoluble in water – none of the atoms carry an electrical charge so they are not attracted to water molecules – hydrophobic.
  • A diet rich in saturated fats increases the cholesterol level in the blood increasing the risk of developing CHD.
  • A saturated fat is one in which the fatty acids contain as much hydrogen as they possibly can – e.g. no double bonds between Carbon atoms.
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Triglycerides (ii)

  • An unsaturated fat has one or more fatty acids in which at least one carbon atom is connected to another carbon atom with a double bond. This forms a kink in the chain.
  • Triglycerides are rich in energy, often used as energy stores in living organisms.
  • One gram of triglyceride can release twice as much energy as one gram of carbohydrate.
  • In humans cells in adipose tissue are almost filled with globules or triglycerides and they make very good thermal insulators. Animals that live in cold environments have thick layers of adipose tissue beneath the skin.
  • Stored triglycerides also provide a place in which fat-soluble vitamins, especially A and D can be stored.
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Phospholipids, Cholesterol and Steroids

Phospholipids

  • Like a triglyceride when one of the fatty acids is replaced by a phosphate group.
  • Fatty acids are hydrophobic, phosphate heads are hydrophilic, due to δ- charge on head.

  • Make up basic cell membrane structure, arranged as a bilayer.

Cholesterol and Steroids

  • Cholesterol is a type of lipid, and other molecules with similar structures are also classified as lipids. Cholesterol, other molecules with similar structures to cholesterol and compounds containing cholesterol are known as steroids.

  • Many are hormones, e.g. testosterone and oestrogen

  • Cholesterol itself is a major constituent of cell membranes where it helps to regulate fluidity of cell membranes.

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Polynucleotides and DNA 1

Polynucleotides

A DNA is a double helix. It is made of two long chains of nucleotide molecules linked together to form a twisted ladder. Each chain is called a polynucleotide.

DNA

  • DNA stands for deoxyribonucleic acid

  • Found in nuclei of cells, slightly acidic

  • Each nucleotide in a DNA molecule contains:

    • A phosphate group, a Deoxyribose (5 carbon sugar) and an organic base (adenine, guanine, cytosine, thymine, uracil

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Polynucleotides and DNA 2

  • Thymine and cytosine only have one ring – pyrimidine
  • Adenine and guanine have two rings – purine
  • A joins with T
  • G joins with C
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