Biological Molecules

Biological Molecules Glossary
monomer – a single subunit making up a long chain of identical repeating unity, called a polymer polymer – a long chain of repeating subunits (monomers) monosaccharide – the smallest subunit of carbohydrate (glucose, galactose, fructose) amino acid – the smallest subunit of a polypeptide; there are 20 different naturally occurring amino acids nucleotide – smallest subunit of DNA and RNA condensation reaction – a reaction releasing water molecules, forming larger molecules in the process (polymers) from monomers hydrolysis reaction – reaction using water to break down larger molecules into their smaller substitute not parts, breaking chemical bonds.

Monomers and Polymers

• Condensation reactions
  • Join monomers together into larger molecules, releasing water
  • Monosaccharides → Disaccharides → Polysaccharides: glycosidic bonds formed
  • Amino acids → Polypeptides: peptide bond
  • Glycerol + fatty acids → Triglycerides: ester bonds

Carbohydrates

• Made up of monosaccharides (monomers of carbohydrates)
• Common monosaccharides - glucose, galactose, fructose
• Disaccharides
  • Formed by condensation reaction of 2 monosaccharides
  • Maltose → Glucose + Glucose
  • Sucrose → Glucose + Fructose
  • Lactose → Glucose + Galactose

α-glucose form, with the -OH group on the right-most carbon pointing down

Glucose

Two isomers:

• α-glucose: Carbon atom 1 has hydrogen pointing up, and hydroxyl group pointing down
• β-glucose: Carbon atom 1 has hydrogen and hydroxyl groups flipped

β-glucose, showing the right-most -OH group pointing up

The acronyms 'ADDUD' and 'BDDUD' can be used to remember which way the -OH groups point. ADDUD - α-glucose, down, down, up, down. BUDUD - β-glucose, up, down, up down.

Polysaccharides

• Formed by condensation of many monosaccharides
  • Glycogen → condensation of α-glucose
  • Starch → condensation of α-glucose
  • Cellulose → condensation of β-glucose
• Structure of Glycogen
  • Energy store in animals
  • Highly branched structure, coiled – so compact
  • Unable to diffuse out of cells, so stays where it is needed until energy is required

• Structure of Cellulose
  • Unbranched, linear chains
  • Used in plant cell wall – provides rigidity to plants

    

    The structures of starch, glycogen, and cellulose. The way the molecules pack together can be seen, with all molecules in cellulose being parallel and tightly packed. The starch and glycogen molecules have a much more branched structure, causing less tight packing

  • Fibres group together to form microfibrils – hydrogen bonds (strength in large numbers)
• Structure of Starch
  • Forms granules – unable to move out of cells it is formed in – doesn’t have to diffuse far, so reasonably quick access to energy
  • Branched chains, coiled – compact

Lipids

• Triglycerides
  • Glycerol + 3 fatty acid tails
  • Form oils, waxes, fats
  • Hydrophobic – do not mix with water

Molecular structure of a triglyceride

• Phospholipids
  • Form the cell wall – phospholipid bilayer
  • Phosphate + glycerol + 2 fatty acid tails
  • Polar molecules – phosphate head is hydrophilic (water loving) // fatty acid tails are hydrophobic (water hating)

Molecular structure of a phospholipid

• Fatty acids
  • Saturated – all carbon atoms have single bonds – with the maximum number of hydrogens possible
  • Unsaturated
    • Monounsaturated – 1 pair of carbon atoms have a double bond; removes 2 hydrogens, causes a kink in the chain
    • Polyunsaturated – More than 1 pair of carbon atoms have a double bond; removes more than 2 hydrogens, causes many kinks in the chain
    • Have less energy content than unsaturated fatty acids

A polyunsaturated fatty acid

Proteins

• Made up of amino acids

General structure of an amino acid, the monomer of a protein (polypeptide)

• Amine group: NH2 Carboxyl group: COOH
• R group – the side chain causing the amino acid to be unique
• Dipeptides – condensation of two amino acids
• Polypeptides – condensation of many amino acids

• Proteins can be made up of multiple polypeptide chains

Protein Keywords
amino acids – the monomers from which proteins are made from dipeptide – 2 amino acids joined together with 1 peptide bond polypeptide – Many amino acids joined together with peptide bonds primary structure]] – first structure of a protein. Chain of amino acids + order secondary structure – second structure of a protein. α-helix and β-pleated sheet tertiary structure – third structure of a protein. Folding of α-helix and β-pleated sheet into 3D structure quaternary structure – joining of tertiary structure proteins together into larger molecules enzyme – a protein molecule able to catalyse the break down / formation of molecules induced-fit model – the theory stating that the enzyme’s active site changes shape slightly when a substrate attaches lock and key model – the theory stating that the enzyme’s active site is rigid and never changes shape

• Primary structure: order of amino acids – polypeptide chain

• Secondary structure: α-helix or β-pleated sheet – formed by hydrogen bonds between R-groups
• Tertiary structure: further coiling of α-helix / β-pleated sheet – more compact
• Quaternary structure: linking together of multiple tertiary structure polypeptide chains
• Hydrogen bonds – hold together the polypeptide chains in quaternary structure
• Ionic bonds – join together amino acids into polypeptide chain
• Disulphide bridges – strong bonds between R-groups holding α-helix / β-pleated sheet together

  

  The four structures a protein can be in

Enzymes

• Lower the activation energy of the reaction it catalyses
• Lock and Key model of enzyme action
  • Substrate fits perfectly in the enzyme
  • No explanation as to how the enzyme catalyses the reaction
• Induced Fit model of enzyme action
  • Enzyme active site changes shape slightly to allow the substrate to bind to it
  • Active site puts stresses on the substrate, causing bonds to brake
  • Reaction is catalysed, causing the product(s) to be released
• Enzymes are only able to have 1 substrate fit it – amylase only catalyses starch hydrolysis

• Enzyme concentration – a higher concentration will cause the substrate to be broken down faster. The rate of reaction will plateau as the substrate concentration decreases, as collisions are less likely to occur
• Substrate concentration – higher concentration of substrate means that the enzymes are more likely to collide with substrate. Increase rate of reaction, to a point. Once all of the enzyme has substrate in active site, reaction cannot continue further

  

  Competitive and non-competitive inhibitors

• Inhibitor concentration – higher concentration of competitive inhibitors will cause reaction to slow, as more competitive inhibitor blocks active sites Non-competitive inhibitors will have an impact, however it is not based on concentration as they do not block the active site

• pH – outside of the enzymes optimum pH, the active site denatures quickly. This prevents the reaction from being catalysed
• Temperature – below the optimum temperature, the reaction slows, as less energy to cause collisions Above optimum temp – reaction stops – enzymes denature

  

  Enzyme activity at differing temperatures

  

  Enzyme activity at differing pH's

Nucleic Acids

Nucleic Acids Glossary
DNA – deoxyribonucleic acid; molecule making up the genetic material in all living cells. Double stranded RNA – ribonucleic acid; molecule used to transfer genetic material to ribosomes; contains (some) viruses entire genome, but not all. Single stranded nucleotide – a single monomer making up DNA and RNA base – cytosine, guanine, thymine, uracil, adenine; complementary to bases, only allowing (A,T/U), (G,C) to bind together (with H-bonds) semi-conservative replication – the theory stating that, during DNA replication, 1 strand is new, and 1 strand is old. Ensures genetic continuity between cells, reducing the likelihood of mutations

The double helix of DNA

• Genetic material for living organisms
• Adenine (purine), Thymine / Uracil (pyramidal), Guanine (purine), Cytosine (pyramidal)

  

  Semi-conservative replication: the purple strands are the original, and the orange strands are new

• Semi-Conservative Replication
  • DNA unzips: DNA Helicase
  • Base pairs move in between the unzipped strands
  • DNA Polymerase used to bind the new bases to the old strands
  • Forms 2 DNA strands, each with 1 old strand and 1 new strand
• Proof for semi-conservative replication
  • DNA replicated until all Nitrogen is ¹⁵N – this is heavier, causing the strand to be lower in solution
  • DNA then replicated 1 generation with ¹⁴N – this creates a hybrid DNA, with 50% ¹⁵N and 50% ¹⁴N
  • DNA replicated 1 further generation in ¹⁴N solution – creating DNA with 25% ¹⁵N and 75% ¹⁴N
  • This is repeated, eventually forming DNA only containing ¹⁴N
  • The solution can be centrifuged, DNA containing different Nitrogen isotopes to be identified

ATP – Adenosine Triphosphate

ATP, the base (adenosine) is circled in red

• Used to transfer energy within cells
• Made of: Adenine, 3× Phosphate groups, Ribose sugar
• $ATP+H_{2}O\rightarrow ADP+P_{i}$ – condensation on ATP, forming ADP and a phosphate group; breaking the bond releases energy
• Low activation energy, so it is easy to release energy
• ATPase – enzyme catalysing hydrolysis of ATP (break down of ATP into ADP)
• Photophosphorylation
• Photosynthesis: Plants only, Using light to synthesise ADP → ATP
• Oxidative Phosphorylation
  • Using respiration to synthesise ADP → ATP; Plants and Animals
• Substrate-level Phosphorylation
  • When phosphate groups are transferred from donors; plants and animals
  • Uses of ATP
  • Metabolic Processes – provides energy to build up molecules from subunits
  • Movement – energy is required for muscular contraction
    • Active Transport – movement of molecules against a concentration gradient
    • Secretion – ATP is needed to form lysosomes to encase cell products
    • Activation of Molecules – inorganic phosphate released in hydrolysis of ATP can phosphorylate other molecules

Water

A diagram of water molecules, showing the more negative and more positive ends interacting through a hydrogen bond

• Essential for all living organisms
• Polar Molecule
  • Hydrogen bonds between water molecules require lots of energy to break
  • Causes water to have a high surface tension
• Solvent
  • As water is polar, other polar molecules are able to dissolve in it
  • Ionic compounds are surrounded by water molecules when dissolved
  • Allows gases to be dissolved – CO2, O2, NH3…
• High Specific Heat Capacity
  • A lot of energy is required to increase the temperature by 1° - this is due to the strength of the hydrogen bonds
  • This means that water acts as a buffer, reducing temperature fluctuations
• High Latent Heat of Vaporisation
  • A lot of energy is required to evaporate water (into steam)
  • Ideal for cooling an organism – sweating (animals) or transpiring (plants)
• Cohesion between Molecules
  • High surface tension means that column of water is able to be pulled up a vessel (such as a xylem)
• Metabolite
  • Used in condensation / hydrolysis reactions to break / form bonds

Inorganic Ions

• Occur in solution in the cytoplasm / bodily fluids
• Some are in high concentrations, others in low concentrations
• Each ion has a specific role
  • Iron ions Haemoglobin
  • Sodium ions co-transport of Glucose and Amino Acids
  • Phosphate ions Part of DNA and ATP