Proteins have a very wide range of functions in living organisms. Topic 2.4 IB Biology Miss Werba

TOPIC 2 – MOLECULAR BIOLOGY 2.1 MOLECULES TO METABOLISM 2.2 WATER 2.3 CARBOHYDRATES & LIPIDS 2.4 PROTEINS 2.5 ENZYMES 2.6 STRUCTURE OF DNA & RNA 2.7 DNA REPLICATION, TRANSCRIPTION & TRANSLATION 2.8 CELL RESPIRATION 2.9 PHOTOSYNTHESIS J WERBA – IB BIOLOGY 2

THINGS TO COVER U.1 U.2 U.3 U.4 U.5 U.6 U.7 U.8 Statement Guidance Amino acids are linked together by condensation to form polypeptides. U.2 There are 20 different amino acids in polypeptides synthesized on ribosomes. Most organisms use the same 20 amino acids in the same genetic code although there are some exceptions. Specific examples could be used for illustration. U.3 Amino acids can be linked together in any sequence giving a huge range of possible polypeptides. U.4 The amino acid sequence of polypeptides is coded for by genes. U.5 A protein may consist of a single polypeptide or more than one polypeptide linked together. U.6 The amino acid sequence determines the three-dimensional conformation of a protein. U.7 Living organisms synthesize many different proteins with a wide range of functions. U.8 Every individual has a unique proteome. J WERBA – IB BIOLOGY 3

THINGS TO COVER Statement Guidance A.1 A.2 S.1 NOS 3.1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions. The detailed structure of the six proteins selected to illustrate the functions of proteins is not needed. A.2 Denaturation of proteins by heat or by deviation of pH from the optimum. Egg white or albumin solutions can be used in denaturation experiments. S.1 Drawing molecular diagrams to show the formation of a peptide bond. NOS 3.1 Looking for patterns, trends and discrepancies J WERBA – IB BIOLOGY 4

POLYPEPTIDES U.4 S.1 Amino acids are linked together by condensation to form polypeptides. The bonds formed are covalent. The bonds formed are peptide bonds. The bonds form in the ribosomes. J WERBA – IB BIOLOGY 5

POLYPEPTIDES U.4 S.1 Peptide bond: J WERBA – IB BIOLOGY 6

ESSENTIAL AMINO ACIDS U.2 There are 20 essential amino acids found in polypeptides synthesised by the ribosomes. The source of these amino acids would be the absorbed products of digestion. J WERBA – IB BIOLOGY 7

ESSENTIAL AMINO ACIDS U.2 J WERBA – IB BIOLOGY 8

PEPTIDE SYNTHESIS U.2 Ribosomes are the molecules (structures) within cells that facilitate the formation of peptide bonds. J WERBA – IB BIOLOGY 9

POLYPEPTIDES There are infinite possibilities for polypeptides U.3 There are infinite possibilities for polypeptides 20 amino acids in any order or combination or length A 7 amino acid peptide has 1,280,000,000 possible combinations. Some polypeptides (eg. titin) are 30,000 amino acids in length! J WERBA – IB BIOLOGY 10

POLYPEPTIDES The sequence of amino acids is coded for by genes. DNA stored in the nucleus is read and “transcribed” into an RNA message. This RNA message (mRNA) can leave the nucleus and head to the ribosomes. Here, the instructions contained within the message are “translated” into a polypeptide. J WERBA – IB BIOLOGY 11

Each amino acid has unique properties. POLYPEPTIDES U.6 Each amino acid has unique properties. J WERBA – IB BIOLOGY 12

POLYPEPTIDES U.6 U.5 The properties of each amino acid influence how a polypeptide will be able to fold up into a protein. There are four levels of structure in proteins: Primary structure Secondary structure Tertiary structure  folding gives the tertiary structure of a protein Quaternary structure J WERBA – IB BIOLOGY 13

PROTEIN STRUCTURE Primary (1˚) structure: Secondary (2˚) structure: Amino acid sequence Involves peptide bonds Secondary (2˚) structure: Repeating local structures Generally found in fibrous proteins These include: α-helices: peptide chain wound into a helix β-pleated sheets: peptide strands lie in a plane J WERBA – IB BIOLOGY 14

PROTEIN STRUCTURE Tertiary (3˚) structure: Quaternary (4˚) structure: Single protein folds into a 3D shape Generally form globular proteins Important for function of the protein Quaternary (4˚) structure: Two or more polypeptide chains linked together eg. Hemoglobin subunits becoming haemoglobin J WERBA – IB BIOLOGY 15

FIBROUS & GLOBULAR PROTEINS Proteins can be separated into two groups based on their shape: Fibrous Globular J WERBA – IB BIOLOGY 16

FIBROUS & GLOBULAR PROTEINS FIBROUS PROTEINS GLOBULAR PROTEINS SOLUBILITY (usually) insoluble (usually) soluble SHAPE Long, narrow shape (strands/sheets) Rounded shape SENSITIVTY TO CHANGES Less sensitive to changes in pH/temperature/salt More sensitive to changes in pH/temperature/salt ROLE Have structural roles Have functional roles EXAMPLES keratin / fibrin / elastin / collagen / actin / myosin insulin / immunoglobulin / haemoglobin / amylase / Na+/K+ pump J WERBA – IB BIOLOGY 17

PROTEIN FUNCTIONS Proteins have a variety of uses in organisms: Catalysis – speeds up chemical reactions – Rubisco Muscle contraction Cytoskeletons – give animal cells their shape Tensile strengthening – provide strength – collagen Blood clotting Transport of nutrients and gases Cell adhesion Membrane transport J WERBA – IB BIOLOGY 18

PROTEIN FUNCTIONS Proteins have a variety of uses in organisms: Hormones – insulin Receptors – binding sites in membranes and cytoplasm for hormones, neurotransmitters, tastes, smells and receptors for light – rhodopsin Packing of DNA Immunity – immunoglobulins J WERBA – IB BIOLOGY 19

PROTEIN FUNCTIONS: Rubisco A.1 Full name = ribulose bisphosphate carboxylase It is an enzyme involved in photosynthesis It “fixes” carbon from a gaseous state to one able to be utilised by the plant. J WERBA – IB BIOLOGY 20

PROTEIN FUNCTIONS: Insulin A.1 It is a hormone involved in maintaining glucose levels in the blood within narrow limits. It is secreted by the β cells in the pancreas. Insulin signals the liver cells to absorb glucose and convert it to glycogen. This takes it out of the bloodstream. Not produced by people with type I diabetes. J WERBA – IB BIOLOGY 21

PROTEIN FUNCTIONS: Immunoglobulins A.1 Also known as antibodies Produced by the immune cells in response to the presence of an antigen The binding site of the protein is highly variable allowing them to respond to a range of pathogens. They also signal other immune cells to help destroy the pathogen once it has been identified. J WERBA – IB BIOLOGY 22

PROTEIN FUNCTIONS: Rhodopsin A.1 A pigment that can absorb light. Found in rod cells within the retina at the back of the eye. The absorption of light causes a chemical and conformational change to the molecule. This results in a nerve impulse being sent to the brain. Rods work well in even dim light, and are responsible for monochrome vision. rhodopsin mitochondria nucleus J WERBA – IB BIOLOGY 23

PROTEIN FUNCTIONS: Collagen A rope-like structural protein. Forms a mesh of fibres in skin and in the blood vessel walls that resists tearing. Gives tendons, ligaments, skin and blood vessel walls their strength. Forms part of teeth and bones, preventing cracks and fractures. J WERBA – IB BIOLOGY 24

PROTEIN FUNCTIONS: Spider silk A.1 Fibrous proteins Spiders can produce different types of silk with different properties for different purposes. Some of the silk is comparable to steel in regards to its tensile strength. J WERBA – IB BIOLOGY 25

PROTEOME Every individual has a unique proteome. Proteome: a term given to all of the proteins produced by a cell, tissue or an organism. The proteome is a function of both the organism’s genome (genes) and environmental factors. Environmental factors such as nutrition, temperature, etc can affect a cell’s activities Epigenetics: field of study of how much influence the environment has on the genome of an organism J WERBA – IB BIOLOGY 26

PROTEOME eg. DNA methylation can stop translation! U.8 eg. DNA methylation can stop translation! J WERBA – IB BIOLOGY 27

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PROTEIN DENATURATION A.2 High temperatures or extremes of pH (high or low) can cause denaturation of proteins. Denaturation affects the bonds holding the secondary, tertiary and quaternary structures together. This will result in an irreversible loss of shape and therefore function. eg. Cooking an egg denatures its proteins, causing them to harden J WERBA – IB BIOLOGY 29

Determine the temperature stability of albumen. PROTEIN DENATURATION A.2 Determine the temperature stability of albumen. Available equipment: Electronic hot plates (for water baths) Albumen (egg white) Thermometers Beakers Test tubes J WERBA – IB BIOLOGY 30

PROTEINS The interaction of polypeptide subunits and prosthetic groups Q1 Which best describes the tertiary structure of a protein? The interaction of polypeptide subunits and prosthetic groups Interactions forming hydrogen bonds between the amino acids The sequence of amino acids in the polypeptide chain The structure formed from interactions between the amino acid side groups J WERBA – IB BIOLOGY 31

PROTEINS Q2 Other than acting as catalysts state three functions of proteins, giving an example of each. [3] J WERBA – IB BIOLOGY 32