PROTEINS AHL Topic 7.5 IB Biology Miss Werba

AHL TOPIC 7 – NUCLEIC ACIDS AND PROTEINS 7.1 DNA STRUCTURE 7.2 DNA REPLICATION 7.3 TRANSCRIPTION 7.4 TRANSLATION 7.5 PROTEINS 7.6 ENZYMES J WERBA – IB BIOLOGY 2

THINGS TO COVER 4 levels of protein structure Fibrous v globular proteins Polar v non-polar amino acids Functions of proteins J WERBA – IB BIOLOGY 3

PROTEIN STRUCTURE Proteins have a complex structure. 7.5.1 PROTEIN STRUCTURE Proteins have a complex structure. They are built up from amino acids. The sequence of amino acids determines their shape and function. J WERBA – IB BIOLOGY 4

PROTEIN STRUCTURE There are four levels of structure in proteins: 7.5.1 PROTEIN STRUCTURE There are four levels of structure in proteins: Primary structure Secondary structure Tertiary structure Quaternary structure J WERBA – IB BIOLOGY 5

PROTEIN STRUCTURE Primary (1˚) structure: Amino acid sequence 7.5.1 PROTEIN STRUCTURE Primary (1˚) structure: Amino acid sequence Bonding involved: peptide linkages ie. covalent bonds J WERBA – IB BIOLOGY 6

PROTEIN STRUCTURE Secondary (2˚) structure: Repeating local structures 7.5.1 PROTEIN STRUCTURE Secondary (2˚) structure: Repeating local structures These include: α-helices: peptide chain wound into a helix β-pleated sheets: peptide strands lie in a plane Bonding involved: hydrogen bonding J WERBA – IB BIOLOGY 7

PROTEIN STRUCTURE Tertiary (3˚) structure: 7.5.1 PROTEIN STRUCTURE Tertiary (3˚) structure: Single protein folds into a 3D shape Can form either globular or fibrous proteins J WERBA – IB BIOLOGY 8

PROTEIN STRUCTURE Tertiary (3˚) structure: Bonding involved: 7.5.1 PROTEIN STRUCTURE Tertiary (3˚) structure: Bonding involved: disulfide bridges (covalent) R-group interactions hydrophobic interactions ionic bonds polar bonds hydrogen bonds van der Waals’ interactions J WERBA – IB BIOLOGY 9

PROTEIN STRUCTURE Quaternary (4˚) structure: 7.5.1 PROTEIN STRUCTURE Quaternary (4˚) structure: Two or more polypeptide chains linked together Bonding involved: Same as for 3˚ hydrogen bonding salt bridges disulfide bridges (covalent) J WERBA – IB BIOLOGY 10

FIBROUS and GLOBULAR PROTEINS Command term = OUTLINE with EXAMPLES 7.5.2 FIBROUS and GLOBULAR PROTEINS Command term = OUTLINE with EXAMPLES Proteins can be separated into two groups based on their shape: Fibrous Globular J WERBA – IB BIOLOGY 11

FIBROUS and GLOBULAR PROTEINS Command term = OUTLINE with EXAMPLES 7.5.2 FIBROUS and GLOBULAR PROTEINS Command term = OUTLINE with EXAMPLES 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 12

POLAR and NON-POLAR AMINO ACIDS 7.5.3 POLAR and NON-POLAR AMINO ACIDS Amino acids can be divided into two types according to the characteristics of their R groups: Polar amino acids = hydrophilic R groups (12) Non-polar amino acids = hydrophobic R groups (8) Amine group Carboxyl group J WERBA – IB BIOLOGY 13

POLAR and NON-POLAR AMINO ACIDS 7.5.3 POLAR and NON-POLAR AMINO ACIDS In membrane channels: Polar amino acids are positioned on the external surfaces of the membrane Allow channel proteins to be transmembrane and retain their position in membrane Allow facilitated diffusion by lining the channels Non-polar amino acids are positioned on the internal surfaces of the membrane Allow channel proteins to embed in a membrane J WERBA – IB BIOLOGY 14

POLAR and NON-POLAR AMINO ACIDS 7.5.3 POLAR and NON-POLAR AMINO ACIDS Polar sections allow ions through + + + + + + Non polar sections bind with the hydrophobic tails + J WERBA – IB BIOLOGY 15

POLAR and NON-POLAR AMINO ACIDS 7.5.3 POLAR and NON-POLAR AMINO ACIDS J WERBA – IB BIOLOGY 16

POLAR and NON-POLAR AMINO ACIDS 7.5.3 POLAR and NON-POLAR AMINO ACIDS In enzymes: Polar and non-polar amino acids contribute to the specificity of an enzyme. On the enzyme surface: polar amino acids allow the enzyme to dissolve in water non-polar amino acids allow the enzyme to embed in a membrane At the enzyme’s active site: polar amino acids attract polar substrates positively charged amino acids attract negatively charged substrate negatively charged amino acids attract positively charged substrate non-polar amino acids attract non-polar substrates J WERBA – IB BIOLOGY 17

POLAR and NON-POLAR AMINO ACIDS 7.5.3 POLAR and NON-POLAR AMINO ACIDS substrate Polar regions of active site and substrate attract enzyme Non polar region of enzyme J WERBA – IB BIOLOGY 18

POLAR and NON-POLAR AMINO ACIDS 7.5.3 POLAR and NON-POLAR AMINO ACIDS J WERBA – IB BIOLOGY 19

PROTEIN FUNCTIONS Command term = STATE 7.5.4 PROTEIN FUNCTIONS Command term = STATE FUNCTION NAME TYPE STRUCTURE collagen fibrous TRANSPORT haemoglobin Na+/K+ pump globular CATALYST lipase amylase MOVEMENT actin myosin tubulin HORMONES insulin ANTIBODIES immunoglobulin STORAGE albumin J WERBA – IB BIOLOGY 20

Sample questions 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 21

Sample questions Q2. Explain primary structures and tertiary structures of an enzyme. [3] Q3. Explain how polar and non-polar amino acids help channel proteins and enzymes carry out their functions.[5] J WERBA – IB BIOLOGY 22

Sample questions A1. D A2. primary structure is (number and) sequence of amino acids; joined by peptide bonds; tertiary structure is the folding of the polypeptide / secondary structure / alpha helix; stabilized by disulfide / ionic / hydrogen bonds / hydrophobic interactions; tertiary structure gives three dimensional globular shape / shape of active site; 3 max J WERBA – IB BIOLOGY 23

Sample questions A3. non-polar amino acids cause channel proteins to embed in a membrane; polar amino acids at either end cause channel proteins to be transmembrane / retain protein position in membrane; polar amino acids lining pore allow polar particles to pass through/form hydrophilic channels through membranes; polar amino acids on surface of enzyme allow it to dissolve in water; polar and non-polar amino acids contribute to the specificity of an enzyme; non-polar amino acids of surface of enzyme allow it to embed in a membrane; polar amino acids at active site of enzyme attract polar substrates; positively charged amino acids attract negatively charged substrate / vice versa; non-polar amino acids at active site attract non-polar substrate; 5 max Award any of the above points if clearly drawn in an annotated diagram. J WERBA – IB BIOLOGY 24