7.5 Proteins

The 20 different amino acids

7.5.1: Explain the four levels of protein structure, indicating the significance of each level.

Peptide bonds link the amino acids together

Polypeptide with five amino acids.

7.5.1: Primary structure

Sequence of amino acids.May have disulfide bridges (sulfur linkage between two cysteines)

7.5.1: Secondary Structures

Alpha Helix Beta Pleated Sheet

Hydrogen bonding stabilises the secondary structure

Secondary structures: alpha helix and beta pleated sheets

Alpha helix

Beta pleated sheet

Beta pleated sheet

7.5.1: Tertiary StructureBeta pleated sheet

Alpha helix

Tertiary structures: Attractions between alpha helices and beta sheets – hydrophobic interactions between R groups cause folding of the polypeptide at the tertiary level.

Bonding in the tertiary structure

IB Question: Explain primary structures and tertiary structures of an enzyme.

M09/4/BIOLO/HP2/ENG/TZ2/XX

IB Question: Explain primary structures and tertiary structures of an enzyme.

M09/4/BIOLO/HP2/ENG/TZ2/XX

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]

7.5.1: Quaternary StructureThe structure of a protein that results from the interaction of two or more individual polypeptides to give larger functional molecules.

7.5.1: Conjugated Protein

Prosthetic group. The non-protein part of a protein required for the protein to be functional. E.g the heme molecule of haemoglobin.

IB Question: Explain the four levels of protein structure [8]

IB Question: Explain the four levels of protein structure [8]

primary structure is sequence / number of amino acids;determined by base sequence in the gene;(largely) determines higher level structures/secondary structure/tertiary structure;secondary structure is regular repeating patterns;such as alpha/α helix and beta/β (pleated) sheet;determined by H bonds (within chain);contributes to the strength of fibrous proteins;tertiary structure refers to overall 3-D shape;conformation can determine function;tertiary structure determined by R-group interactions / ionic interactions /hydrophobic interactions / disulfide bridges / H-bonds;quaternary structure is only found in proteins formed from more than onepolypeptide;e.g. hemoglobin; (accept other suitable example)quaternary structure may involve the binding of a prosthetic group;

IB QUESTION: Outline the first three levels of protein structure, including the types of bonding within each and the significance of each level. [5]

primary structure/level: order/sequence of amino acids;linked by peptide bonds;determines the type/function of protein / 2º and 3º structures;secondary structure/level: regular folding / beta-pleated sheets / spiralling /alpha-helices;held through hydrogen bonding;tertiary structure/level: 3-dimensional conformation of a polypeptide/protein;held with ionic bonds, hydrogen bonds, disulfide bonds/bridges and hydrophobic bonds; (must give at least two bonds)determines overall shape / a named example e.g.: active sites on enzymes; [5 max]To receive full marks the candidate must mention each of the three levels,otherwise award [4 max].

IB Question: Bt proteins act as toxins to insects, primarily by destroying epithelial cells in the insect’s digestive system. Below is the three-dimensional structure of one such protein.

(i) State the type of structure shown in the region marked A in the diagram above.[1](ii) Outline how this structure is held together.[2](iii) Region A inserts into the membrane. Deduce, with a reason, the nature of theamino acids that would be expected to be found in this region. [2]

(i) helix / alpha helix [1]

(ii) hydrogen bonds; between the turns of the helix (rather than between R-groups); bonds between carboxyl and NH groups/C-O---H-N; [2 max]

(iii) non-polar amino acids/R-groups; (inner part of phospholipid) bilayer is hydrophobic/non-polar; [2]

7.5.2: Outline the difference between fibrous and globular proteins, with reference to two examples of each protein type.

enzymes

antibodies

•Globular proteins are near soluble (colloids). •They have more compact and rounded shapes.

7.5.2:Fibrous Proteins

collagen

Myosin and actin

Fibrous proteins are water insoluble, long and narrow proteins.

Fibrous Proteins Globular Proteins

general shape strands rounded

solubility (usually) insoluble (usually) soluble

general roles structural metabolic reactions

sensitivity to changes in pH

less sensitive than globular proteins

more sensitive than fibrous proteins

sensitivity to changes in temperature

less sensitive than globular proteins

more sensitive than fibrous proteins

examples myosin, actin, collagen insulin, antibodies, haemoglobin, enzymes (lactase)

structure little or no tertiary structure.

have complex tertiary and sometimes quaternary structures

Distinguish between fibrous and globular proteins

IB Question: Distinguish between fibrous and globular proteins with reference to one example of each protein type. [6]

fibrous proteins are strands/sheets whereas globular proteins are rounded; fibrous proteins (usually) insoluble whereas globular proteins (usually) soluble; globular more sensitive to changes in pH/temperature/salt than fibrous; fibrous proteins have structural roles/globular proteins used for metabolic activitiesnamed fibrous proteins e.g. keratin/fibrin/collagen/actin/myosin/silk protein; named globular protein e.g. insulin/immunoglobulin/hemoglobin/named enzyme; [6 max] Do not accept statements about fibrous proteins having only secondary structure and globular proteins having only tertiary structure.

7.5.3 : Explain the significance of polar and non-polar amino acids.Polar amino acids HYDROPHILIC (+ve or –ve charge)

Non-polar amino acidsHYDROPHOBIC (R-groups stay close together in water)

7.5.3The polarity of R groups plays a role in the tertiary structure of globular proteins. Thus, polarity plays a role in shaping enzymes and their active sites.

Active site of an enzyme

Membrane proteins are firmly anchored in the phospholipid bilayer because they have two polar ends and a non-polar center. One end of a membrane protein contacts the watery extracellular fluid and the other end extends to the watery cytoplasm. The non-polar center remains inside the membrane because it is hydrophobic.

7.5.3

7.5.3Protein channels facilitate the passage of polar molecules across cellular membranes because the polar amino acids line the inside of the channel and non-polar amino acids line the outside.

IB Question: Explain the significance of polar and non-polar amino acidsActual question: Outline how polar amino acids and non-polar amino acids control the position of proteins in plasma membranes. [8]

Actual IB mark scheme from a past papermembrane is a lipid bi-layer;membrane has hydrophobic interior / lipid hydrophobic tails oriented inward;hydrophilic on cytoplasmic and extracellular side / lipid hydrophilic heads orientedoutward;polar amino acids are hydrophilic/water soluble/attracted to outside of membrane;non-polar amino acids are hydrophobic/attracted to inside of membrane;integral proteins embedded in the membrane;non-polar amino acids cause proteins to be embedded in membrane;peripheral proteins associated with surface of membrane;polar amino acids cause parts of proteins to protrude from membrane;transmembrane proteins have both polar and non-polar amino acids;polar amino acids create channels through which (hydrophilic) substances/ionscan diffuse;

7.5.4: State four functions of proteins, giving a named example of each.

Enzymes e.g. lactase

Structure e.g. collagen

Transport e.g. haemoglobin

Movement e.g. myosin and actin

Antibodies e.g. flu antibodies