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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.

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

7 5 1 primary structure
7.5.1: Primary structure

Sequence of amino acids.

May have disulfide bridges (sulfur linkage between two cysteines)

7 5 1 secondary structures
7.5.1: Secondary Structures

Secondary structures: alpha helix and beta pleated sheets

Alpha Helix Beta Pleated Sheet

Hydrogen bonding stabilises the secondary structure

7 5 1 tertiary structure
7.5.1: Tertiary Structure

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

Beta pleated sheet

Alpha helix


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



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


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 structure
7.5.1: Quaternary Structure

The 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
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]

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 one


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.


(ii) Outline how this structure is held together.


(iii) Region A inserts into the membrane. Deduce, with a reason, the nature of the

amino acids that would be expected to be found in this region. [2]


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



7 5 2 fibrous proteins
7.5.2:Fibrous Proteins

Fibrous proteins are water insoluble, long and narrow proteins.


Myosin and actin


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 activities

named 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
7.5.3 : Explain the significance of polar and non-polar amino acids.

Polar amino acids

HYDROPHILIC (+ve or –ve charge)


Non-polar amino acids

HYDROPHOBIC (R-groups stay close together in water)

7 5 3

The 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.



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 31

Protein 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 acids

Actual question: Outline how polar amino acids and non-polar amino acids control the position of proteinsin plasma membranes. [8]

Actual IB mark scheme from a past paper

membrane is a lipid bi-layer;

membrane has hydrophobic interior / lipid hydrophobic tails oriented inward;

hydrophilic on cytoplasmic and extracellular side / lipid hydrophilic heads oriented


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/ions

can diffuse;

7 5 4 state four functions of proteins giving a named example of each
7.5.4: State four functions of proteins, giving a named example of each.


e.g. haemoglobin

Enzymes e.g. lactase


e.g. collagen

Antibodies e.g. flu antibodies

Movement e.g. myosin and actin