2.1.2 - Biologial Molecules (set D - Proteins)

Question 1

What are peptides, how do they relate to proteins?

Answer 1

Polymers made up of amino acid molecule (monomers)

Proteins consist of one or more polypeptides arranged as complex macromolecules, proteins all contain the elements carbon, hydrogen, oxygen and nitrogen

Question 2

Describe what amino acids are, mention the different types?

Answer 2

Amino acids are monomer which all have a basic structure (carboxyl and amine group) but varying R-groups, which results in different amino acids (20 different ones commonly found in cells)

• 5 of these are non-essential
• 9 are essential and only obtained from what we eat
• further 6 are conditionally essential (only needed by infants and growing children)

Question 3

Explain the synthesis of peptides?

Answer 3

Amino acids join when the hydrogen (H) of the amine group and hydroxyl (OH) in carboxylic acid group react during a condensation reaction forming a peptide bond between the amino acids and a water molecule - results in a compound called dipeptide

Question 4

What is the general structure of an amino acid?

Answer 4

• -COOH - carboxylic acid group
• -R variable side group, which consists of carbon chains
• amine/amino group (NH2)

Question 5

Explain the formation of a peptide bond with reference to chemical symbols and groups?

Answer 5

The hydroxyl (OH) of the carboxylic acid group (COOH) of an amino acid reacts with the hydrogen (H) of the amine group (NH2) of another amino acid resulting in a water molecule (H20) and a peptide bond (-CO-NH-)

• happens during a condensation reaction

Question 6

Explain how polypeptides are formed?

Answer 6

When many amino acids are joined together by peptide bonds a polypeptide is formed, the enzyme peptidyl transferase present in ribosomes (site of protein synthesis) catalyses the reaction

Question 7

Explain how proteins are formed mention polypeptides and bonding?

Answer 7

The different R-groups of the amino acids are able to interact with each other (R-group interactions) forming different types of bond - these bonds lead to long chains of amino acids forming into complex structures (proteins)

• Different sequences of amino acids leads to different structures, with different shapes being produced

Question 8

How many levels of protein structure are there, give them all?

Answer 8

4 levels of protein structure
- primary
- secondary
- tertiary
- quaternary

Question 9

Define ‘primary structure’ of a protein, what types of bonds are involved ext?

Answer 9

Sequence in which the amino acids are joined, particular amino acids in the sequence influence how the polypeptide folds to give the proteins final shape (determining its function)

• only bonds involved are peptide bonds

Question 10

Define ‘secondary structure’ of a protein, what types of bonds are involved, what is formed?

Answer 10

oxygen,hydrogen and nitrogen atoms of the basic repeating structure of amino acids interact - hydrogen bonds form which pull the amino chain into a coil shape called an alpha Helix

Question 11

Describe the 2 types of secondary protein structure?

Answer 11

Alpha helix
- all N-H bonds on same side of protein chain
- spiral shape
- H-bonds parallel to helical axis

Beta pleated sheet
- N-H and C=O groups alternate from one side to the other

Question 12

Explain how the structure of proteins in the secondary level can be beta plated sheets?

Answer 12

Polypeptide chains can also lie parallel to one another joined by hydrogen bonds - pattern formed by the individual amino acids cause the structure to appear pleated

Question 13

Define ‘tertiary structure’ of a protein, what types of bonds are involved, what is formed?

Answer 13

Further folding of protein into its 3D structure, often includes sections of secondary structure

• disulphide bridges - strong covalent S-S bonds between molecule of the amino acid cysteine
• ionic bonds - relatively strong bonds between charged R groups
• hydrogen bonds - numerous and easily broken

Question 14

Explain the types of bonds found in tertiary protein structure, describe factors about them?

Answer 14

• disulfide bridges - strong covalent S-S bonds between molecule of the amino acid cysteine
• ionic bonds - relatively strong bonds between charged R groups (pH changes cause these bonds to break)
• hydrogen bonds - numerous and easily broken

Question 15

Explain why the types of bonds formed in the tertiary protein structure are able to form?

Answer 15

Coiling and folding of sections of proteins into their secondary structure bring R-groups of different amino acids closer together so they are able to interact - leading to further folding of these sections
- leads to hydrogen bonds, ionic bonds and disulfide bonds/bridges

Question 16

Define ‘quaternary structure’ of a protein?

Answer 16

• fucntion proteins may consist of two or more individual proteins (subunits)
• precise 3D structure held together by the same types of bond as tertiary structure
• may involve addition of prosthetic groups eg metal ions or phosphate groups

Question 17

Explain what determines the way a protein folds and why this is the case?

Answer 17

Hydrophilic and hydrophobic interactions - proteins are assembled in an aqueous environment in the cytoplasm, which means the way a protein will fold will depend on wether the R-group are hydrophobic or hydrophilic

Question 18

Explain the breakdown of peptides?

Answer 18

Peptides are created by amino acids linking together in condensation reactions to form peptide bonds - in the reverse reaction (catalysed by enzyme proteases) they are turned back into amino acids - a water molecule is required to break the peptide bond in a hydrolysis reaction and reform the amine and carboxylic acid groups

Question 19

Describe what globular proteins are, give an example?

Answer 19

Form when proteins fold into their tertiary structures, they are compact, water soluble and usually roughly spherical in shape

• an example is insulin - which is involved in regulation of blood glucose concentration - travels in the bloodstream and must have a precise shape to fit into specific receptors on cell-surface membranes

Question 20

Explain why globular proteins are soluble in water?

Answer 20

they form in way that means the hydrophobic (water repelling) r-groups on the amino acids are kept away from the aqueous environment and the hydrophilic (water loving) r-groups are on the outside of the protein - so the proteins are soluble in water

Question 21

Explain why its important globular proteins are soluble, give an example?

Answer 21

Solubility is important for different functions of globular proteins like chemical reactions ext

• for example the globular protein insulin must be soluble in order to travel in the bloodstream

Question 22

Describe what conjugate proteins are, give an example?

Answer 22

Are globular proteins which contain a non-protein component called a prosthetic group (different types - lipids or carbohydrates can combine with proteins forming lipoproteins or glycoproteins, metal ions and molecules derived from vitamins also form prosthetic groups)

• for example Haemoglobin

Question 23

What is Haemoglobin?

Answer 23

An example of a conjugated protein

It is a quaternary protein made from four polypeptides (2 alpha and 2 beta sub units which each contain a prosthetic haem group)

• iron 2 ions present in the haem groups are each able to combine reversibility with an oxygen molecule

Question 24

Describe the structure of Haemoglobin?

Answer 24

• globular conjugated protein with prosthetic group
• 2 alpha, 2 beta chains and 4 prosthetic haem groups
• Fe2+ haem group form coordinate bond with O2
• tertiary structure changes so it is easier for subsequent O2 molecule to bind (cooperative binding)

Question 25

Describe what catalase is, with reference to its structure and function?

Answer 25

Quaternary protein containing 4 haem prosthetic groups which contain Iron (II) ions which allow catalase to interact with hydrogen peroxided and speed up its breakdown

• catalase is an enzyme

Question 26

Describe what fibrous proteins are, with reference to their structure give some examples?

Answer 26

Formed from long insoluble molecules, the amino acid sequence in the primary structure is usually quite repetitive, leads to a very organised structure - can form long chains or fibres

• for example keratin, elastin and collagen

Question 27

Describe the functions of fibrous proteins?

Answer 27

• can form long chains or fibres
• insoluble in water
• useful for structure and support (eg collagen in skin)

Question 28

Explain why fibrous proteins are insoluble in water?

Answer 28

Due to the presence of a high proportion of amino acids with hydrophobic R-groups in their primary structure

Question 29

Describe what keterain is, with reference to its structure, where its found?

Answer 29

Group of fibrous proteins present in hair,skin and nails - it has a large proportion of the sulfur-containing amino acid,cysteine allowing for many strong disulfide bonds, forming strong, inflexible and insoluble materials

Question 30

Explain why there is a high presence of disulfide bonds/bridges in keratin,what is the significance of this?

Answer 30

Keratin has a large proportion of the sulfur-containing amino acid, cysteine which allows for disulfide bonds to form

• degree of disulfide bonds determines the flexibility (eg hair contains less disulfide bonds making it more flexible than nails)

Question 31

Describe what elastin is, with reference to its structure, where its found?

Answer 31

quaternary proteins made from stretchy molecules called tropoelastin

• fibrous proteins found in elastin fibres which are present in in walls of blood vessels and in the alveoli of lungs (allows for flexibility and expansion when needed but also so they can return to their normal size)

Question 32

Describe what collagen is, with reference to its structure, where its found?

Answer 32

made up of three polypeptides wound together in a long and strong rope-like structure (does have flexibility)

• Fibrous proteins which acts as a connective tissue found in skin,tendons,ligaments and the nervous system

Question 33

List the functions of collagen, elastin and keratin?

Answer 33

Collagen - component of bones, cartilage, connective tissue and tendons

Elastin - provides elasticity to connective tissue, arteries, skin, lungs, cartilage and ligaments

Keratin - structural component of hair,nails, hooves and epithelia cells of outer layer of skin