2.9 Proteins structure and amino acids

Define what a protein is and state the uses of proteins

proteins are polymers made on repeating units of monomers called amino acids

• used for: enzymes, cell membrane, hormones, structural proteins, transport proteins e.g haemolglobin

Describe and draw what an amino acid consists of

amino acids are the monomers of polypeptides

they consist of:

• an amine group -NH₂

• a carboxylic acid group -COOH

• an R group (this is what makes each amino acid unique)

• a hydrogen atom

Draw and explain how a peptide bond is formed, include:

• how a dipeptide bond is formed

• how a polypeptide bond is formed

a peptide bond is formed through a condensation reaction producing a water molecule, whereby it is between the C on the carboxylic acid group of one amino acid and the N of the amine group on the other

• dipeptide bond is formed by the condensation of two amino acids

• polypeptide is many (3 or more) amino acids joined together by many peptide bonds

Describe and explain the primary structure of a protein

this is a single chain of a sequence of amino acids held together by covalent polypeptide bonds

Describe and explain the secondary structure of proteins

this occurs when the weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms —→ held together by hydrogen bonds between non-adjacent amino acids

• this forms an α-helix —→ which occurs between every fourth peptide bond

• this forms β-pleated sheet —→ protein folds so the two parts of the polypeptide chain are parallel forming hydrogen bonds

Describe and explain the tertiary structure of a protein

this is the combination of different secondary structures within the same polypeptide chain, leading to the formation of different bonds between the R groups

• disulphide bridges

• hydrogen bonds

• ionic bonds

• hydrophobic bonds

Describe each of the following covalent bonds:

• hydrogen bonds

• ionic bonds

• disulphide bonds

• hydrophobic interactions

• hydrogen bonds - weak interactions between C=O and the N-H groups on different amino acids

• ionic bonds - occurs between oppositely charged R groups

• disulphide bonds - occurs between the sulfur atoms of two cysteine amino acid residues

• hydrophobic interactions - between non-polar R groups

Describe and explain the quaternary structure of a protein

this occurs in proteins that have more than one polypeptide chain

• contains all of the bonds within a tertiary structure i.e hydrogen, ionic, hrydrophobic interactions and disulphide bridges

Describe the structure of globular proteins

compact and spherical shape

• this is because they have hydrophilic R groups on the outside and hydrophobic R groups facing inwards

• They have VERY specific shapes (due to tertiary structure) allowing them to carry out very specific functions (like enzymes)

Describe and explain the function of globular proteins and give examples of globular proteins

• soluble in water - this is because the hydrophilic R groups are on the outside so can form hydrogen bonds with water molecules

• this allows it to attract other polar hydrophilic R groups → hence can be easily transported

e.g haemolglobin, enzymes, insulin, oestrogen

Describe the structure of fibrous proteins

• have long chains

• little or no tertiary structure

• hydrophobic R groups face outwards whilst hydrophilic R groups face inwards

Describe and explain the function of fibrous proteins and include examples

• insoluble - hydrophobic R groups face outside whereas hydrophilic R groups face inside so cannot form hydrogen bonds in water

• structural roles - strong / high tensile strenghth (made of many polypeptide chains)

e.g collagen, keratin and elastin

Describe the structure of collagen and how it realtes to its function

collagen has a tertiary three dimensional structure: main function is a structural component found in ligaments, tendons, the skin

• consists of three polypeptide chains (a triple helix structure) held together by hydrogen bonds —→ thus has a high tensile strength

• has it’s hydrophobic R groups on the outside and the hydrophilic R groups on the inside —→ thus it is insoluble so cannot form hydrogen bonds with water molecules

• has kinks in the protein chain —→ this makes it flexible

Describe the structure of haemoglobin

haemoglobin is a quaternary structure consists of:

• 4 polypeptide chains whereby there are 2 alpha-subunits and 2 beta-subunits

• the four subunits are held togther by hydrogen bonds, ionic bonds and hydrohphobic interactions between R groups

• hydrophobic R groups face inwards and hydrophilic R groups face outwards

• it also has 4 haem prosthetic groups (non-protein) containing iron —→ this binds to oxygen to form oxyhaemoglobin

Explain how the structure of haemoglobin relates to it’s function

• soluble - hydrophobic R groyps face inwards and hydrophilic R groups face outwards —→ allows it to be a transport molecule transporting oxygen around the body to be used in aerobic respiration

• iron in the prosthetic haem group allows oxygen to reversibly nind as none of the amino acids that make up the polypeptide chains in haemoglobin are suited to bind it oxygen

Compare and contrast the molecular structures of globular and fibrous proteins (4)

• both chains of amino acids joined by peptide bonds

• both contain hydrogen, ionic and disulphide bridges holding the molecule in it’s three dimensional shape

• globular proteins have hydrophilic groups on the outside wheras fibrous proteins have hydrophobic groups on the outside

• globular have tertuary or quaternary structures whereas fibrous have little or nor tertiary structure

• globular proteins are folded into compact shapes wheras fibrous have long chains