B1.2 Protein

Question 1

What are amino acids?

Answer 1

The building blocks of proteins.

Each amino acid has a central carbon atom called the alpha carbon.
Amino acids are amphiprotic, carboxyl group is acidic as it can donate a proton, amine group is basic as it can accept one.

Question 2

What is bonded to the alpha carbon in the amino acid?

Answer 2

Single covalent bonds to nitrogen atom of an amine group (H2N), another carbon of carboxyl group (COOH), hydrogen atom and a side chain called the R group, which can one be a wide range of other possibilities.

Question 3

What is a dipeptide?

Answer 3

Two amino acids linked by a condensation reaction,

Question 4

What is a oligopeptide?

Answer 4

Chains of fewer than 20 amino acids. Polypeptides can contain any number of amino acids. Linked by peptide bonds

Question 5

What are peptide bonds?

Answer 5

C-N bonds formed by condensation between amine of one amino acid and the carboxyl group of another at end of growing chain. This is catalysed by ribosomes. Peptide bonds are made using groups part of all amino acids, bond is the same, no matter what the R groups are.

Question 6

How do plants obtain amino acids?

Answer 6

There are two different amino acids used by ribosomes to make polypeptides. Plants make these by photosynthesis.

Question 7

How do animals obtain essential amino acids?

Answer 7

Obtained by food, as animals cannot synthesise in sufficient quantities.

Question 8

What is an essential amino acid?

Answer 8

Amino acids that cannot be synthesised in sufficient quantities by the animal, so must be obtained from diet. There are 9 amino acids essential to us.

Question 9

What are non essential amino acids?

Answer 9

Amino acids that can be synthesised by an animal using metabolic pathways, transforming one amino acid into another.

Question 10

Foods vary in…

Answer 10

Amino acid content, possible to eat a protein rich diet and be deficient in an essential amino acid. Have a balance of amino acids similar to what is needed in the human diet.

Question 11

What amino acids are gained from plant based foods?

Answer 11

Different balance and efficient in specific amino acids, cereals and wheat with low lysine content, peas and beans low in methionine. Both are essential to humans.

Question 12

Function of ribosomes?

Answer 12

Linking amino acids together one at a time until a polypeptide is fully formed, can make peptide bonds between any amino acid pair. Ribosomes do not make random sequences, receive instructions by genetic code.

Question 13

How do we calculate possible amino acid sequences?

Answer 13

Starting with dipeptides, both amino acids can be any of the 20, so there are 20^2 possible sequences. There are 20^3 possible tripeptide sequences. For a polypeptide of n amino acids, there are 20^n possible sequences.

Question 14

What are some examples of polypeptides

Answer 14

• Beta endorphin, painkiller secreted by pituitary gland,31 amino acids.
• insulin, small protein, two short polypeptides, one with 21, the other with 30.
• alpha amylase, enzyme in saliva that starts the digestion of starch, 496 amino acids, with one chloride ion and one calcium ion associated.
• titin is the largest polypeptide discovered. It is part of a structure of muscle. In humans, 34,350 amino acids

Question 15

How is the 3d dimensional conformation of proteins stabilised?

Answer 15

By bonds between R-group amino acids within the molecule e.g hydrogen bonds, disulfide bonds, ionic bonds etc. Most bonds are weak, and can be disrupted/broken, resulting a change to conformation. This is known as denaturation. Unable to return to former structure. Soluble proteins often become insoluble and form a precipitate.

Question 16

Why is a precipitate formed?

Answer 16

Due to hydrophobic R-groups in the centre of the molecule becoming exposed to water by change in conformation.

Question 17

Why heat causes denaturation?

Answer 17

Causes vibrations within the molecule that can break intermolecular bonds or interactions. Proteins vary in their heat tolerance.

Question 18

What other factors cause proteins to denature?

Answer 18

Extremes of pH, can cause denaturation, because positive and negative charges of R groups are changed, breaking ionic bonds within the protein/causing new ionic bonds to form. As with heat, 3d structure is altered, protiens that are dissolved in water become insoluble.

Question 19

What happens when amino acids are linked up into a polypeptide?

Answer 19

Their amine and carboxyl groups are used to make peptide bonds, leaving the amine group (NH2) at one end and carboxyl at the other. Hydrogen atom has little effect on properties. It is the R groups that determine chemical characteristics.

Question 20

How is an R group varied?

Answer 20

R groups determine chemical characteristics, some are hydrophobic, others are hydrophilic. Some are polar, and others become charged by acting as an acid or a base. This broad diversity allows living organisms to make and use an amazingly wide range of proteins.

Question 21

Why do some proteins contain amino acids that are not in the basic repertoire of 20?

Answer 21

Most cases, this is due to one of the 20 being modified after a polypeptide has been synthesised. Examples include collagen, a structural protein used to provide tensile strength in tendons, ligaments, skin and blood vessel walls. collagen polypeptides made by ribosomes contain proline in many positions, but at some positions it is converted to hydroxyproline, making collagen more stable.

Question 22

What are the 4 levels of complexity in the structure of proteins?

Answer 22

Primary, secondary, tertiary, quaternary.

Question 23

What is the primary structure of proteins?

Answer 23

A linear sequence of amino acids in a polypeptide.

Question 24

What is the backbone of a polypeptide?

Answer 24

A repeating sequence of atoms linked by covalent bonds (C C N C C N and so on). Bond angles are all tetrahedral, there can be rotation about the bonds between the alpha carbon atoms and adjacent nitrogen and carbon atoms. Allows polypeptides to fold into almost any 3d shape.

Question 25

What is conformation?

Answer 25

The 3d arrangement of atoms in a polypeptide or protein. Most polypeptides self assemble into a specific conformation determined by sequence of amino acids and their R groups. Conformation determines their functions and through this the behaviour of cells.

Question 26

What remains of carboxyl and amine groups after they have been used to make peptide bonds? (secondary structure)

Answer 26

there are C=O and N-H bonds, both are polar, with oxygen having a slight negative charge, hydrogen, slight positive charge. hydrogen bonds can form between this groups, although weak, the frequency of C=O and N-H groups along chains allow many of them to form and collectively are strong enough to stabilize distinctive conformational structures within protein molecules.

Question 27

What are the two commonly occurring types of structure stabilized by hydrogen bonding? (secondary structure)

Answer 27

The alpha helix, polypeptide is wound into helical shape, with hydrogen bonds between adjacent turns of the helix. The beta pleated sheet, two or more sections of polypeptide are arranged in parallel with hydrogen bonds between them. Sections of a polypeptide run in opposite directions, forming as sheet that is pleated because of the tetrahedral bond angles.

Question 28

What is the tertiary structure of polypeptides? And what are the 4 main interactions?

Answer 28

The folding of a whole polypeptide chain into a three dimensional structure, stabilized by interactions between R groups. 4 main types of interactions: - ionic - hydrogen bonds - disulphide bonds - hydrophobic interactions

Question 29

Explain the ionic bonds within tertiary structure of a polypeptide

Answer 29

ionic bonds between positively charged and negatively charged R groups. Amine groups become positively charged by accepting a proton (-NH2 + H+ -> NH3+). Carboxyl groups become negatively charged by donating a proton (-COOH -> COO- + H+) because of the involvement of protons (hydrogen ions), ionic bonds in proteins are sensitive to pH changes.

Question 30

Explain the hydrogen bonds within tertiary structure of a polypeptide

Answer 30

Formed between polar R groups, hydrogen atoms forms link between two electronegative atoms (O/N etc), and is covalently bonded to one of them. Results in hydrogen with a positive charge, making it attractive to the others electronegative atom which has a slight negative charge.

Question 31

Explain the disulphide bonds within tertiary structure of a polypeptide

Answer 31

There are disulfide bonds between pairs of cysteines. A covalent bond and is the strongest of all interactions

Question 32

Explain the hydrophobic interactions within tertiary structure of a polypeptide

Answer 32

amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, hydrophilic amino acids on the outside interact with surrounding water molecules.

Question 33

How is the tertiary structure of a polypeptide developed?

Answer 33

Develops as polypeptide is synthesised by the ribosome. Sometimes, chaperone protein helps with process ensuring a correctly folded/fully functional protein.

Question 34

Amino acids in proteins can be divided into what broad categories?

Answer 34

1) Non polar + hydrophobic 2)Polar/charged therefore hydrophilic.

Question 35

What amino acids do proteins that are routinely in contact with non polar substance have?

Answer 35

Hphobic amino acids on surface, integral proteins embedded in membranes have these, in contact with the non-polar hydrocarbon core of the membrane.

Question 36

How do Channel proteins in membranes allow hydrophilic solutes or water to diffuse across hydrophobic core of membrane?

Answer 36

They have hydrophilic regions with hydrophobic region in between, holds them in transmembrane position. In addition they have a tunnel lined with hydrophilic amino acids through centre of protein. Width and charge distribution of this channel allows specific hydrophilic ions/molecules to pass through.

Question 37

All proteins must consist of?

Answer 37

At least one polypeptide, but many consist of two or more linked together, some have one or more non-polypeptide components. In proteins that consist of more than one polypeptide, the 3d arrangement of subunits is the quaternary structure.

Question 38

In a non conjugated protein (formed by combining with another compound) there are only?

Answer 38

Polypeptide subunits, to form the quaternary structure, polypeptides are linked by the same types of interactions as in the tertiary structure.

Question 39

Conjugated proteins have one or more? haemoglobin as an example

Answer 39

non polypeptide subunits in addition to their polypeptides. Haemoglobin consists of polypeptide chains, each associated with a haem group. Inclusion of non polypeptide components increases chemical and functional diversity of proteins. Haem group binds oxygen, allowing haemoglobin to transprot oxyygen.

Question 40

What does the function of a protein depend on?

Answer 40

Dependent on form, and can be illlustrated by considering the difference between fibrous and globular proteins.

Question 41

What do fibrous proteins consist of?

Answer 41

Elongated polypeptides that lack the folding of typical tertiary structure. Polypeptides in fibrous proteins do not develop secondary structures, e.g alpha helices. Their quaternary structure is developed by linking together polypeptide chains into narrow fibres/filaments, with hydrogen bonds between chains.

Question 42

Explain collagen as an example of a fibrous protein.

Answer 42

- Collagen, fibrous protein, the quaternary structure is three polypeptides, wound together into a triple helix. - Primary structure is a repeating sequence of P-G-X. - P as in (hydroxy)proline, which has a special property in preventing formation of a alpha helix. The winding together of polypeptides would be impossible if they were alpha helices. - R group of every third amino acid faces inwards towards centre of triple helix and glycine is the only amino acid with an R group small enough to fit. It is a single hydrogen atom. - rope like structure of collagen gives high tensile strength - R group of amino acid X faces outwards and is variable, allowing many variations of collagen to be produced for variety of uses in skin, tendons, ligaments etc.

Question 43

Globular proteins consist of?

Answer 43

A rounded shape, formed by folding up of polypeptides. Shape is very intricate and is stabilized by bonds between the R groups of the amino acids that have been brought together by the folding. - An insulin molecule has conformation needed to bind to a specific site on the insulin receptor. This allows a specific and unambiguous signal to be sent to body cells when blood sugar concentration is too high.

Question 44

What is a cysteine?

Answer 44

a non-essential amino acid important for making protein, and for other metabolic functions

Question 45

What shapes of polypeptides can be produced during formation of tertiary structure?

Answer 45

Wide range of 3d shapes, most are globular some are fibrous, within tertiary structures are often parts with secondary structures, alpha helices or beta pleated sheets. Some polypeptides do not become folded and instead remain elongated, no tertiary structure.

Question 46

why are many globular proteins soluble in water, what amino acids are on their surface?

Answer 46

Soluble in water to carry out function in the cytoplasm/aqueous solution. Have hydrophilic amino acids on surface, and are in contact with water. hydrophobic amino acids clustered in centre. arrangement stabilises tertiary structure, maximises (hphobic) interactions between amino acids in the centre, and hydrogen bonding between amino acids on the surface and the water around.

Question 47

in transmembrane proteins what is the hydrophobic region considered as?

Answer 47

a belt, with hydrophilic regions inside and outside that are in contact with aqueous solutions inside and out of cell. This stabilises the tertiary structure of the protein, and ensures it is positioned correctly int he membrane where its function can be performed.