B1.2 proteins

Question 1

how many types of amino acids are there?

Answer 1

20

Question 2

in a molecular structure common to all 20, what letter represents the type of amino acids and what do they tend to call it?

Answer 2

• R
• variable group or the side chain

Question 3

what are the 2 parts of a molecular structure common to all 20 amino acid called?

Answer 3

amine functional group
carboxyl functional group

Question 4

the molecular structure common to all 20 amino acids?

Answer 4

. H R O
I I II
H - N - C - C - OH
I
H

Question 5

word equation for a dipeptide

Answer 5

amino acid 1 + amino acid 2 –> dipeptide + water

Question 6

the covalent bond linking amino acids is called

Answer 6

peptide bond

Question 7

dipeptide structure

Answer 7

. H R O R O
I I II I II
N - C - C - N - C - C
I I I I I
H H H H OH

Question 8

where does the water come from when a dipeptide is formed?

Answer 8

a hydroxyl group (-OH) from the carboxyl group of one amino acid and a hydrogen ion (H+) from the amine functional group of the other amino acid.

Question 9

what does the formation of water allow to happen to the two amino acids?

Answer 9

this frees electrons to be shared between carbon and nitrogen atoms that allows the bonding of two amino acids together into a dipeptide

Question 10

a chain of many amino acids is called

Answer 10

a polypeptide

Question 11

essential amino acids

Answer 11

they cannot be synthesised and must be obtained from food ( 9 types of amino acids come from diet)

Question 12

non-essential amino acids

Answer 12

those that the body can produce on its own. 11 out of 20 amino acids can be synthesised by our cells.

Question 13

why do vegans require attention to ensure essential amino acids are consumed?

Answer 13

vegans may be limited to types of amino acids
(no need to memorize):
white rice is deficient in the amino acid lysine
legumes/ beans contain low levels of amino acid methonine

Question 14

some examples of common polypeptides

Answer 14

1- heamoglobin (oxygen carrying protein in red blood cells)
2- keratin (found in nails claws hooves and hair)
3- lipase (a digestive enzyme that helps hydrolyse ingested lipids)
4- collagen (found in connective tissue in the body)
5-histones (proteins found in the nucleus of cells that help form chromatin and chromosomes)
6-insulins (helps regulate blood glucose levels)

Question 14

why is there a huge variety of polypeptides?

Answer 14

1- DNA codes for the number and order of amino acids within polypeptides
2- 20 different amino acids
3- polypeptides vary in length (a few to thousands)
4- some polypeptides are modified by cells after their intial synthesis
5- amino acids can be arranged into any order

Question 15

importance of protein structures

Answer 15

the function of a protein is very dependant on its structure; some are shaped like fibres and some are folded to form globular proteins

Question 16

whats denaturation?

Answer 16

loss of shape and function

Question 17

how does a protein denature from temperature?

Answer 17

when protein molecule is placed into a environment that higher temperature than their physiological optimum, the increased molecular motion puts stress on the weak intermolecular bonds. peptide bonds tend to stay in pact but the intermolecular bonds that help the shape of the protein do not. therefore protein loses shape and function. if peptide bonds break then the protein won’t be able to reshape itself.

Question 18

how does a protein denature from ph?

Answer 18

when a protein is placed in an environment that is not close to its optimum pH. a protein will lose its three-dimentional shape thus its functionality. when a fluid environment like blood or cytoplasm is flooded with H+ ions or -OH (acid or a base), the extra charges can prevent normal hydrogen bonding.

Question 19

what happens to a protein in an aqueous solution?

Answer 19

when in aqueous solution both amine and carboxyl groups ionize. this happens because the carboxyl group acts as an acid and donates a hydrogen ion while the anime group acts as a base and accepts a hydrogen ion. so the carboxyl group would have a net negatove charge and the amine group would have a net positive charge.

Question 20

what divides the amino acids into polar and non-polar categories?

Answer 20

R-groups

Question 21

non polar amino acids are hydrophobic or hydrophilic?

Answer 21

hydrophobic

Question 22

polar amino acids are hydrophobic or hydrophilic?

Answer 22

hydrophilic

Question 23

non-polar amino acids information

Answer 23

• 9 amino acids
• R-groups are hydrocarbons

Question 24

polar amino acids information

Answer 24

• 6 amino acids
• R-groups contains elements that form a polar covalent bond (oxygen, nitrogen or sulfur)

Question 25

polar (+) due to ionization charge amino acids information

Answer 25

• 3 amino acids
• R-groups acts as a base

Question 26

polar (-) due to ionization charge amino acids information

Answer 26

• 2 amino acids
• R-groups acts as an acid

Question 27

primary structure of a protein

Answer 27

the number and sequence of amino acids held together by peptide bonds, determined by a gene. (sequence of amino acids in polypeptide chain) the sequence of amino acids also determine the which intermolecular bonds will form to make its three-dimentional shape.

Question 28

influence of polar and non polar R-groups on the amino acid

Answer 28

if the R-groups are non-polar then the R-groups do not influence the shape of the molecule. whilst Polar R-groups can connect with other parts of the protein or with water, influencing how the protein folds.

Question 29

do all amino acids have charges even if their R-groups do not?

Answer 29

yes

Question 29

residues

Answer 29

residues charges on amino acids come from amine groups and carboxyl groups that make up peptide bonds.

Question 30

the two possible shapes that can result when the primary structure of a protein contains only non-polar R-groups

Answer 30

• alpha helix
• beta pleated-sheet

they are often insoluable
protiens with this structure are often called fibrous - having a function related to movement

Question 31

Secondary Structure of a protein

Answer 31

Localized folding patterns within a protein chain

Question 32

alpha helix

Answer 32

A coiled structure stabilized by hydrogen bonds between amino acids along the chain.

Question 33

beta pleated-sheet

Answer 33

A structure where the protein chain folds back and forth on itself, forming a sheet-like structure.

Question 34

bondings in a secondary structure of a protein

Answer 34

they are held together in shape by hydrogen bonds. the R-group and a hydrogen that connects to the alpha/centeral carbon has been omitted this is because theyre are not involved in the shaping of the moelcule and not needed to explain the secondary structure. all of the hydrogen bonding is between non-adjacent amine and carboxyl residues which are portions of peptide bonds.

Question 35

where are the hydrogen bond in the alpha helix and beta pleated sheets

Answer 35

the hydrogen bonds have fromed between the oxygen atoms (partial negatove charge) of the carboxyl residues and the hydrogen atoms (partial positive charge) of the amine residues.

Question 36

examples of bonding interactions that can occur between amino acids at the teritary level

Answer 36

• ionized R-groups
• Non polar amino acids
• pairs of cysteine forming disulfate bonds
• polar amino acids will form hydrogen bonds with eachother

Question 37

Ionized R-groups bonding interactions

Answer 37

Ionized R-groups, (some - or +) will align with eachother to form an ionic bond. amino acid with a carboxyl in their R-group will dissociate, lose the hydrogen ion and become negativley charged. Amino acids with amine within their R-groups will bind to a hydrogen ion and become positivley charged. the two opposite charged R-groups can then form an ionic bond.

Question 38

Non polar amino acids bonding interactions

Answer 38

being hydrophobic, will fold into an area within the interior of the polypeptide in an attempt to avoid the polar water molecules. this is known as a hydrophobic interaction

Question 39

pairs of cysteine forming disulfate bonds, bonding interactions

Answer 39

pairs of cysteine form a covalent bond between themselevs and within the polypeptide. Cysteine R-groups contain a sulfur atom bonded to a hydrogen atom. when a two non-adjacent cysteine atoms get close to eachother, the two hydrogens can be removed and the two sulfur become covalently bonded to eachother. the resulting covalent bond is called disulfate bond and the strongest