2.4 Proteins

Question 1

what are proteins compromised of?

Answer 1

long chains of recurring monomers (amino acids)

Question 2

what are the basic structures of a central carbon atom? (4)

Answer 2

• an amine group (NH2)
• a carboxylic acid group (COOH)
• hydrogen atom (H)
• a variable side chain (R)

Question 3

how many different amino acids are universal to all organisms?

Answer 3

around 20

Question 4

how are amino acids joined together?

Answer 4

amino acids are joined together on the ribosome to form long chains (polypeptide), which make up proteins

Question 5

how does each type of amino acid differ?(2)

Answer 5

• differ in the composition of the variable side chain
• with distinct chemical properties and cause the protein to fold and function differently according to its specific position within the polypeptide chain

Question 6

how are amino acids joined together?

Answer 6

joined together by a covalent bond (peptide bond) in a condensation reaction to form a dipeptide and water

Question 7

what are long chains of covalently bonded amino acids called?

Answer 7

polypeptides

Question 8

how can polypeptide chains be called?

Answer 8

can be broken down via hydrolysis reaction (required water to reverse the process)

Question 9

where are peptide bonds formed? (2)

Answer 9

between the amine and carboxylic acid groups of adjacent amino acids
- the amine group loses a hydrogen atom (H) and the carboxylic acid loses a hydroxyl (OH) - this forms water (H2O)

Question 10

what is the order of the amino acid sequence called? (3)

Answer 10

primary structure
- determines the way the chain will fold
- different amino acid sequences will fold into different configurations due to the chemical properties of the variable side chain

Question 11

what will amino acid sequences commonly fold into? (3)

Answer 11

secondary structures
- alpha helices -> when amino acid sequence folds into a coil/spiral arrangement
- beta-pleated sheets -> when the amino acid sequence adopts a directionally orientated staggered strand configuration

Question 12

how are alpha-helices and beta-pleated sheets formed?(2)

Answer 12

from hydrogen bonds fomring between non-adjacent amine and carboxyl groups
(when no secondary structure exists, the polypeptide chains will form a random coil)

Question 13

what is the overall 3D configuration of the protein called?

Answer 13

tertiary structure

Question 14

how are tertiary structures determined? (2)

Answer 14

• tertiary structure of a polypeptide chain will be determined by the interactions between the variable side chain
• these interactions may include hydrogen bonds, disulphide bridges, ionic interactions, polar associations

Question 15

what can change the overall shape of the polypeptide chain and are determined by the position of specific amino acids within a sequence?

Answer 15

the affinity/repulsion of the side chains
(so, the order of the amino acid sequence (primary structures) determines all subsequent levels of protein folding)

Question 16

what is the fourth level of structural organisation called?

Answer 16

quaternary structure

Question 17

what are quaternary structures made of?

Answer 17

proteins that consist of more than one polypeptide chain linked together

Question 18

what is an example of a protein with a quaternary structure? (3)

Answer 18

haemoglobin
- haemoglobin is composed of 4 polypeptide chains (2 a and 2 b)
- it is composed of iron-containing haeme groups (prosthetic groups responsible for binding oxygen)

Question 19

what is denaturation?

Answer 19

structural change in a protein that results in the loss (usually permanent) of its biological properties
(because the way a protein fold determines its function, any change or abrogation of the tertiary structure will alter its activity)

Question 20

what two things usually cause the denaturation of proteins?

Answer 20

• temperature
• pH

Question 21

how does temperature denature a protein?(3)

Answer 21

• high levels of thermal energy may disrupt the H-bonds that hold the protein together
• as these bonds are broken, the protein will begin to unfold and lose its capacity to function as intended
• temperature at which proteins denature may vary, but most human proteins function optimally at body temperature

Question 22

how does pH denature a protein? (3)

Answer 22

• amino acids are zwitterions, neutral molecules possessing both negatively (COO-) and positively (NH3+) charged regions
• changing the pH will alter the charge of the protein solubility and overall shape
• all proteins have optimal pH which is dependent on the environment in which it functions

Question 23

what is a gene?

Answer 23

gene is a sequence of DNA which encodes a polypeptide sequences

Question 24

what process is a gene sequence converted into a polypeptide sequence? (2)

Answer 24

• transcription - making mRNA transcript based on a DNA template (occurs in the nucleus)
• translation - using the instructions of the mRNA transcript to link amino acids together (occurs at the ribosome)

Question 25

usually, one gene will code for one polypeptide, but what exceptions to this rule? (3)

Answer 25

• genes may be alternatively spliced to generate multiple polypeptide variants
• genes encoding tRNA sequences are transcribed but never translated
• genes may be mutated (their base sequence is changed) and consequently produce an alternative polypeptide sequence

Question 26

what is the proteome?

Answer 26

the totality of proteins expressed within a cell. tissue or organism at a certain time

Question 27

why will any given individual proteome be unique?

Answer 27

as protein expression patterns are determined by an individual’s genes

Question 28

what are the factors which cause the proteome to be significantly larger than the number of genes in an individual?

Answer 28

• gene sequences may be alternatively spliced following transcription to generate multiple protein variants from a single gene
• proteins may be modified (eg. glycosylated, phosphorylated) following translation to promote further variations

Question 29

what are 7 roles of a proteins?

Answer 29

structure - collagen, spider silk
hormones - insulin, gucagon
immunity - immunoglobins
transport - haemoglobin, cytochrome
sensation - rhodopsin
movement - actin, myosin
enzymes - rubisco