Lecture 13 - Amino Acids & Polypeptides

Question 1

we can draw protein structures using a:

Answer 1

PDB file

Question 2

two aspects of amino acid structure:

Answer 2

• shared properties
• properties unique to each amino acid

Question 3

what is the central carbon of an amino acid referred to be?

Answer 3

the “alpha carbon”

Question 4

charge distribution of a zwitterion:

Answer 4

amine (NH3+) end = positive

carboxyl (COO-) end = negative

Question 5

what happens to amino acids at basic/acidic pH conditions:

Answer 5

in basic and acidic conditions the amino acid can act as it own buffer:

acidic (low pH) = amine group gains a proton = amino acid becomes (+)

basic (high pH) = carboxyl group gives off proton = amino acid becomes ( - )

Question 6

amino acids are CHRIAL so we structure them accordingly:

Answer 6

“CORN crib” mnemonic for the hand of L^2-amino acids (L - left handed to which the VAST majority of amino acids exist as in biological systems)

[CORN refers to reading the tetrahedral structure from left to right ]

Question 7

during protein synthesis each amino acid is joined to the next via:

Answer 7

a peptide bond - forming a polypeptide

Question 8

a peptide bond results from:

Answer 8

the linkage of the carboxyl group of one amino acid to the amine group of it neighbour, with the elimination of a molecule of water

Question 9

formation of a peptide bond is:

Answer 9

CONDENSATION - i.e loss of water

Question 10

destruction of a peptide bond is:

Answer 10

HYDROLYSIS - i.e usage of one water

Question 11

how to remember peptide bond structure:

Answer 11

CONH

Question 12

what sort of bond is a peptide bond?

Answer 12

peptide bonds are PLANAR therefore they do not have any spin

Question 13

what are peptide bonds planar because of?

Answer 13

peptide bonds are planar due to the sharing of electrons between carbon and nitrogen which creates a resonance that restricts any movement around your bond

Question 14

the trans-peptide group:

Answer 14

the majority of peptide bonds, whereby -NH point sin one direction and -CO in the other: this allows SOME rotation between the alpha carbons, a little bit of flexibility but not very much

Question 15

the cis-peptide group:

Answer 15

• very rare where for the peptide bond to be a cis-peptide, only for when it is useful in structure
• the enzyme that makes the peptide bond ‘cis’ is called an isomerase

Question 16

fully extended conformation of a polypeptide chain shows the:

Answer 16

planarity of each of its peptide groups

Question 17

the 20 amino acids posses unique properties:

Answer 17

• this is due to the different side chain groups (R-groups)
• in 19 amino acids the alpha carbon is CHIRAL (asymmetrical) because it has four different groups
• can exist as stereoisomers
• the exception is glycine, this is because it’s R group is a hydrogen

Question 18

enenatiomers - amino acids can be:

Answer 18

• L (laevus = left) or D (dexter = right) isomers
• only L amino acids are found in proteins in living organisms

Question 19

example which shows the vast combinations of amino acids even from a 100 residue protein (where residue = amino acids):

Answer 19

for a 100 residue protein = 20^100 combinations

Question 20

the common amino acids are grouped according to whether the side chains are:

Answer 20

acidic

basic

uncharged polar

non-polar

Question 21

what abbreviations are each amino acids given?

Answer 21

all amino acids are given either a three letter or a one letter abbreviation

Question 22

what do all non-polar amino acids essentially have as their R-groups?

Answer 22

all non-polar amino acids have hydro-carbon (just C & H) based R-groups

Question 23

what do all polar amino acids contain within their R groups?

Answer 23

all polar amino acids either have an alcohol (-OH) or (O=C–NH2) within their R-group side chains

Question 24

what do acidic amino acids have in their R-group side chains?

Answer 24

acidic amino acids have carboxyl groups on the ends of their R-groups

Question 25

what do all basic amino acids all have on the ends of their R-groups?

Answer 25

all basic amino acids all have amino groups on the ends of their R-groups

Question 26

unique properties of glycine and proline and their purpose:

Answer 26

glycine - the R-group side chain is only —H, this allows glycine to pack together very closely in a small region

proline - is an actual cyclic amino acid which allows for the introduction of a “kink” in the chain to form a cis-backbone

Question 27

aliphatic R groups:

Answer 27

more CH = increasingly hydrophobic

Question 28

aromatic R-groups:

Answer 28

Phe, Tyr & Trp are the aromatic amino acids and they are called aromatic amino acids as they can absorb ultraviolet light (UV)

at a neutral pH Trp & Tyr absorb light at 280nm whereas Phe absorbs light at 260nm

absorbance is routinely used to estimate the protein concentration

Question 29

disulphide bonds & purpose:

Answer 29

• side chain of cysteine contains highly reactive thiol group
• two thiol groups forms a disulphide bond
• they are there to link together distant amino acids

Question 30

sequence of the pol,peptide chain is:

Answer 30

the primary strucutre

Question 31

what does comparison of the primary structure of proteins reveal?

Answer 31

primary structure amino acids reveals evolutionary relationships through comparison of structures

for example cytochrome-c is found in all aerobic organisms

Question 32

the more identities between two molecules…

Answer 32

… the more recently they have evolved from a common ancestral molecule and thus the closer the kinship of their owners

Question 33

what gene codes haemoglobin?

Answer 33

the globin gene

Question 34

in adults haemoglobin =

Answer 34

iron containing heme molecule surrounded by 4 globin proteins: 2 alpha globin and 2 beta globin

Question 35

how does haemoglobin change during human development?

Answer 35

during developemtrn, different globin genes are expressed which alter the oxygen affinity of embryonic and fetal haemoglobin

Question 36

sickle cell anaemia:

Answer 36

genetic disease - heterozygous=carriers, homozygous=diseased

sickle-cell anaemia results from defective haemoglobin which causes the haemoglobins to stick together and consequently damaged red blood cells

this causes complications from low oxygen supply to tissues [pain, organ damage, strokes, increased infections]

incidents are highest in african and indian populations

Question 37

sickle cell haemoglobin:

Answer 37

significant change in structure caused by the single mutation

Question 38

how are amino acids classified?

Answer 38

amino acids are classified via their properties