amino acids and proteins

Question 1

what are the 4 constituents of an amino acid?

Answer 1

-amino group
-carboxyl group
-single hydrogen
-side chain (R)

Question 2

what is the backbone of the amino acid?

Answer 2

N-C-C

Question 3

what are the characteristics of non-polar amino acids?

Answer 3

-hydrophobic
-help the protein fold and create hydrophobic exclusion or Van der Waals attraction

Question 4

what are the characteristics of polar uncharged amino acids?

Answer 4

-tend to make H-bond
-hydrophilic

Question 5

what are the characteristics of charged amino acids?

Answer 5

-have a side chain that can ionize
-opposite charged side chain of amino acids can interact and create ionic bond
-same charges side chains are repelled by each other

Question 6

what are characteristics of amino acids that have benzene ring (non-polar)?

Answer 6

-non-polar side chain
-hydrophobic
-hydrophobic exclusion or Van der Waals attraction

Question 7

what are characteristics of amino acids that have benzene ring (polar)?

Answer 7

-polar due to hydroxyl functional group (phenol)
-hydrophilic
-arrange themselves towards water molecules, create H-bond

Question 8

what are characteristics of amino acids that have benzene ring (charged)?

Answer 8

-charged due to NH+ in ring
-can create ionic bond (oppositely charged)
-if same charged, will repel

Question 9

what is the special function of methionine?

Answer 9

it is always the first amino acid of a polypeptide in eukaryote and archaea

Question 10

what is the special function of proline?

Answer 10

it induces a kink in the alpha helix

Question 11

what is the special function of cysteine?

Answer 11

-contains a side chain with sulfhydryl, which will link together to create disulfide bridge
-disulfide bridge is a type of covalent bond (strongest bond between side chains)

Question 12

what are the polymers of amino acids?

Answer 12

polypeptides composed of monomers of unbranched amino

Question 13

what is a protein made out of?

Answer 13

one or more polypeptides and can only be called a protein if the polypeptide(s) have a function

Question 14

what is the name of the bond formed between the amino end and carboxyl end of two adjacent amino acids?

Answer 14

peptide bond

Question 15

true or false: the peptide bond is planar and does not permit rotation

Answer 15

true

Question 16

can rotation occur along the c(alpha)-c bond?

Answer 16

yes (it makes the side chain (R) be on the same or opposite side)

Question 17

what is the primary structure of an amino acid?

Answer 17

it is the sequence of amino acids linked together by peptide bonds

Question 18

what is the secondary structure of amino acids?

Answer 18

it is the interaction of atoms in the peptide backbone (NCC):
-H-bond between amino acids of the backbone

Question 19

what are the two structures that are part of the secondary structure level of an amino acid?

Answer 19

-alpha helix
-beta pleated sheet: always composed of 2+ beta strands

Question 20

what are unstructured regions?

Answer 20

they are regions between secondary structures

Question 21

what is the tertiary structure of an amino acid?

Answer 21

it is the 3D structure formed by the interaction between the side chains (R) of the other amino acids and also with the environment

Question 22

true or false: only a polypeptide with a tertiary structure can form a functioning protein

Answer 22

true

Question 23

what is the quaternary structure of an amino acid?

Answer 23

it is the arrangement of 2+ polypeptide chains in a functional protein

Question 24

what are motifs?

Answer 24

-they are similarities between otherwise dissimilar proteins
-also called super-secondary structures

Question 25

describe the motif helix-turn-helix

Answer 25

-major structural motif capable of binding DNA -each monomer incorporates two alpha-helices, joined by a short strand of amino acids, that bind to the major groove of the DNA -occurs in many proteins that regulate gene expression

Question 26

describe the motif beta barrel

Answer 26

-beta sheet folded around to form a tube -involved in membrane transport

Question 27

describe the motif beta-alpha-beta

Answer 27

-contains two beta sheets which are connected by an alpha helix -creates a fold/crease at the core of nucleotide binding site in a wide variety of proteins e.g. FAD, NAD+, NADP+

Question 28

true or false: motifs have not been useful to determine the function of unknown proteins

Answer 28

false

Question 29

what are domains?

Answer 29

-functional units within a larger structure -can be thought of as a substructure within the tertiary structure of a protein -most proteins are made up of multiple domain that perform different parts of the protein's function

Question 30

name the different protein functions

Answer 30

-enzyme catalysis -defense -transport -support -motion -regulation

Question 31

what are some environmental factors that can change the structure and function of proteins?

Answer 31

-temperature -pH -organic solvent

Question 32

how will temperature affect the shape of a protein?

Answer 32

-function of a protein will be outside if the temperature is outside of its nominal range

Question 33

how will pH affect the shape of a protein?

Answer 33

-will cause disruption of the ionic bond -will cause disruption of the hydrogen bond

Question 34

how will high ion concentration (salt) affect the shape of a protein?

Answer 34

-disrupts ionic bonds

Question 35

what is the denaturation of a protein?

Answer 35

-environmental exceed the limitation of a protein, the secondary, tertiary, and quaternary bonds are overcome -the protein will no longer function, the damage is irreversible

Question 36

explain the denaturation of keratin

Answer 36

-composed of long alpha-helix with hydrophobic amino acids -lots of disulfide bonds -permanent wave is made by reducing the disulfide bond and generating a new one