lecture 1: amino acids

Question 1

what are the monomers of proteins?

Answer 1

amino acids

Question 2

what are the polymers of proteins?

Answer 2

polypeptide

Question 3

by which bond are amino acids linked?

Answer 3

peptide bond

Question 4

what are the components to each amino acid?

Answer 4

-central carbon
-hydrogen group
-amino group (NH2)
-carboxyl group (COOH)
-R group

Question 5

what differentiates the 20 different amino acids?

Answer 5

the R group

Question 6

in what form is the amino group more stable? what are the 2 forms it can exist as?

Answer 6

it can exist as NH2 or NH3+, but its more stable as NH3+ in our bodies so thats how it exists.

Question 7

what is common between each amino acid?

Answer 7

backbone

Question 8

what is another word for R group?

Answer 8

side chain

Question 9

what are the properties of a non-basic/acidic hydrophilic amino acid? (polar side chains)

Answer 9

the side chains contain hydroxyl (OH), carbonyl (C=O) and sulfhydryl (SH) groups

Question 10

what happens if you see an oxygen in the side chain of an amino acid?

Answer 10

it must be at least polar

Question 11

what are the properties of a basic hydrophilic amino acid? (electrically charged side chains) what is the charge?

Answer 11

the side chain is charged positivly. the charge is due to a positive amino group (NH2/NH3) in the R group. CHARGED AT PH 7

Question 12

what are the properties of an acididc hydrophilic amino acid? (electrically charged side chains) what is the charge? CHARGED AT PH 7

Answer 12

the side chain is charged negatively. this charge is due to a negatively charged carboxyl group (COO/COOH)

Question 13

how does carboxyl exist in our bodies in the backbone of amino acids?

Answer 13

as COO-

Question 14

what are the properties of a hydrophobic amino acid? (polar side chains)

Answer 14

the side chains are made up of carbons, hydrogens and methyl groups (CH3)

Question 15

What happens to an amino acid in very acidic conditions?

Answer 15

Backbone becomes positively charged. The carbonyl group gains an H+, due to the fact that there are more H+ in the environment

Question 16

What happens to an amino acid in very basic conditions?

Answer 16

The amino group loses its proton, therefore it is no longer positively charged and the negative charge of the carboxyl takes over.

Question 17

What does an amino acid look like at PH 7?

Answer 17

Question 18

what is the isoelectric point?

Answer 18

PH at which a protein has a neutral charge (charge of 0)

Question 19

by which reaction are peptide bonds formed? how does this happen?

Answer 19

dehydration reaction. the H of the amino group of one amino acid is lost along with the OH of the carboxyl group of the next amino acid. this continues until we have a chain

Question 20

what is the directionality of the peptide bond?

Answer 20

c terminus first (carboxyl end)
n terminus at the end (amino end)

Question 21

why are proteins able to carry out so many diverse functions in cells?

Answer 21

-because they can form many different shapes which makes them really diverse comapred to other structures

Question 22

what are the 4 levels of protein structure?

Answer 22

-primary structure
-secondary structure
-tertiary structure
-quaternary structure

Question 23

what type of bonds are peptide bonds? why?

Answer 23

covalent bonds. anything formed by a dehydration reaction is a covalent bond.

Question 24

what is a primary structure?

Answer 24

-Linear sequence of amino acids coded for by a gene sequence
-Has directionality (N-C terminus)
-linear chain of amino acids

Question 25

what is a secondary structure?

Answer 25

spatial arangement of amino acids to form alpha helices of beta sheets.

Question 26

how is a secondary structure formed?

Answer 26

by H bonding between amino (N-H) group of one amino acid and carbonyl (C=O) (since we lost OH during dehydration) group of another amino acid

Question 27

are R groups involved in the the formation of secondary structures?

Answer 27

NO! only the backbone!

Question 28

what are the characteristics of alpha helix?

Answer 28

-H-bonding between amino acids 4 places apart -R groups oriented away from the axis -looks like a curl

Question 29

what are the characteristics of beta sheet?

Answer 29

-two regions of polypeptide chain lie parallel to each other like a folded sheet

Question 30

what is a tertiary structure?

Answer 30

-structure formed when alpha helix and beta sheets interact to form a variety of shapes -formed through the interactions between amino acid side chains

Question 31

what type of bonds happen in tertiary structure?

Answer 31

side chains interact again through covalent and non-covalent interactions to form tertiary structures

Question 32

what type of non-covalent bonds are involved in a tertiary structure?

Answer 32

-H bonding (between R groups) -hydrophobic interactions between hydrophobic amino acids (2 hydrophobic) -van der Waals (2 hydrophilic or 2 hydrophobic) -ionic bond (charged amino acids interact through salt bridges)

Question 33

what type of covalent bonds are involved in a tertiary structure?

Answer 33

disulphide bridge (amino acids interact with a sulfhydyl group)

Question 34

what are van Der Waals?

Answer 34

a way in which 2 polar or 2 hydrophobic amino acids can interact with each other in a tertiary structure.

Question 35

what is a quaternary structure?

Answer 35

-more than one polypeptide chain interacting together to form a protein

Question 36

how are polypeptides held together in the quaternary structures?

Answer 36

by the same interactions as a tertiary structure

Question 37

what is denaturation?

Answer 37

disrupting protein structure. proteins become unfolded as all bonds are broken. we are left with polypeptides.

Question 38

is renaturation possible?

Answer 38

sometime possible, but highly unlikely

Question 39

what are the conditions that can denature a protein? why?

Answer 39

-temperature (alters vibrational and rotational energy and disrupts non-covalent interactions such as H-bonds -PH (changes the ionic state of the charged side chains, which disturbs bonds and makes for the protein to unfold) -salt (changes the ionic environment. there are now more charges in the environment which disrupts the charges of the protein causing it to unfold) -detergent (disrupts hydrophobic regions) -reducing agent (breaks covalent disulphide bonds. smells and. something that you add to the protein that causes a reduction)

Question 40

what is the movement od hydrophobic/hydrophilic side chains when we add detergent?

Answer 40

-hydrophobic side chains move from the interior of protein to the exterior of protein -hydrophilic Side chains move to the interior of protein

Question 41

what levels of protein structure are affected by denaturation?

Answer 41

4th, 3rd, 2nd, NOT FIRST! (cant break peptide bonds)