day 1

Question 1

Some proteins can switch between two or more conformations. The switch often involves :

Answer 1

noncovalent binding of another molecule

Question 2

weak bonds

Answer 2

noncovalent bonds

Question 3

Types of noncovalent interactions

Answer 3

ionic, polar, LDF’s, hydrophobic exclusions

Question 4

of amino acids essential for humans

Answer 4

9

Question 5

polypeptide chain: Formation of peptide bond by energy-requiring ___ rxn

Answer 5

condensation

Question 6

Hydrogen bonding is not involved in forming which level of protein structure?

Answer 6

primary

Question 7

Proper folding of a newly synthesized protein is accomplished by:

Answer 7

the hydrophobic effect

electrostatic attractions and repulsions

Van der Waals attraction

help from chaperone proteins

Question 8

Functioning proteins change between conformations when

Answer 8

a small molecule binds noncovalently

Question 9

combustion: exer or endergonic?

Answer 9

exergonic

Question 10

which things contribute to a proteins function?

Answer 10

shape

order of amino acids in primary sequence

positioning of R groups

secondary struture

Question 11

The R group of which amino acid would form a covalent bond with another R group?

Answer 11

cysteine

Question 12

Which of the following defines the polypeptide backbone?

Answer 12

anything that’s not an R group

Question 13

how would you calculate an isoelectric point and what does it mean

Answer 13

1. take the average of the pKa’s of its various forms
2. its the point at which it stops migrating in an electric field which is equal to its average pH

Question 14

aspartic acid vs serine; which is more water solube and why?

Answer 14

aspartic acid. COO- >> OH. ionic wins

Question 15

Enzymes differ from chemical catalysts because they lose activity at high temperature or extremes of pH. This difference can be explained by

Answer 15

the loss of the 3-D shape of the enzyme

the loss of the shape of the active site

the loss of noncovalent interactions

the loss of ionic bonds

Question 16

name an amino acid with an R group capable of hydrogen bonding

Answer 16

serine, threonine, tyrosine

Question 17

If a crystal of NaCl is dropped into a beaker of polar solvent such as methanol, how would the electrostatic attraction of Na+ for Cl- in the salt bridge change?

Answer 17

The electrostatic attraction is weaker

Question 18

DNA Polymerase is the enzyme involved in

Answer 18

Replication

Question 19

are hydrophobic exclusions a true type of bond? where do they exist and what do they mainly depend on? give an example

Answer 19

• Not a true bond. Only exists in water
• Depends on entropy more than any binding
• Benzene: nonpolar molecule.

If you put benzene in water, benzene clusters together

Question 20

T/F: membrane formation is powered by the hydrophobic effect

Answer 20

T

Question 21

entropy of protein folding

Answer 21

disorder -> order

Question 22

name some hydrophobic R groups

Answer 22

hydrophobic R groups: alanine, leucine, isoleucine

Question 23

ways to denature a protein

Answer 23

Since proteins are held together with these weak forces, they can be unfolded fairly easily.

• Heat up to 50 degrees celcius,
• Detergent also denatures protein. (amphipathic molecule- highly polar salt bridge on one side, long hydrophobic tail on other side. Surrounds molecule- unfolds the molecule)
• Urea: has a lot of polar properties (2 dipoles) .
• Changing the pH of the system. Changes the molecules ability to ionize- titrates amino acids- lowering pH means adding H+ to the system. Swamping your negative R groups with positively charged hydrogen.

Question 24

T/F: protein folding occurs via hydrogen bonding between backbone atoms and weak interactions of the R groups

Answer 24

True

Question 25

what kinds of bonds can aspartic acid make?

Answer 25

ionic, hydrogen , LDF’s

Question 26

Weak acids and bases are good at buffering pH changes if acid or base is added because

Answer 26

they easily protonate and deprotonate.

Question 27

a buffer is most effective near:

Answer 27

its pka

Question 28

Any given amino acid molecule in solution is constantly losing and gaining protons so as to shift among the forms drawn below. However, more time is spent in this form: ____ when the pH is near 7. If the pH is made very acidic (more H+) then more time is spent: ____

Answer 28

1. zwitter ion
2. with H+ on both the amine and carboxyl ends because there is more H+ available.

Question 29

histidine structure- why is it special?

Answer 29

aromatic

Question 30

STY CNQ- what group are these?

Answer 30

polar uncharged

Question 31

what are some essential amino acids

Answer 31

histidien, menthionine, leucine, valine, tryptophan

Question 32

secondary protein structure

Answer 32

‘local interactions’ alpha helix, beta pleated sheet,

hydrogen bonding between polar backbone

Question 33

tertiary protein structure

Answer 33

overall 3-D shape. results from all R group and backbone interactions combined. can be globular or filamentous

Question 34

when would you have quaternary structure?

Answer 34

more than one chain of polypeptides