Proteins

Question 1

4 parts of an amino acid

Answer 1

*all are bonded to common carbon core

1. H - hydrogen atom
2. NH2 - amino functional group
3. COOH - carboxyl functional group
4. a distinctive “R-group”

Question 2

What happens to amino acids in water?

Answer 2

They ionize due to the pH of 7

Question 3

What acts as a base in an amino acid?

Answer 3

Amino group (NH2)

Question 4

What acts as an acid in an amino acid?

Answer 4

Carboxyl group (COOH)

The two highly electronegative oxygens pull the hydrogen away

Question 5

What makes the amino acids unique?

Answer 5

The r-group

Question 6

What happens if an R-group just contains carbon and hydrogen?

Answer 6

They will not participate in many chemical reactions

Question 7

Hydrophilic R-groups

Answer 7

Polar and electrically charged

Question 8

Hydrophobic R-groups

Answer 8

Nonpolar R-groups or highly electronegative atoms capable of forming hydrogen bonds with water

Question 9

Does the R-group have a negative charge?

Answer 9

If yes, it is acidic and will lose a proton

Question 10

Does the R-group have a positive charge?

Answer 10

If yes, it is basic and will pick up a proton

Question 11

If the R-group is uncharged, does it have an oxygen atom?

Answer 11

If yes, then the highly electronegative oxygen atom will form a polar covalent bond, thus making it uncharged

Question 12

Dehydration reactions

Answer 12

also called condensation reactions

newly formed bond results in the loss of water

Question 13

What type of bond is a peptide bond?

Answer 13

Covalent

Question 14

What do peptide bonds occur between?

Answer 14

carboxyl group of one amino acid and the amino group of another amino acid

2 hydrogens from (NH2) react with one oxygen from (COOH) to form the peptide bond

Question 15

Are peptide bonds stable?

Answer 15

Yes due to the degree of electron sharing

Question 16

Residues

Answer 16

amino acids that are linked together in a chain

Question 17

R-group orientation in residue

Answer 17

Side chains (R-group) stick out which makes it possible for them to react with eachother and to react with water

Question 18

What is the directionality of the residue?

Answer 18

N-terminus (amino group) to C-terminus (carboxyl group)

Question 19

Oligopeptide

Answer 19

a polymer with fewer than 50 amino acids

Question 20

Polypeptide

Answer 20

a polymer with more than 50 amino acids

Question 21

Primary structure

Answer 21

refers to the distinct amino acid sequence

R-groups affect chemical reactivity and solubility

Question 22

Secondary structure

Answer 22

distinctively shaped sections that are stabilized by hydrogen bonding that occurs between the oxygen on the C=O group of one amino acid residue and the N-H groups on another

Question 23

a-helix

Answer 23

the polypeptide’s backbone is coiled

Question 24

B-pleated sheet

Answer 24

segments of the peptide chain fold in the same plane

Question 25

Proline

Answer 25

rarely found in a-helixes

Question 26

Tertiary structures

Answer 26

form using a variety of bonds and interactions between R-groups or between R-groups and the backbone

Question 27

Types of interactions used for tertiary structures

Answer 27

1. Hydrogen bonding 2. Hydrophobic interactions 3. van de Waals interactions 4. Covalent bonding 5. Ionic bonding

Question 28

Hydrogen bonding

Answer 28

form between polar side chains and opposite partial charges either in the peptide backbone or other R-groups

Question 29

Hydrophobic interactions

Answer 29

water molecules force the hydrophobic nonpolar side chains to merge into globular masses

Question 30

van der Waals interactions

Answer 30

once hydrophobic side chains are close to one another, electrical attractions take place constant motion of elections produces tiny asymmetry in charge this makes nonpolar molecules slightly attracted to eachother

Question 31

Covalent bonding

Answer 31

can form between two cysteines disulfide bonds create strong links

Question 32

Ionic bonding

Answer 32

form between groups that have full and opposing charges

Question 33

Quaternary structure

Answer 33

proteins that involve multiple polypeptides

Question 34

Dimers

Answer 34

proteins with two polypeptide subunits

Question 35

Macromolecular machines

Answer 35

groups of multiple proteins that assemble to carry out a particular function ex: ribsome

Question 36

Is folding spontaneous?

Answer 36

It tends to be

Question 37

Denatured

Answer 37

unfolded proteins

Question 38

How do we know that folding affects function?

Answer 38

Anfinsen studied denatured proteins and found that they could not function

Question 39

Molecular chaperones

Answer 39

special proteins that can facilitate protein folding

Question 40

Prions

Answer 40

proteins that can be induced to fold into infectious, disease causing agents shapes are different Ex: mad cow disease

Question 41

What are proteins used for?

Answer 41

``` Catalysis Defense Movement Signaling Structure Transport ```

Question 42

Active site

Answer 42

location where substrates bind to enzyme and react

Question 43

Where can hydrogen bonding occur to form the secondary structure?

Answer 43

Every 4th amino acid Between carboxyl (-) and amino (+) group