Week 4

Question 1

The ____ ____ of amino acids in a protein determine the shape and function of the protein.

Answer 1

exact order

Question 2

Describe the structure of an amino acid.

Answer 2

It consists of a central carbon atom, called the 𝛼 (alpha) carbon, connected by covalent bonds to four different chemical groups: an amino group (–NH2, a carboxyl group (–COOH), a hydrogen atom (–H), and a variable side chain or R group.

Question 3

define alpha carbon

Answer 3

The central carbon atom of each amino acid.

Question 4

define amino group

Answer 4

NH2; a nitrogen atom bonded to two hydrogen atoms, covalently linked to the central carbon atom of an amino acid.

Question 5

define carboxyl group

Answer 5

COOH; a carbon atom with a double bond to oxygen and a single bond to a hydroxyl group.

Question 6

define side chain or R group

Answer 6

A chemical group attached to the central carbon atom of an amino acid, whose structure and composition determine the identity of the amino acid.

Question 7

What generally makes amino acids hydrophobic?

Answer 7

They are hydrophobic when their R group is a non polar hydrocarbon chain or ring

Question 8

What causes the aggregation of hydrophobic amino acids?

Answer 8

The tendency of water to hydrogen bonds with itself and because of weak van der waals forces (temporary dipole interactions)

Question 9

Why are hydrophobic amino acids usually burried deep in the interior of folded proteins?

Answer 9

to keep them away from water

Question 10

Why are hydrophilic amino acids usually located on the outside surface of folded proteins?

Answer 10

Because the R groups may gain or lose an electron due to the pH of the cell causing them to interact with water and therefore want to be near the surface

Question 11

Do charged R groups on the surface of proteins bond?

Answer 11

yes they bond with one another and with other charged molecules which is why that can associate with one another or other macromolecules such as DNA

Question 12

The R groups of the basic and acidic amino acids are ____ _____

Answer 12

strongly polar

Question 13

Basic R groups ____ a proton to become ____ charged in the pH of the cell

Answer 13

gain

positively

Question 14

Acidic R groups ____ a proton to become ____ charged in the pH of the cell

Answer 14

lose

negatively

Question 15

What make glycine different from other amino acids?

Answer 15

It has H as an R group so it is symmetric, non polar, and smaller than other amino acids. The H as an R group allows for free rotation around the C-N bond because H group is not big enough to interact enough with the other hydrogen on the N

Question 16

How is proline different from other amino acids?

Answer 16

Its R group is bonded back to the amino group causing a kink or bend in peptide chains which puts restraints on protein folding

Question 17

How is cytosine different from other amino acids?

Answer 17

the sulfur in the R group allows it to make disulfide bonds which are stronger than the ionic interactions of other pairs of amino acids

Question 18

Define peptide bond

Answer 18

A covalent bond that links the carbon atom in the carboxyl group of one amino acid to the nitrogen atom in the amino group of another amino acid.

Question 19

What is released when a peptide bind is formed?

Answer 19

water

Question 20

what is the name of a C double bonded to and O?

Answer 20

carbonyl

Question 21

what is the name of an H bonded to an N

Answer 21

amide group

Question 22

Polypeptides have an ____ end that is ____ charged and a _____ end that is _____ charged

Answer 22

amino, positively

carboxyl, negatively

Question 23

Define amino end

Answer 23

The end of a polypeptide chain that has a free amino group.

Question 24

Define Carboxyl end

Answer 24

The end of a polypeptide chain that has a free carboxyl group.

Question 25

Define residues

Answer 25

In the context of protein synthesis, any of the amino acids that is incorporated into a protein.

Question 26

What are amino acids which are Incorporated in the protein called?

Answer 26

residues

Question 27

Define primary structure

Answer 27

The sequence of amino acids in a protein.

Question 28

The sequence of amino acids in a polypeptide is the proteins ____ _____

Answer 28

primary structure

Question 29

Define secondary structure

Answer 29

The structure formed by interactions between stretches of amino acids in a protein.

Question 30

What is the secondary structure of a protein a result of?

Answer 30

interactions between stretches of amino acids

Question 31

What is the tertiary structure of a protein a result of?

Answer 31

long-range itneractions between the secondary structures

Question 32

Define tertiary structure

Answer 32

The overall three-dimensional shape of a protein, formed by interactions between secondary structures.

Question 33

Define quartenary structure

Answer 33

The structure that results from the interactions of several polypeptide chains.

Question 34

The function of a protein is dependent on….?

Answer 34

the 3D shape of the protein

Question 35

What are the two types of secondary structures found in found in different proteins?

Answer 35

alpha helix and beta sheet

Question 36

Secondary structures are a result of ____ bonding between…?

Answer 36

hydrogen

the carbonyl group of one amino acid and the amide group of another amino acid

Question 37

B sheets are typically denoted by…?

Answer 37

Broad arrows, where the direction of the arrow goes from the amino end to the carboxyl end

Question 38

Tertiary structure is determined by the spatial distribution of?

Answer 38

Hydrophilic and hydrophobic R groups along the molecule and the various attractions between R groups

Question 39

Define denaturation

Answer 39

The unfolding of proteins by chemical treatment or high temperature; the separation of paired, complementary strands of nucleid acid.

Question 40

When a protein is denatured what happens to the R group?

Answer 40

It loses its functional activity

Question 41

Quarternary structures are made up of…?

Answer 41

Two or more proteins that are complete and fully functional in their tertiary structure

Question 42

Define chaperone (in terms of protein folding)

Answer 42

A protein that helps shield a slow-folding protein until it can attain its proper three-dimensional structure.