Lecture 2

Question 1

what are the four steps of protein formation?

Answer 1

1. primary
2. secondary
3. tertiary
4. quaternary

Question 2

what are proteins made of?

Answer 2

amino acids

Question 3

what is the part that varies within amino acid structures?

Answer 3

the R group

Question 4

what are the four main categories of amino acids?

Answer 4

acidic, basic, nonpolar, and uncharged polar amino acids

Question 5

which type of amino acids makes disulphide bonds?

Answer 5

cysteine

Question 6

how are peptide bonds formed?

Answer 6

when the oxygen of a carboxyl group of one amino acid reactions with the hydrogen of the amino group of an adjacent amino acid

Question 6

what are the ends of polypeptide chains like?

Answer 6

an N terminus or amino group on one end and a C terminus or carboxyl group on the other end

Question 7

why does the difference in primary amino acid sequences matter?

Answer 7

the unique sequence determines the unique structure and function of a protein

Question 7

what is an alpha helix?

Answer 7

a spiral staircase protein structure

Question 8

how are the hydrogen bonds in the alpha helix formed in terms of carbon number?

Answer 8

between every four amino acids

Question 9

what are beta pleated sheets?

Answer 9

a flat arrangement of amino acids

Question 10

how are hydrogen bonds formed in alpha helixes?

Answer 10

the hydrogen of one amino acid reacts with the oxygen in the carbonyl of an adjacent amino acid on the same strand

Question 11

what are the R groups like in beta pleated sheets?

Answer 11

they alternate pointing up and down

Question 12

what does antiparallel mean?

Answer 12

when the amino acids on one strand run in one direction and the amino acids on another strand run in the opposite direction

Question 12

what are the two types of beta-pleated sheets?

Answer 12

1. anti parallel
2. parallel

Question 13

what does parallel mean?

Answer 13

amino acids on both strands run in the same direction

Question 14

how are hydrogen bonds formed in beta-pleated sheets?

Answer 14

the hydrogen of one amino acid reacts with the oxygen in the carbonyl of an adjacent amino acid on the opposite strands

Question 14

what is the coiled coil?

Answer 14

when structures of alpha helixes wind around one another

Question 15

what is the property of coiled coils?

Answer 15

amphipathic

Question 16

what does amphipathic mean?

Answer 16

a molecule that has both hydrophobic and hydrophilic parts

Question 17

what is the tertiary stage of protein formation?

Answer 17

a 3D folded structure of a protein

Question 18

what forces hold the tertiary structure together?

Answer 18

1. hydrophobic forces
2. non-covalent parts
3. disulphide bonds

Question 19

what are non-covalent bonds?

Answer 19

bonds within a protein formed by weak attractions

Question 20

what are hydrophobic interactions?

Answer 20

part of the protein that fears water

Question 21

what are disulphide bonds?

Answer 21

a bond that forms between the sulphur of two cysteine groups in two different amino acids

Question 22

why do proteins fold in a certain way in terms of energy?

Answer 22

they fold in a certain way that makes them most energetically stable

Question 23

what proteins help in the shaping process of making proteins?

Answer 23

chaperone proteins

Question 24

how many domains do eukaryotic proteins have?

Answer 24

two or more

Question 25

what are protein domains?

Answer 25

a specialized part of the tertiary structure that is semi-independent

Question 26

what are domains in eukaryotic proteins connected by?

Answer 26

intrinsically disordered sequences

Question 27

what are protein families?

Answer 27

proteins that have similar amino acid sequences and 3D structures

Question 28

how do protein domains play a role in protein evolution?

Answer 28

protein domains can be rearranged and altered during protein evolution

Question 29

what do proteins in protein famlies do in terms of evolution?

Answer 29

evolve to have different structures

Question 30

how are proteins in protein families similar in terms of domain structure?

Answer 30

they have similar domain structures even though they might have different overall structures

Question 31

what is hemoglobin made of?

Answer 31

two subunits, 2 alpha and 2 beta

Question 32

what are examples of different multiprotein complexes?

Answer 32

1. actin filament;; structure with the same subunits 2. viruses and ribosomes: structures made from different protein and DNA 3. molecular machines; structures made of many different proteins to perform complex tasks

Question 32

What is each subunit like in hemoglobin?

Answer 32

the subunits function independently

Question 32

what are ways to study a protein in terms of purification?

Answer 32

electrophoresis and chromatography

Question 33

what is a way to study the protein in terms of amino acid sequences?

Answer 33

mass spectroscopy