Chapter 3: Protein Structure and Function

Question 1

building blocks of proteins in living organisms

Answer 1

amino acids

Question 2

how many amino acids can be found in nature

Answer 2

500 amino acids

Question 3

number of amino acids the human genetic code directly encodes

Answer 3

20 amino acids

Question 4

must be obtained from the diet

Answer 4

essential amino acids

Question 5

can be synthesized in the body

Answer 5

non-essential amino acids

Question 6

aliphatic amino acids

Answer 6

1. alanine
2. glycine
3. isoleucine
4. leucine
5. proline
6. valine

Question 7

aromatic amino acids

Answer 7

1. phenylalanine
2. tryptophan
3. tyrosine

Question 8

acidic amino acids

Answer 8

1. aspartic acid
2. glutamic acid

Question 9

basic amino acids

Answer 9

1. arginine
2. histidine
3. lysine

Question 10

hydroxylic amino acids

Answer 10

1. serine
2. threonine

Question 11

suflur-containing amino acids

Answer 11

1. cysteine
2. methionine

Question 12

amidic amino acids

Answer 12

1. asparagine
2. glutamine

Question 13

What are the nine (9) essential amino acids? (PriVaTe ThIM HiLL)

Answer 13

1. Phenylalanine
2. Valine
3. Tryptophan
4. Threonine
5. Isoleucine
6. Methionine
7. Histidine
8. Lysine
9. Leucine

Question 14

What are the 11 non-essential amino acids?
(Almost All Girls Go Crazy After Going To A Pretty Shop)

Answer 14

1. Alanine
2. Arginine
3. Glycine
4. Glutamine
5. Cysteine
6. Asparagine
7. Glutamic Acid
8. Tyrosine
9. Aspartic Acid
10. Proline
11. Serine

Question 15

often referred to as the 21st amino acid

Answer 15

Selenocysteine

Question 16

glycine

Answer 16

gly

Question 17

alanine

Answer 17

ala

Question 18

valine

Answer 18

val

Question 19

leucine

Answer 19

leu

Question 20

isoleucine

Answer 20

Ile

Question 21

methionine

Answer 21

met

Question 22

tryptophan

Answer 22

trp

Question 23

phenylalanine

Answer 23

phe

Question 24

proline

Answer 24

pro

Question 25

serine

Answer 25

ser

Question 26

threonine

Answer 26

thr

Question 27

cysteine

Answer 27

cys

Question 28

tyrosine

Answer 28

tyr

Question 29

asparagine

Answer 29

asn

Question 30

glutamine

Answer 30

gln

Question 31

aspartic acid

Answer 31

asp

Question 32

glutamic acid

Answer 32

glu

Question 33

lysine

Answer 33

lys

Question 34

arginine

Answer 34

arg

Question 35

histidine

Answer 35

his

Question 36

where is the word protein derived from

Answer 36

Greek, proteios

Question 37

proteios

Answer 37

first

Question 38

What are proteins

Answer 38

• large molecules made up of chains of amino acids
• found in every cell in the body
• involved in most of body’s functions and life processes
• sequence of amino acids is determined by DNA

Question 39

Different classes of proteins

Answer 39

1. structural
2. contractile
3. transport
4. storage
5. hormone
6. enzyme
7. protection

Question 40

provide structural components

Answer 40

structural protein

Question 41

examples of structural protein

Answer 41

1. collagen
2. keratin

Question 42

collagen examples

Answer 42

• tendons
• cartilage

Question 43

keratin examples

Answer 43

• hair
• skin
• wool
• nails

Question 44

make muscles move

Answer 44

contractile protein

Question 45

examples of contractile protein

Answer 45

1. myosin
2. actin

Question 46

myosin and actin

Answer 46

contract muscle fibers

Question 47

carry essential substances throughout the body

Answer 47

transport protein

Question 48

examples of transport proteins

Answer 48

1. hemoglobin
2. lipoproteins

Question 49

hemoglobin

Answer 49

transports oxygen

Question 50

lipoproteins

Answer 50

transports lipids

Question 51

store nutrients

Answer 51

storage proteins

Question 52

examples of storage proteins

Answer 52

1. casein
2. ferritin

Question 53

casein

Answer 53

stores protein in milk

Question 54

ferritin

Answer 54

stores iron in spleen and liver

Question 55

regulate body metabolism and the nervous system

Answer 55

hormone

Question 56

examples of hormone

Answer 56

1. insulin
2. growth hormone

Question 57

insulin

Answer 57

regulates blood glucose level

Question 58

growth hormone

Answer 58

regulates body growth

Question 59

catalyze biochemical reactions in the cells

Answer 59

enzymes

Question 60

example of enzymes

Answer 60

1. sucrase
2. trypsin

Question 61

sucrase

Answer 61

catalyzes hydrolysis of sucrose

Question 62

trypsin function

Answer 62

catalyzes hydrolysis proteins

Question 63

recognize and destroy foreign substances

Answer 63

protection proteins

Question 64

example of protection protein

Answer 64

immunoglobulins

Question 65

immunoglobulins

Answer 65

stimulate immune responses

Question 66

structure, characteristic, and classes of amino acids differ in

Answer 66

R groups

Question 67

amino acids vary in

Answer 67

1. size
2. shape
3. charge
4. polarity
5. solubility in water

Question 68

attached to four different substituents

Answer 68

α-Carbon

Question 69

Four substiuents of amino acids

Answer 69

1. hydrogen atom
2. carboxyl group
3. amino group
4. R group

Question 70

nonionic form:
amino group

Answer 70

NH2

Question 71

nonionic form:
carboxyl group

Answer 71

COOH

Question 72

Zwitterionic form:
amino group

Answer 72

NH3+

Question 73

Zwitterionic form:
carboxyl group

Answer 73

COO-

Question 74

two forms of amino acid

Answer 74

1. nonionic form
2. Zwitterionic form

Question 75

compounds that form amino acids

Answer 75

• amine
• acid

Question 76

α-amino acids

Answer 76

amine is adjacent to the carboxylate group

Question 77

19 out of the 20 amino acids are __

Answer 77

stereoisomers

Question 78

amino acid that is not a stereoisomer

Answer 78

Glycine

Question 79

compounds that have the same constitution but differ in the spatial arrangement of their atoms

Answer 79

stereoisomers

Question 80

α-carbon of amino acids is __

Answer 80

chiral

Question 81

chiral molecules

Answer 81

nonsuperimposable on their mirror images

Question 82

achiral molecules

Answer 82

superimposable on their mirror images

Question 83

have the hydroxy group attached to the left side of the asymmetric carbon furthest from the carbonyl

Answer 83

L isomers

Question 84

have the hydroxy group on the right side

Answer 84

D isomers

Question 85

where do the differences of amino acids depend upon

Answer 85

side-chain R groups

Question 86

Amino acids form classes based on what?

Answer 86

polarity of side chains

Question 87

Nonpolar

Answer 87

hydrophobic R groups

Question 88

Polar neutral

Answer 88

• high affinity for water
• not ionic at pH

Question 89

Polar acidic

Answer 89

• ionized carboxyl groups
• negatively charged

Question 90

Polar basic

Answer 90

• basic as side chain reacts with water to release hydroxide ion
• positively charged

Question 91

What are the polar uncharged amino acids

Answer 91

1. serine
2. threonine
3. asparagine
4. glutamine
5. tyrosine
6. cysteine

Question 92

R groups of polar uncharged amino acids

Answer 92

• OH
• amide group
• sulfhydryl/ thiol groups
• H-bond with water

Question 93

where are polar uncharged amino acids found

Answer 93

surface of globular proteins

Question 94

polar uncharged amino acids are __ in aqueous solutions

Answer 94

soluble

Question 95

bears hydroxylic R group

Answer 95

• serine
• threonine

Question 96

has amide-bearing side chain

Answer 96

• asparagine
• glutamine

Question 97

• has a phenolic group
• together with aromatic groups of F and W, acounts for most of UV absorbance and fluorescence exhibited by proteins

Answer 97

tyrosine

Question 98

tyrosine account for most of what

Answer 98

• UV absorbance
• fluorescence

exhibited by proteins

Question 99

forms a disulfide bond to another residue through oxidation of their thiol groups

Answer 99

cysteine

Question 100

how does the cysteine form a disulfide bond to another

Answer 100

through oxidation of thiol groups

Question 101

what is formed between two cysteine residue after oxidaton of their thiol groups

Answer 101

disulfide bond

Question 102

non-polar/hydrophobic amino acids

Answer 102

aliphatic
1. glycine
2. alanine
3. valine
4. leucine
5. isoleucine
6. methionine
7. proline

aromatic
1. phenylalanine
2. tryptophan

Question 103

aliphatic non-polar/hydrophobic amino acids

Answer 103

1. glycine
2. alanine
3. valine
4. isoleucine
5. leucine
6. proline
7. methionine

Question 104

aromatic non-polar/hydrophobic amino acid

Answer 104

1. phenylalanine
2. tryptophan

Question 105

where are non-polar/hydrophobic amino acids found

Answer 105

• globular proteins
• insoluble core

Question 106

has the smallest possible side chain, an H atom

Answer 106

glycine

Question 107

has methyl group -CH3

Answer 107

alanine

Question 108

has aliphatic hydrocarbon side chain

Answer 108

valine

Question 109

has isomeric butyl groups

Answer 109

• leucine
• isoleucine

Question 110

has thiol ether side chain that resembles an n-butyl group in many of its physical properties

Answer 110

methionine

Question 111

methionine: C and S have nearly equal __ and S is about the size of a __ __

Answer 111

• electronegativities
• methylene group

Question 112

cyclic secondary amino acid has conformational constraints imposed by the cyclic nature of its pyrrolidine side chain, which is unique among the standard amino acids

Answer 112

proline

Question 113

side chain” from the α carbon connects to the nitrogen

Answer 113

pyrrolidine loop

Question 114

has phenyl moiety

Answer 114

phenylalanine

Question 115

with indole group, contain aromatic side chains, which are characterized by bulk as well as nonpolarity

Answer 115

tryptophan

Question 116

D (position)

Answer 116

dexter (right)

Question 117

L (position)

Answer 117

laevus (left)

Question 118

electrically charged amino acids

Answer 118

Negative (acidic)
1. aspartic acid
2. glutamic acid

Positive (basic)
1. lysine
2. arginine
3. histidine

Question 119

• negatively charged above pH 3

Answer 119

• aspartic acid
• glutamic acid

Question 120

in its ionized state, aspartic acid is often referred to as what?

Answer 120

aspartate

Question 121

in its ionized state, glutamic acid is often referred to as what?

Answer 121

glutamate

Question 122

positively charged at pysiological pH values

Answer 122

• lysine
• arginine
• histidine

Question 123

what kind of side chain does lysine have

Answer 123

butylammonium side chain

Question 124

what group does arginine have

Answer 124

guanidino group

Question 125

guanidino group contains __ __ __, rather than only one as in the lysine side chain, it shows a more diverse chemistry

Answer 125

two reactive nitrogens

Question 126

what does histidine carry

Answer 126

imidazolium moiety

Question 127

glycine one letter

Answer 127

G

Question 128

alanine one letter

Answer 128

A

Question 129

valine one letter

Answer 129

V

Question 130

leucine one letter

Answer 130

L

Question 131

isoleucine one letter

Answer 131

I

Question 132

methionine one letter

Answer 132

M

Question 133

proline one letter

Answer 133

P

Question 134

phenylalanine one letter

Answer 134

F

Question 135

tryptophan one letter

Answer 135

W

Question 136

serine one letter

Answer 136

S

Question 137

threonine one letter

Answer 137

T

Question 138

asparagine one letter

Answer 138

N

Question 139

glutamine one letter

Answer 139

Q

Question 140

tyrosine one letter

Answer 140

Y

Question 141

cysteine one letter

Answer 141

C

Question 142

lysine one letter

Answer 142

K

Question 143

arginine one letter

Answer 143

R

Question 144

histidine one letter

Answer 144

H

Question 145

aspartic acid one letter

Answer 145

D

Question 146

glutamic acid one letter

Answer 146

E

Question 147

Animal protein: complete

Answer 147

• egg
• milk
• meat, fish, poultry

Question 148

Animal protein: incomplete

Answer 148

gelatin (denatured collagen)

Question 149

what is missing in gelatin

Answer 149

Trp

Question 150

vegetable protein: incomplete

Answer 150

Grains
- wheat
- corn
- rice (brown, white)
- oats

Legumes
- beans
- peas

Nuts
- almonds
- walnuts

Question 151

what is missing in grains

Answer 151

lys (wheat, rice, oats)
lys, trp (corn)

Question 152

what is missing in legumes

Answer 152

met (peas)
met, trp (beans)

Question 153

what is missing in nuts

Answer 153

lys, trp

Question 154

top 10 complete vegetarian protein foods with all the essential amino acids

Answer 154

1. firm tofu
2. lentils
3. low-fat yogurt
4. cottage cheese
5. green peas
6. squash and pumpkin seeds
7. quinoa
8. peanut butter
9. eggs
10. mushrooms

Question 155

chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O)

Answer 155

peptide bond

Question 156

how is peptide bond formed

Answer 156

dehydration synthesis

Question 157

what does peptide bond have that limits rotation about this bond

Answer 157

partial double bond

Question 158

what is formed from the condensind or dehydrating of two amino acids

Answer 158

dipeptide

Question 159

amino acid with free -NH3+

Answer 159

amino terminal amino acid

Question 160

short for amino terminal amino acid

Answer 160

N-terminal

Question 161

amino acid with free -COO-

Answer 161

carboxyl terminal amino acid

Question 162

short for carboxtyl terminal amino acid

Answer 162

C-terminal

Question 163

how are amino acid structures written

Answer 163

N-terminal on the left

Question 164

unbranched chain of amino acids

Answer 164

polypeptide chain

Question 165

may consists of one or more polypeptide chains

Answer 165

protein

Question 166

read from N to C terminal

Answer 166

simple peptide

Question 167

naming:
ex. alanine

Answer 167

alanyl

Question 167

naming peptides

Answer 167

1. far AA residue retains the name of amino acids
2. all AAs (except trp) –> -ine or -ic acid is replaced by -yl
3. tryptophan –> tryptophanyl

Question 168

naming:
ex. glycine

Answer 168

glycyl

Question 169

naming:
ex. serine

Answer 169

seryl

Question 170

naming:
ex. alanine, glycine, serine

Answer 170

alanylglycylserine
(Ala-Gly-Ser)

Question 171

4 steps of writing strucutre of peptides

Answer 171

1. write backbone
2. add oxygens to carboxyl carbons, and hydrogens to amino nitrogens
3. add hydrogens to alpha-carbon
4. add side chains

Question 172

backbone of peptide

Answer 172

N-C-C-N-C-C-N-C-C

Question 173

peptide chain of nine amino acid residues

Answer 173

nonapeptide

Question 174

examples of nonapeptides

Answer 174

• oxytocin
• vasopressin

Question 175

where do oxytocin and vasopressin differ

Answer 175

amino acid position
- 3
- 8

Question 176

stimulates uterine contraction in labor

Answer 176

oxytocin

Question 177

• antidiuretic hormone
• regulates blood pressure by adjusting amount of water reabsorved by kidneys

Answer 177

vasopressin

Question 178

Variety of Functions of Peptides

Answer 178

1. hormones and pheromones
2. neuropeptides
3. antibiotics
4. protection

Question 179

hormones and pheromones

Answer 179

• insulin (think sugar)
• oxytocin (think childbirth)
• sex-peptide (think fruit fly mating)

Question 180

neuropeptides

Answer 180

substance P (pain mediator)

Question 181

antibiotics

Answer 181

• polymyxin B (Gram - bacteria)
• bacitracin (Gram + bacteria)

Question 182

ex. of toxins that protection proteins defend against

Answer 182

• amanitin
• conotoxin
• chlorotoxin

Question 183

amanitin

Answer 183

mushrooms

Question 184

conotoxin

Answer 184

cone snails

Question 185

chlorotoxin

Answer 185

scorpions

Question 186

fewer than 50 amino acids

Answer 186

peptides

Question 187

2 amino acids

Answer 187

dipeptides

Question 188

3 amino acids

Answer 188

tripeptides

Question 189

more than 10 amino acids

Answer 189

polypeptides

Question 190

more than 50 amino acids

Answer 190

proteins

Question 191

proteins are typically __ to __ amino acids linked together

Answer 191

100 - 10,000 amino acids

Question 192

how are chains of proteins synthesized

Answer 192

based on specific bodily DNA

Question 193

Functions of proteins

Answer 193

1. enzymes
2. defense proteins
3. transport proteins
4. regulatory proteins
5. structural proteins
6. movement proteins
7. nutrient proteins

Question 194

are biological catalysts

Answer 194

enzymes

Question 195

include antibodies which are specific protein molecules produced by specialized cells of the immune system in response to foreign antigens

Answer 195

defense proteins

Question 196

other term for antibodies

Answer 196

immunoglobulins

Question 197

__ has regions that precisely fit and bind to a single __

Answer 197

• antibody
• antigen

Question 198

carry materials from one place to another in the body

Answer 198

transport proteins

Question 199

• carry lipids, vitamins, minerals, and oxygen in the body
• act as pumps in cell membranes, transferring compounds from one side of the cell to the other

Answer 199

transporters

Question 200

responsible for transport and storage of oxygen in higher organisms, respectively

Answer 200

• hemoglobin
• myoglobin

Question 201

myoglobin

Answer 201

1 subunit
1 heme group

Question 202

hemoglobin

Answer 202

4 subunits
4 heme groups

Question 203

• control many aspects of cell function, including metabolism and reproduction
• we can only function within limited set of conditions

Answer 203

regulatory proteins

Question 204

where are insulin released

Answer 204

beta cells of pancreas

Question 205

where are glucagon released

Answer 205

alpha cells of pancreas

Question 206

promotes growth

Answer 206

growth hormone

Question 207

regulate blood glucose

Answer 207

insulin and glucagon

Question 208

regulates the body’s metabolic rate

Answer 208

thyroxine

Question 209

regulate blood calcium

Answer 209

• calcitonin
• parathormone

Question 210

regulates fluid and electrolyte balance

Answer 210

antidiuretic hormone

Question 211

provide mechanical support to large animals and provide them with outer coverings

Answer 211

structural proteins

Question 212

hair and fingernail are composed of what

Answer 212

keratin

Question 213

necessary for all forms of movement

Answer 213

movement proteins

Question 214

how do muscles move

Answer 214

interaction of actin and myosin proteins

Question 215

serve as sources of amino acids for embryos or infants

Answer 215

nutrient proteins

Question 216

examples of nutrient storage proteins

Answer 216

• egg albumen
• casein in milk

Question 217

Levels of protein structure

Answer 217

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

Question 218

primary structure

Answer 218

amino acid residues

Question 219

secondary structure

Answer 219

three-dimensional spatial arrangements

Question 220

tertiary structure

Answer 220

polypeptide chain

Question 221

quaternary structure

Answer 221

assembled subunits

Question 222

bond that holds primary structure

Answer 222

peptide bonds

Question 223

smalles protein

Answer 223

insulin (51 amino acids in two chains)

Question 224

what links the two chains of insulin

Answer 224

cysteine (disulfide) cross links

Question 225

bonds in secondary strucure

Answer 225

hydrogen bond
(-NH group of peptide bond and carbonyl oxygen of another peptide bond)

Question 226

two regular arrangements in secondary structure

Answer 226

1. α-Helix
2. beta sheet

Question 227

stabilized by hydrogen bonds between nearby residues

Answer 227

α-Helix

Question 228

stabilized by hydrogen bonds between adjacent segemtns that may not be nearby

Answer 228

beta sheet

Question 229

most common type of secondary structure

Answer 229

α-Helix

Question 230

shape of α-Helix

Answer 230

coiled, helical

Question 231

important features of α-Helix

Answer 231

1. amide H and carbonyl O involved in H bonds
2. carbonly O links to amide H, 4 AA away
3. H bonds parallel to long axis of helix
4. right handed
5. 5.4 angstorms repeat distance
6. 3.6 amino acids per turn

Question 232

second most common secondary structure appears similar to folds of fabric

Answer 232

β-pleated sheet

Question 233

two possible orientations of β-pleated sheet

Answer 233

1. parallel
2. antiparallel

Question 234

if the N-termini are head-to-head

Answer 234

parallel

Question 235

if the N-terminus of one chin is aligned with the C-terminus of the other

Answer 235

antiparallel

Question 236

• gives a specific three dimensional shape of the polypeptide chain
• involves interactions and cross links between different parts of peptide chain

Answer 236

tertiary structure

Question 237

tertiary structure is stabilized by what

Answer 237

1. hydrophobic and hydrophilic interactions
2. salt bridges
3. hydrogen bonds
4. disulfide bonds

Question 238

globular tertiary structure forms spontaneously and is maintained by what

Answer 238

interactions among side chains or R groups

Question 239

between two cysteine residues

Answer 239

disulfide bridges

Question 240

S-S linkage can occur within the same chain

Answer 240

intrachain

Question 241

S-S linkage can occur between 2 or more chains

Answer 241

interchain

Question 242

ionic interaction/electrostatic attraction between ionic side chains -COO- and - NH3+

Answer 242

salt bridges

Question 243

interaction between polar residue chains

Answer 243

hydrogen bonds

Question 244

interaction between nonpolar groups attracted by mutual repulsion of water

Answer 244

hydrophobic interactions

Question 245

results from the aggregation of two or more polypeptide subunits

Answer 245

quaternary structure

Question 246

fibrous protein of three polypeptides that are supercoiled like a rope

Answer 246

collagen

Question 247

globular protein with two copies of two kinds of polypeptides

Answer 247

hemoglobin

Question 248

Two major classes of protein

Answer 248

1. fibrous proteins
2. globular proteins

Question 249

• typically insoluble inw ater and serve structural roles
• 3D structure is usually long and rod shaped

Answer 249

fibrous proteins

Question 250

• coiled into compact shapes with hydrophilic outer surfaces making them water-soluble
• compact shape like a ball with irregular surfaces
• enzymes

Answer 250

globular proteins

Question 251

α-keratin function

Answer 251

tough, rigid, hard (nails, horns)

Question 252

α-keratin structure

Answer 252

• cross-linked α-helixes
• rigid linker (S–S)

Question 253

collagen function

Answer 253

tensile strength, non-stretching (tendons, cartilage)

Question 254

collagen structure

Answer 254

• cross linked triple-helixes
• flexible linker (Lys-HyLys)

Question 255

silk fibroin function

Answer 255

soft, flexible non-stretchy (egg sac, nest, web)

Question 256

silk fibroin structure

Answer 256

• non-covalently held β-sheets
• van der Waals interaction

Question 257

shape of globular proteins

Answer 257

roughly circular

Question 258

shape of fibrous proteins

Answer 258

long strands

Question 259

amino acid sequence globular

Answer 259

irregular and wide range of R groups

Question 260

amino acid sequence fibrous

Answer 260

repetitive with limited range of R groups

Question 261

function globular

Answer 261

physiological/functional

Question 262

function fibrous

Answer 262

structural

Question 263

examples of globular

Answer 263

• hemoglobin
• enzymes
• insulin
• immunoglobulin

Question 264

examples of fibrous

Answer 264

• collagen
• keratin
• myosin
• actin
• fibrin

Question 265

solubility globular

Answer 265

generally soluble in water

Question 266

solubility fibrous

Answer 266

generally insoluble in water

Question 267

chemistry of permanent waving

Answer 267

• reduce
• curl
• oxidize