Chem 2B Ch. 07 Amino Acids And Proteins

Front 1

The principal classes of biomolecules are:

Back 1

proteins, carbohydrates, lipids, and nucleic acids

Front 2

Proteins are polymers of:

Back 2

amino acids

Front 3

Every amino acid contains:

Back 3

an amine group (-NH₂), a carboxyl group (-COOH), and an R group called a side chain all bonded to the same carbon atom.

Front 4

The carbon that the amine group (-NH₂), a carboxyl group (-COOH), and an R group called a side chain are all bonded to is called:

Back 4

the alpha carbon (α-carbon)

Front 5

A large biological molecule made of many amino acids linked together through amide (peptide) bonds.

Back 5

Protein

Front 6

A molecule that contains both an amino group and a carboxylic acid functional group.

Back 6

Amino acid

Front 7

The variable group bonded to the central carbon atom in an amino acid; different in different amino acids.

Back 7

Side chain (amino acid)

Front 8

An amino acid in which the amino group is bonded to the carbon atom next to the -COOH group.

Back 8

α-amino acid

Front 9

The α-carbon is:

Back 9

the central carbon in an amino acid to which the amine, carboxyl, and side-chain R groups attach.

Front 10

An amide bond that links two amino acids together.

Back 10

Peptide bond

Front 11

Two amino acids, three amino acids, and many amino acids are called:

Back 11

a dipeptide, tripeptide, and a polypeptide respectively

Front 12

What reaction forms a peptide bond? What groups react?

Back 12

The amine group of one amino acid replaces the hydroxyl group of the carboxylic group on another. An H from the amine and -OH from carboxylic acid form water.

Front 13

The sequence of amino acids in a protein chain.

Back 13

Primary structure

Front 14

The regular and repeating spatial organization of neighboring segments of single protein chains.

Back 14

Secondary Structure

Front 15

The overall shape of a protein molecule produced by regions of secondary structure combined with the overall bending and folding of the protein chain.

Back 15

Tertiary structure

Front 16

The overall structure of proteins composed of more than one polypeptide chain.

Back 16

Quaternary structure

Front 17

What distinguishes one amino acid from another?

Back 17

their different side chains

Front 18

What are some different functions of proteins in the body?

Back 18

-structure and support
-hormones and enzymes
-storage and transport
-protection (immunity)

Front 19

All of the proteins in living organisms are made from _____ amino acids.

Back 19

20 α-amino acids

Front 20

19 of the amino acids differ in _______, but one of the them, _______ differs in:

Back 20

19 of the amino acids differ in the side chain, but one of the them, proline differs in that it is a secondary amine whose N and α-carbon atoms are joined in a five-membered ring.

Front 21

The 20 α-amino acids that make up proteins are classified as:

Back 21

neutral, acidic, or basic, depending on the nature of their side chains.

Front 22

Neutral amino acids are further divided into:
How many of the amino acids are neutral?

Back 22

those with polar or non-polar side chains
15 are neutral

Front 23

What is of central importance in determining the shapes and functions of proteins?

Back 23

Intermolecular forces

Front 24

Non-polar side chains are described as:

Back 24

hydrophobic

Front 25

Polar, acidic, and basic side chains are described as:

Back 25

hydrophilic

Front 26

Forces of attraction other than covalent bonds that can act between molecules or within molecules.

Back 26

Noncovalent forces

Front 27

"Water-fearing"; does not dissolve in water:

Back 27

hydrophobic

Front 28

"Water-loving"; dissolves in water.

Back 28

hydrophilic

Front 29

Amino acids contain both an acidic group (carboxyl group) and a basic group (amine group), can they undergo an intramolecular acid-base reaction?

Back 29

yes, the result is a transfer of the hydrogen from the hydroxyl group of the carboxylic acid to the amine group.

Front 30

The intramolecular acid base reaction of an amino acid forms a:

Back 30

dipolar ion, an ion that has one positive charge (ammonium ion) and one negative charge (carboxylic acid anion).

Front 31

Dipolar ions are known as:

Back 31

zwitterions

Front 32

What is the charge of zwitterions?

Back 32

neutral

Front 33

A neutral dipolar ion that has one positive charge and one negative charge.

Back 33

zwitterion

Front 34

Because they are zwitterions, amino acids have many of the physical properties of:

Back 34

salts

Front 35

What are the properties of amino acids?

Back 35

-can form crystals
-high melting points
-soluble in water, not soluble in hydrocarbons solvents

Front 36

In acidic solutions, zwitterions:

Back 36

ACCEPT protons on the carboxylic acid anion, leaving only the positively charged amine group.

Front 37

In basic solutions, zwitterions:

Back 37

LOSE protons on the amine cation, leaving only the negatively charged carboxylic acid anion group.

Front 38

Draw the reaction of a NH₃⁺CH(R)COO⁻ + H⁺

Back 38

NH₃⁺CH(R)COO⁻ + H⁺ → NH₃⁺CH(R)COOH

Front 39

Draw the reaction of a NH₃⁺CH(R)COO⁻ + OH⁻

Back 39

NH₃⁺CH(R)COO⁻ + OH⁻ → NH₂CH(R)COO⁻ + HOH

Front 40

Do amino acids ever exist in a completely un-ionized form in either the solid state or in aqueous solution?

Back 40

No

Front 41

THe charge of an amino acid molecule at any given moment depends on:

Back 41

the particular amino acid and the pH of the solution.

Front 42

Define the isoelectric point (pl)

Back 42

The pH at which the net positive and negative charges are evenly balanced for a particular amino acid.

Front 43

The point at which the net charge of all the molecules of a particular amino acid in a pure sample is zero.

Back 43

isoelectric point (pl)

Front 44

Is the (pl) the same for all amino acids?

Back 44

No, the (pl) is different for each amino acid, due to differences in their side chains.

Front 45

Pl influences:

Back 45

protein stability and determines which amino acids in an enzyme participate.

Front 46

The acidic and basic side chains are particularly important because:

Back 46

at physiological pH, these groups are fully charged and can participate not only in ionic bonds within a protein chain but can also transfer H⁺ from one molecule to another during reactions.

Front 47

Which amino acids are hydrophilic and which are hydrophobic?

Back 47

The polar, acidic, and basic side chains are hydrophilic since they can interact with water.
The non-polar side chains are hydrophobic since they cannot interact with water.

Front 48

Describe hydrolysis:

Back 48

A reaction in which a bond or bonds are broken and the H- and -OH of water add to the atoms of the broken bond or bonds.

Front 49

What reaction is involved in the formation of peptide bonds?

Back 49

amide formation where: an H from the amine is added to the carboxyl group -OH forming water as the N-chain is added to the carbonyl group C.

Front 50

Alanine

Back 50

Ala

Front 51

Glycine

Back 51

Gly

Front 52

Isoleucine

Back 52

Ile

Front 53

Leucine

Back 53

Leu

Front 54

Methionine

Back 54

Met

Front 55

Phenylalanine

Back 55

Phe

Front 56

Proline

Back 56

Pro

Front 57

Tryptophan

Back 57

Trp

Front 58

Valine

Back 58

Val

Front 59

Asparagine

Back 59

Asn

Front 60

Cysteine

Back 60

Cys

Front 61

Glutamine

Back 61

Gln

Front 62

Serine

Back 62

Ser

Front 63

Threonine

Back 63

Thr

Front 64

Tyrosine

Back 64

Tyr

Front 65

Aspartic acid

Back 65

Asp

Front 66

Glutamic acid

Back 66

Glu

Front 67

Arginine

Back 67

Arg

Front 68

Histidine

Back 68

His

Front 69

Lysine

Back 69

Lys

Front 70

Having right or left-handedness with two different mirror image forms that cannot be superimposed.

Back 70

chiral

Front 71

The opposite of chiral; having superimposable mirror images and thus no right or left-handedness.

Back 71

achiral

Front 72

Define a chiral carbon atom aka chiral center:

Back 72

A carbon atom bonded to four different groups.

Front 73

The two mirror image forms of a chiral molecule.

Back 73

Enantiomers (optical isomers).

Front 74

Define stereoisomers:

Back 74

Isomers that have the same molecular and structural formulas but different spatial arrangements of their atoms.

Front 75

Does the presence of a chiral atom always produce a chiral molecule?

Back 75

yes

Front 76

Pairs of enantiomers always differ in:

Back 76

their affects on polarized light and in how they react with other molecules that are chiral.

Front 77

Pairs of enantiomers often differ in:

Back 77

their biological activity, odors, tastes or activity as drugs.

Front 78

Of the 20 alpha amino acids, how many are chiral?

Back 78

19 of them; only glycine is achiral.

Front 79

Even though the 19 chiral α-amino acids can exist as either D- or L- enantiomers, nature exclusively uses only:

Back 79

L-amino acids for making proteins

Front 80

Which amino acids have abbreviations that are not the first 3 letters?

Back 80

G.A.I.T.
Glutamine Gln
Asparagine Asn
Isoleucine Ile
Tryptophan Trp

Front 81

How do you determine if a molecule is chiral?

Back 81

Make a list of the different carbon atoms and the groups bonded to them. If a carbon has 4 different groups, it is chiral.

Front 82

Define primary protein structure:

Back 82

The sequence in which amino acids are linked by peptide bonds in a protein.
ie.. Alanine + Serine → Alanylserine but,
Serine + Alanine → Serylalanine

Front 83

In the primary structure, the electrons of each carbonyl group double bond are shared to a considerable extent with:

Back 83

the adjacent C-N bond (the α-carbon-nitrogen bond).

Front 84

Does the C-N unit that shares electrons with the carbonyl group double bond carbons rotate?

Back 84

No, this sharing of bonds makes it sufficiently rigid that there is no rotation.

Front 85

One planar unit consists of:

Back 85

the carbonyl carbon, -NH group bonded to it, and the two adjacent α-carbons.

Front 86

Are the side chains on the same or opposite side of the backbone of the primary structure?

Back 86

On opposite sides.

Front 87

The amino acid with the free -NH₃⁺ group at the end of a protein.

Back 87

Amino-terminal (N-terminal) amino acid.

Front 88

The amino acid with the free -COO⁻ group at the end of a protein.

Back 88

Carboxyl-terminal (C-terminal) amino acid

Front 89

An amino acid unit in a polypeptide.

Back 89

Residue

Front 90

By convention, peptides and proteins are always written with the amino-terminal amino acid on the ______ and the carboxyl-terminal amino acid on the _______.

Back 90

left; right

Front 91

The individual amino acids joined in the chain are called:

Back 91

residues

Front 92

How are peptides named?

Back 92

Starting at the N-terminal amino acid and ending at the C-terminal amino acid, all residues are named in order. The residue name endings are changed from -ine to -yl for all except the C-terminal amino acid.
They can also be named by listing their 3-letter abbreviation in order, separated by hyphens.
ie... serine + tyrosine + glycine = seryltyrosylglycine or Ser-Tyr-Gly.

Front 93

In L-forms of amino acids, the amino group is on the:

Back 93

left

Front 94

When drawing the 3-D primary protein structure of a L-hand form, the H atoms on the top are on the ____ side and point:

Back 94

left side; away from you

Front 95

When drawing the 3-D primary protein structure of a L-hand form, the H atoms on the bottom are on the ____ side and point:

Back 95

right side; toward you

Front 96

The planar unit square connects:

Back 96

The α-carbon, carboxyl O, -NH group H, and second α-carbon.

Front 97

Where there are ionized acidic and basic side chains, the attraction between their positive and negative charges creates:

Back 97

salt bridges

Front 98

Where there are interactions between hydrocarbon side chains, the attraction is from:
These interactions are called:

Back 98

london-dispersion forces; hydrophobic

Front 99

What is the one type of covalent bond in the formation of protein structure?

Back 99

covalent sulfur-sulfur bonds.

Front 100

covalent sulfur-sulfur bonds are formed between these residues:

Back 100

between the thiol-containing side chains of two cysteine amino acids which form a sulfide bond.

Front 101

What are the different types of bonds that determine protein structure?

Back 101

-H bonds
-Salt bridges
-Hydrophobic interactions
-Sulfur-Sulfur bonds

Front 102

An S-S bond formed between two cysteine side chains; can join two separate peptide chains together or cause a loop in a single peptide chain.

Back 102

Disulfide bond

Front 103

Describe the reaction of a disulfide bond:

Back 103

-SH + -SH [O]⟶ S-S + HOH
Sulfide + Sulfide (with oxidizer) ⟶ Disulfide + HOH (two H's from each S add to an O from the oxidizer to form the HOH)

Front 104

In the covalent disulfide bond between two cysteine residues, if they are in different protein chains, then:

Back 104

the chains become linked together

Front 105

In the covalent disulfide bond between two cysteine residues, if they are in the same protein chain, then:

Back 105

a loop is formed in the chain

Front 106

The regular and repeating structural patterns (ie.. α-helix, β-sheet) created by hydrogen bonding between backbone atoms in neighboring segments of protein chains.

Back 106

Secondary protein structure

Front 107

Secondary protein structure in which a protein chain forms a right-handed coil stabilized by hydrogen bonds between peptide groups along its backbone.

Back 107

Alpha helix (α-helix)

Front 108

Secondary protein structure in which adjacent protein chains either in the same molecule or in different molecules are held together by hydrogen bonds along the backbones, forming a flat sheet-like structure.

Back 108

Beta-sheet (β-sheet

Front 109

A tough, insoluble protein whose protein chains form fibers or sheets.

Back 109

Fibrous protein

Front 110

A water-soluble protein whose chain is folded in a compact shape with hydrophilic groups on the outside.

Back 110

Globular protein

Front 111

Define secondary protein structure:

Back 111

The spatial arrangement of the polypeptide backbones of proteins.

Front 112

The secondary structure includes two kinds of repeating patterns known as:

Back 112

α-helix and β-sheet

Front 113

In both α-helix and β-sheet patterns, what holds the polypeptide in place?

Back 113

H bonding between backbone atoms

Front 114

In both α-helix and β-sheet patterns, the H bonds connect:

Back 114

the carbonyl oxygen atom of one peptide unit to the amide H atom of another.

Front 115

an α-helix is:
and resembles:

Back 115

A single protein chain coiled in a spiral with a right-handed (clockwise) twist. It resembles a coiled telephone cord.

Front 116

What is the spatial arrangement of the H bonds and amino acid R-groups in the α-helix?

Back 116

The H-bonds lie vertically along the helix and the amino acid R groups extend to the outside of the coil.

Front 117

What is the spatial arrangement of the H bonds and amino acid R-groups in the β-sheet?

Back 117

H-bonds connect different protein chains, which are fully extended, with their R-groups extending above and below the sheet.

Front 118

Proteins are classified in several ways, one of which is to identify them as either:

Back 118

fibrous or globular proteins.

Front 119

How are the N-terminals and C-terminals arranged among the protein chains in a β-sheet?

Back 119

They run in an antiparallel arrangement

Front 120

Which structure is primarily responsible for the nature of fibrous proteins?

Back 120

secondary protein structure

Front 121

The way in which an entire protein chain is coiled and folded into its specific 3-dimentional shape.

Back 121

Tertiary protein structure

Front 122

A protein with the shape (secondary, tertiary, and quaternary structure) in which it exists naturally in living organisms.

Back 122

Native protein

Front 123

Secondary structure depends mainly on attraction between ___________, where tertiary structure depends mainly on attraction between ____________.

Back 123

Secondary structure depends mainly on attraction between BACKBONE ATOMS, where tertiary structure depends mainly on attraction between AMINO ACID SIDE CHAINS THAT ARE FAR APART ALONG THE SAME BACKBONE.

Front 124

Define a Simple protein:

Back 124

A protein composed of only amino acid residues.

Front 125

Define a Conjugated protein:

Back 125

A protein that incorporates one or more non-amino acid units in its structure.

Front 126

Which structure determines the overall shape of fibrous proteins? Which structure determines the overall shape of globular proteins?

Back 126

Secondary structure determines the shape of fibrous proteins. Tertiary structure determines the overall shape of globular proteins.

Front 127

A simple protein is made of nothing but __________, while a conjugated protein has:

Back 127

A simple protein is made of nothing but amino acid residues, while a conjugated protein has something else in its structure, i.e... myoglobin which has a heme group in its structure.

Front 128

The way in which two or more protein chains aggregate to form large, ordered structures.

Back 128

Quaternary protein structure

Front 129

Collagen and Hemoglobin both have this structure:

Back 129

quaternary protein structure

Front 130

The most abundant of all proteins in mammals is:

Back 130

collagen; making up 30% or more of the total.

Front 131

Define primary structure:

Back 131

the sequence of amino acids connected by polypeptide bonds.

Front 132

Define secondary structure:

Back 132

the arrangement in space of the polypeptide chain (α-helix and β-sheet)

Front 133

Define tertiary structure:

Back 133

the folding of a protein into a specific 3-D shape

Front 134

Define quaternary structure:

Back 134

two or more protein chains assembled in a large 3-D structure.

Front 135

Describe the bonds involved in each structure.

Back 135

Primary = peptide bonds
Secondary = H-bonds between backbone carbonyl oxygen and amine hydrogens.
Tertiary = interactions between amino acid side chains, (in some cases disulfide bonds), that can be quite far apart along the backbone.
Quaternary = noncovalent interactions.

Front 136

The reverse of protein synthesis is:

Back 136

protein hydrolysis

Front 137

Describe the reaction of protein hydrolysis:

Back 137

Protein reacts with H³O⁺ or enzyme which breaks peptide bonds and adds an -OH group to the carboxyl carbon and an H⁺ to the amine.

Front 138

The loss of secondary, tertiary, or quaternary protein structure due to disruption of non covalent interactions and/or disulfide bonds that leaves peptide bonds and primary structure intact.

Back 138

Denaturation

Front 139

Denaturation is accompanied by changes in:

Back 139

physical, chemical, and biological properties.

Front 140

Is solubility usually increased or decreased by denaturation?

Back 140

decreased

Front 141

What agents cause denaturation?

Back 141

heat, mechanical agitation, detergents, organic solvents, extremely acidic or basic pH, and inorganic salts.

Front 142

How does heat denature proteins?

Back 142

It breaks side-chain interactions in globular proteins.

Front 143

How does Mechanical agitation denature proteins?

Back 143

stiffens the proteins

Front 144

How do Detergents denature proteins?

Back 144

disrupts hydrophobic side chains

Front 145

How do Organic polar solvents denature proteins?

Back 145

Polar solvents such as acetone and ethanol interfere with H bonding by competing for bonding sites.

Front 146

How do Inorganic salts denature proteins?

Back 146

by disrupting salt bridges