CHAPTER 3 Flashcards by Miyaki Jan Lim

Q

a compound that contains both an amino group and a carboxyl group

A

Amino acid

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Q

gives identity to amino acid

A

R group

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Q

has an amino group attached to the carbon adjacent to the carboxyl group

A

a-Amino acid

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Q

Two steroisomers of amino acids are designated

A

L- (naturally occuring ) or D-

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Q

Alanine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Ala
A

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Q

Arginine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Arg
R

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Q

Asparagine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Asn
N

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Q

Aspartic acid

Three-Letter Abbreviation
One-Letter Abbreviation

A

Asp
D

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Q

Cysteine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Cys
C

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Q

Glutamic acid

Three-Letter Abbreviation
One-Letter Abbreviation

A

Glu
E

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Q

Glutamine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Gln
Q

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Q

Glycine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Gly
G

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Q

Histidine

Three-Letter Abbreviation
One-Letter Abbreviation

A

His
H

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Q

Isoleucine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Ile
I

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Q

Leucine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Leu
L

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Q

Lysine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Lys
K

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Q

Methionine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Met
M

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Q

Phenylalanine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Phe
F

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Q

Serine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Ser
S

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Q

Threonine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Thr
T

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Q

Tryptophan

Three-Letter Abbreviation
One-Letter Abbreviation

A

Trp
W

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Q

Tyrosine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Tyr
Y

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Q

Valine

Three-Letter Abbreviation
One-Letter Abbreviation

A

Val
V

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Q

Amino acids with Nonpolar side chains

A

Ala, Val, Leu, Ile, Pro, Phe, Trp, Met

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Amino acids that contain aliphatic hydrocarbon group

Ala, Val, Leu, Ile, Pro

Amino acid that has cyclic structure

Pro

Amino acid that has hydrocarbon aromatic ring

Phe

Amino acid that has indole ring side chain, aromatic

Trp

Amino acid that has sulfur atom in side chain

Met

amino acids without charged groups on side chain exist in neutral solution as

zwitterions

amino acid found only in the thyroid gland

thyroxine

Amino acid that have Acidic Side Chains

Glu, Asp

These amino acids are negatively charged at neutral pH

Acidic Side Chains Amino Acid

Amino Acid that can lose a proton, forming a carboxylate ion

Acidic Side Chains Amino Acid

Group D: Basic side chains:

His, Lys, Arg

Amino Acid that Side chains are positively charged at pH 7

basic Side Chains Amino Acid

Arg-side chain is part of what group

guanidino group

His-side chain part of what group

imidazole group

amino acid side chain with NH3 group is attached to an aliphatic hydrocarbon chain

Lys-side chain

The average pKa of an a-carboxyl group is ______________, which makes them considerably stronger acids than acetic acid (pKa 4.76)

2.19

the greater acidity of the amino acid carboxyl group is due to the electron-withdrawing inductive effect of the __________

NH3+ group

in a-NH3+ groups, The average value of pKa for an a-NH3+ group is

Basicity

group where the side chain of arginine is a considerably stronger base than an aliphatic amine

Guanidine Group

basicity of the ____________ is attributed to the large resonance stabilization of the protonated form relative to the neutral form

guanido group

group where The side chain of histidine is a heterocyclic aromatic amine

Imidazole Group

All ______ essential amino acids are a-amino acids

20

For 19 of the 20, the a-amino group is primary; for ____________, it is secondary

proline

With the exception of ___________, the a-carbon of each is a stereocenter

glycine

________ and ________ contain a second stereocenter

Isoleucine and threonine

amino acid in many organisms

Selenocysteine

amino acid in several archaeal species

Pyrrolysine

amino acid in collagen

Hydroxylysine, hydroxyproline

amino acid in blood-clotting proteins

Carboxyglutamate

amino acid in bacteriorhodopsin

Pyroglutamate

amino acid in epinephrine, histamine, serotonin act as that neurotransmitters and hormones

GABA

amino acid used as a signaling device

Phosphorylated

are less common, but nevertheless found in certain proteins found in connective-tissue proteins

Hydroxylysine and hydroxyproline

are less common, but nevertheless found in certain proteins blood-clotting proteins

carboxy-glutamate

are less common, but nevertheless found in certain proteins found in bacteriorhodopsin

pyroglutamate

Each derived from a common amino acid by a modification are less common, but nevertheless found in certain proteins

Uncommon Amino Acids

Remember, amino acids without charged groups on side chain exist in neutral solution as _________ with no net charge

zwitterions

When an amino acid is titrated, the titration curve represents the reaction of each functional group with the ________

hydroxide ion

a-carboxyl, and a-amino groups have titratable protons. Some side chains do as well

free amino acids

the pH at which the majority of molecules of a compound in solution have no net charge

Isoelectric pH, pI

* most important protein in milk * nutritionally-adequate protein * storage protein

Casein

Casein can be isolated from milk by __________ to bring it to its isoelectric point

acidification

proteins are least soluble in water at their __________ because they tend to aggregate by electrostatic interaction aggregates precipitate out of solution

Isoelectric Point

What kind of charges will be on the casein in its native environment, that is, in milk?

In its native environment (milk), casein will have a negative charge because the pH of milk is higher than the isoelectric point of casein (around 4.6), meaning the casein molecules will be deprotonated and carry a net negative charge.

a method for estimating the amount of protein and nucleic acid in a sample using ultraviolet (UV) light absorption.

Warburg-Christian Assay

Individual amino acids can be linked by forming _______

covalent bonds

the special name given to the amide bond between the a-carboxyl group of one amino acid and the a-amino group of another amino acid

Peptide bond

are unbranched polymers of amino acids

Proteins

Amino acids join _________ through formation of covalent peptide bonds

head-to-tail

Peptide bond formation results in release of _____

water

The peptide backbone of a protein consists of the repeated sequence of

amide - alpha-C - carbonyl carbon

Peptide Bond is usually found in the ______ conformation

trans

Peptide Bond has partial _________ character

(40%) double bond

In a Peptide Bond, N partially ___________; O partially ____________

positive negative

Peptide Bond has a length of about 0.133 nm - shorter than a typical _________ but longer than a _________

single bond double bond

Due to the double-bond character of the peptide bond, the six atoms of the peptide bond group define a plane, called the

amide plane

What is the Fundamental Structural Pattern in Proteins?

(a) The peptide bond has partial double bond character. (b) peptide planar group

Structure of proteins is hydrogen bonded arrangement of backbone of the protein

2˚ of proteins

Two bonds have free rotation:

1) Bond between a-carbon and amino nitrogen in residue 2) Bond between the a carbon and carboxyl carbon of residue phi and psi bond

Short polymers of amino acids

Peptides

in Peptides, Each unit is called a

residue

in Peptides, 2 residues is called

dipeptide

in Peptides, 3 residues is called

tripeptide

in Peptides, 12-20 residues is called

oligopeptide

in Peptides, many residues is called

polypeptide

Protein with One polypeptide chain

monomeric protein

Protein with More than one polypeptide chain

multimeric protein

Protein with one kind of chain

Homomultimer

Protein with two or more different chains

Heteromultimer

It has two alpha chains and two beta chains a heterotetramer

Hemoglobin

polypeptide structures consisting of 1 or more long chains of amino acid residues

Protein

* Is a unique characteristic of every protein * Is encoded by the nucleotide sequence of DNA * Is thus a form of genetic information * Is read from the amino terminus to the carboxyl terminus

The Sequence of Amino Acids in a Protein

β-alanine aids in the production of _________. That's a compound that plays a role in muscle endurance in high-intensity exercise.

carnosine

a non-essential amino acid that is produced naturally in the body aids in the production of carnosine

β-alanine

Oxytocin and vasopressin difference

each have nine amino acids and only differ in two positions.

stimulates uterine contractions, lactation, mother–child bonding, pair bonding, feelings of trust, and altruistic behavior. * In males and females: Influences trust, altruism, social bonding, and recognition of emotions.

Oxytocin

is involved in control of blood pressure, as well as being implicated in male behavior of territoriality, aggression, pair bonding, and social group defense.

Vasopressin

Building proteins requires all ________ amino acids.

20

non Essential amino acids

Alanine Asparagine Isoleucine Cysteine Glutamate Glutamine Glycine Proline Serine tyrosine

Essential amino acids

Arginine* Histidine† Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine