Amino acids, Peptides & Proteins Flashcards
are biopolymers of varying size that are constructed from a set of 20 α-amino acids
Proteins
______ are the chief constituents of skin, bone, hair, and nails.
Collagen and keratin
Virtually all reactions in living systems are catalyzed by proteins called _________
enzymes
Muscles are made up of proteins called __________
myosin and actin
__________ transports oxygen from the lungs to cells, other proteins transport molecules across cell membranes.
Hemoglobin
Many hormones are proteins, among them:
- insulin
- oxytocin
- human growth hormone.
______ in milk and _______ in eggs store nutrients for newborn infants and birds.
- Casein
- ovalbumin
Blood clotting involves the protein ________; the body used proteins called antibodies to fight disease.
fibrinogen
a protein in the liver, stores iron
Ferritin
Certain proteins not only control the ________, but also control when gene expression takes place.
expression of genes
Two major types of Proteins
- fibrous proteins
- globular proteins
insoluble in water and are used mainly for structural purposes
fibrous proteins
more soluble in water and are used mainly
for nonstructural purposes.
globular proteins
A compound that contains both an amino group and a carboxyl group.
Amino acid
they are chains of amino acids
proteins
An amino acid in which the amino group is on the carbon adjacent to the carboxyl group.
a-Amino acid
Although a-amino acids are commonly written in the un-ionized form, they are more properly written in the ___________ form.
zwitterion (internal salt)
With the exception of glycine, all protein-derived amino acids have at least _________ and are chiral.
one stereocenter (the a-carbon)
The vast majority of a-amino acids have the _______ at the a-carbon.
L-configuration
we can classify amino acids into four groups:
- nonpolar
- polar neutral
- acidic
- basic
non-polar side chains are
hydrophobic
polar neutral, acidic, and
basic side chains are ______
hydrophilic
Alanine
Shortcut
Ala
A
Arginine
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Arg
R
Asparagine
Shortcut
Asn
N
Aspartic acid
Shortcut
Asp
D
Cysteine
Shortcut
Cys
C
Glutamic acid
Shortcut
Glu
E
Glutamine
Shortcut
Gln
Q
Glycine
Shortcut
Gly
G
Histidine
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His
H
Isoleucine
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Ile
I
Leucine
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Leu
L
Lysine
Shortcut
Lys
K
Methionine
Shortcut
Met
M
Phenylalanine
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Phe
F
Proline
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Pro
P
Serine
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Ser
S
Threonine
Shortcut
Thr
T
Tryptophan
Shortcut
Trp
W
Tyrosine
Shortcut
Tyr
Y
Valine
Shortcut
Val
V
Give all Non-Polar Amino Acids
- Methionine
- Leucine
- Tryptophan
- Proline
- Phenylalanine
- Alanine
- Isoleucine
- Valine
- Glycine
Give all Polar Amino Acids
- Threonine
- Serine
- Cysteine
- Asparagine
- Tyrosine
- Glutamine
Give all Acidic Amino Acids
- Aspartic acid
- Glutamic acid
Give all Basic Amino Acids
- Histidine
- Lysine
- Arginine
Amino Acids with sulfur
- Cysteine
- Methionine
Amino Acids with amide
- Asparagine
- Glutamine
Amino Acids with aromatic rings
- Phenylalanine
- Tyrosine
- Histidine
- Tryptophan
Amino Acid with non-aromatic ring
Proline
For 19 of the 20, the a-amino group is primary; for proline, it is ___________.
secondary
With the exception of glycine, the a-carbon of each is a _________.
stereocenter
Isoleucine and threonine contain a ____________.
second stereocenter
The __________ on an amino acid depends on the pH of the solution in which it is dissolved.
net charge
If we dissolve an amino acid in water, it is present in the aqueous solution as its ___________
zwitterion
If we add a strong acid such as HCl to bring the pH of the solution to 0.0, the strong acid donates a proton to the -COO- of the zwitterion turning it into a __________.
positive ion
If we add a strong base such as NaOH to the solution and bring its pH to 14, a proton is transferred from the NH3+ group to the base turning the zwitterion into a _____________.
negative ion
The pH at which the majority of molecules of a compound in solution have no net charge.
Isoelectric point, pI
Phenylalanine and tyrosine are precursors to _____________ and ______________, both of which are stimulatory neurotransmitters.
- norepinephrine
- epinephrine
epinephrine The -SH (sulfhydryl) group of cysteine is easily oxidized to an ___________
-S-S- (disulfide).
Hydroxylation (oxidation) of Tryptophan
5-Hydroxytryptophan
Decarboxylation of 5-Hydroxytryptophan
Serotonin
(5-Hydroxytryptamine)
oxidation of Phenylalanine
Tyrosine
oxidation of Tyrosine
3,4-Dihydroxyphenylalanine
(L-DOP A)
decarboxylation of 3,4-Dihydroxyphenylalanine
(L-DOP A)
Dopamine
oxidation and methylation of dopamine
Epinephrine
Hydroxylation (oxidation) of proline
Hydroxyproline
Hydroxylation (oxidation) of Lysine
Hydroxylysine
iodination of Tyrosine
Thyroxine
In 1902, Emil Fischer proposed that proteins are long chains of amino acids joined by ___________.
amide 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.
Peptide bond (peptide linkage)
A short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain.
Peptide
A molecule containing two amino acids joined by a peptide bond.
Dipeptide
A molecule containing three amino acids joined by peptide bonds.
Tripeptide
A macromolecule containing many amino acids joined by peptide bonds.
Polypeptide
A biological macromolecule containing at least 30 to 50 amino acids joined by peptide bonds.
Protein
The individual amino acid units are often referred to as
“residues”
Linus Pauling, however, discovered that there is about 40% ________ character to the C-N bond and that a peptide bond between two amino acids is ________, which Pauling explained using the concept of resonance.
- double bond
- planar
By convention, peptides are written from the left to right, beginning with the free _____ group and ending with the free _______ group.
- -NH3+
- -COO-
the amino acid at the end of the chain having the free -COO- group.
C-terminal amino acid
The amino acid at the end of the chain having the free -NH3+ group.
N-terminal amino acid
Other name for
C-terminal amino acid and N-terminal amino acid
C-terminus and the N-terminus
At its ________, the protein has no net charge
isoelectric point
At any pH above (more basic than) its pI, it has a ______
net negative charge
At any pH below (more acidic than) its pI, it has a _________.
net positive charge
pl of hemoglobin
6.8
pl of Serum albumin
4.9
Proteins are least soluble in water at their _________ and can be ________ from solution when pH = pI
- isoelectric points
- precipitated
The sequence of amino acids in a polypeptide chain. Read from the N-terminal amino acid to the C-terminal amino acid.
Primary structure
Conformations of amino acids in localized regions of a polypeptide chain. Examples are a-helix, b-pleated sheet, and random coil.
Secondary structure
The complete three-dimensional arrangement of atoms of a polypeptide chain.
Tertiary structure
The spatial relationship and interactions between subunits in a protein that has more than one polypeptide chain.
Quaternary structure
The sequence of amino acids in a polypeptide chain.
Primary structure
The number dipeptides possible from the 20 protein-derived amino acids
400
The number tripeptides possible from the 20 protein-derived amino acids
8000
The number of peptides possible for a chain of n amino acids is ___
20n
For a small protein of 60 amino acids, the number of proteins possible is 20^60 =
10^78
The hormone insulin consists of two polypeptide chains, A and B, held together by two ____________.
disulfide bonds
Human insulin consists of two polypeptide chains having a total of ____ amino acids; the two chains are connected by two interchain disulfide bonds.
51
Vasopressin and oxytocin are both __________ but have quite different biological functions.
nonapeptides
Vasopressin is an __________ hormone.
antidiuretic
affects contractions of the uterus in childbirth and the muscles of the breast that aid in the secretion of milk.
Oxytocin
A type of secondary structure in which a section of polypeptide chain coils into a spiral, most commonly a right-handed spiral.
a-Helix
A type of secondary structure in which two polypeptide chains or sections of the same polypeptide chain align parallel to each other; the chains may be parallel or antiparallel.
b-Pleated sheet
In a section of a-helix
there are __ amino acids per turn of the helix.
3.6
In a section of a-helix, The ________ of each peptide bond lie in the same plane.
six atoms
In a section of a-helix, the _________ of peptide bonds point in the same direction, roughly parallel to the axis of the helix.
N-H groups
In a section of a-helix, the ________ of peptide bonds point in the opposite direction, also roughly parallel to the axis of the helix.
C=O groups
In a section of a-helix, the C=O group of each peptide bond is _________ to the N-H group of the peptide bond four amino acid units away from it.
hydrogen bonded
In a section of a-helix, all ________ point outward from the helix.
R- groups
a polypeptide derived entirely from alanine
polyalanine
In a section of b-pleated sheet; The six atoms of each peptide bond of a b-pleated sheet lie in the _________.
same plane
In a section of b-pleated sheet;
The C=O and N-H groups of the peptide bonds from adjacent chains point toward ________ and are in the same plane so that hydrogen bonding is possible between them.
each other
All R- groups on any one chain ___________, first above, then below the plane of the sheet, etc.
alternate
Many globular proteins contain all three kinds of secondary structure in different parts of their molecules:
- a-helix
- b-pleated sheet
- random coil
the overall conformation of an entire polypeptide chain.
Tertiary structure
Tertiary structure is stabilized in four ways:
- Covalent bonds
- Hydrogen bonding
- Salt bridges
- Hydrophobic interactions
for example, the formation of disulfide bonds between cysteine side chains.
Tertiary structure stabilization
Covalent bonds
between polar groups of side chains, as for example between the -OH groups of serine and threonine.
Tertiary structure stabilization
Hydrogen bonding
as for example, the attraction of the -NH3+ group of lysine and the -COO- group of aspartic acid.
Tertiary structure stabilization
Salt bridges
as for example, between the nonpolar side chains of phenylalanine and isoleucine.
Tertiary structure stabilization
Hydrophobic interactions
The arrangement of polypeptide chains into a noncovalently bonded aggregation.
Quaternary structure
Two side chains with the same charge would normally repel each other, but they can also be linked via a metal ion.
Tertiary structure stabilization
Metal Ion Coordination
Two alpha chains of 141 amino acids each, and two beta chains of 146 amino acids each.
Adult hemoglobin
Two alpha chains and two gamma chains. Has a greater affinity for oxygen than does adult hemoglobin. Each chain surrounds an iron-containing heme unit.
Fetal hemoglobin
______________ proteins form quaternary structures in which the outer surface is largely nonpolar (hydrophobic) and interacts with the lipid bilayer.
Integral membrane
The process of destroying the native conformation of a protein by chemical or physical means.
Denaturation
Denaturing agents include:
- Heat
- 6 M aqueous urea
- Surface-active agents
- Reducing agents
- Heavy metal ions
- Alcohols
Heat can disrupt ___________
Denaturing agents
hydrogen bonding
in globular proteins, it can cause unfolding of polypeptide chains with the result that coagulation and precipitation may take place.
Heat
6 M aqueous urea: Disrupts _________
hydrogen bonding
Surface-active agents: Detergents such as _________________ disrupt hydrogen bonding.
sodium dodecylbenzenesulfate (SDS)
Reducing agents: _______________ cleaves disulfide bonds by reducing -S-S- groups to-SH groups.
2-Mercaptoethanol (HOCH2CH2SH)
Heavy metal ions: Transition metal ions such as Pb2+, Hg2+, and Cd2+ form ___________ with -SH groups; Hg2+ for example forms -S-Hg-S-.
water-insoluble salts
Alcohols: 70% ethanol penetrates bacteria and kills them by _________ their proteins. It is used to sterilize skin before injections.
coagulating
