amino acids
20 different amino acids - typical protein contains 1000 amino acids, large contain 100,000; long chains of organic molecules; 5 components: central carbon atom, hydrogen atom, amino group, carboxylic acid group, a variable group (R group/side chain)
carboxyl
an oxygen atom is double bonded to a carbon atom that is also bonded to an -OH group- carboxylic acid
amino group
A functional group that consists of a nitrogen atom bonded to two hydrogen atoms; can act as a base in solution, accepting a hydrogen ion and acquiring a charge of +1.
D and L
a form of stereochemistry; polarization of light; nearly all biological AA's are in the "L" form when produced, "D" is rare
L form
Do natural amino acids occur in the D or L form?
natural amino acids
L-amino acids, only these occur in proteins
side chain
Another term for R-group; variable group of an amino acid that differs with each amino acid and determines the unique characteristics of a particular AA
chiral
A molecule that is not superimposable on its mirror image. Typically a carbon atom bonded to four different atoms or molecules., Two mirror-image forms, that are not superimposable (enantiomers).
Of the standard ?-amino acids, all but glycine can exist in either of two_____
optical isomers
isomers
One of several organic compounds with the same molecular formula but different structures and therefore different properties. The three types are structural , geometric and enantiomers.
structural isomers
compounds that have the same molecular formula but differ in the covalent arrangements of their atoms.
geometric isomers
have the same covalent partnerships, but they differ in their spatial arrangements (cis isomer and trans isomer)
enantiomers
Mirror image isomers (like your left and right hand), molecules with the same molecular formula but structurally create non-superimposable mirror images of each other/ left-handed (L) and right-handed (R) conformations
optical isomers
A class of chiral stereoisomers that results from two possible arrangements of four different atoms or groups of atoms bonded to the same carbon atom.
L-amino acids
represent all of the amino acids found in proteins during translation in the ribosome,
acid and a base at the same time
Amino acids have both amine and carboxylic acid functional groups and are therefore both what?
D-amino acids
_______ are found in some proteins produced by enzyme posttranslational modification
stereocenter
an atom about which exchange of two groups produces a stereoisomer; chiral centers are one type of this
diastereomers
non mirror image stereoisomers; they have the same configuration at one of more chirality centers but differ at other chirality centers.
aliphatic
having carbon atoms linked in open chains
nonpolar, aliphatic R groups
Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine
polar R groups
Serine, Theronine, Cysteine, Asparagine, Glutamine
aromatic R groups
Phenylalanine, Tyrosine, Tryptophan
Negatively charged R groups
Aspartate, Glutamate
D and L
a form of stereochemistry; polarization of light; nearly all biological AA's are in the "L" form when produced, "D" is rare
dipolar compound
is a chemical compound that exists in at least one stable form
nonionic and zwitterionic
the two states an amino acid exist in
zwitterionic
is a dipolar compound, chemical compound that exists in at least one stable form, with a positive and a negative formal charge on different atoms and a total net charge of zero
zwitterionic
Most amino acids at physiological pH are
ribosome
A cell organelle constructed in the nucleolus and functioning as the site of protein synthesis in the cytoplasm; Consists of rRNA and protein molecules, which make up two subunits.
peptide
A ____________ bond is a link between the amino group [-NH2] of one amino acid and the carboxyl group [-COOH] of the next amino acid in the protein chain. All living things (and even viruses) use various combinations of the same twenty amino acids.
peptide bond
The covalent bond between two amino acid units, formed by a dehydration reaction
dehydration reaction
A chemical process in which two molecules become covalently bonded to each other with the removal of a water molecule. Also called condensation.
peptide bond
Condensation of carboxyl group of one amino acid with and amino group of next amino acid
amide
-nitrogen and carbonyl on end carbon -name ends in "amide
carboxyl end
the end of a protein encoded by the 3' end of the mRNA and is the last part of the protein to be synthesized in translation.
carboxyl end
acts as a slight acid
amino end
the end of a protein having a free amino group
side chains
the parts of the amino acids that are not involved in forming peptide bonds
side chains
unique part of aa projecting off backbone
side chain
the unique substituent attached to the alpha carbon.
aliphatic R Groups
glycine,alanine,proline,valine,leucine,isoleucine,methionine
glycine
Gly, G, nonpolar, only A-chiral amino acid residue, in places where you need a lot of flexiblity,
alanine
Ala, A, CH3, nonpolar, CH?; Nonpolar, aliphatic R group; Ala, A;
proline
An amino acid that causes kinks/bends in protein structures., circles back to link to alpha-carbon
valine
CH, CH?--CH?; Nonpolar, aliphatic R group; Val, V;
leucine
CH2-CH-(CH3)2 (v shape), Hydrophobic, Nonpolar, aliphatic R Groups
isoleucine
CH(CH3)-CH2-CH3 (t-shape)
methionine
CH?, CH?, S, CH?; Nonpolar, aliphatic R group; Met, M; start codon
polar uncharged hydrophilic
serine,threonine,cysteine,asparagine,glutamine
serine
CH?OH; Polar, uncharged R groups; Ser, S
cysteine
CH?, SH; Polar, uncharged R groups; Cys, C; R-group pKr 8.18, disulfide bonds; strongest nucleophile of amino acid residues; two could come together to form a cysteine bridge
asparagine
Polar, uncharged R groups; Asn, N C=O:NH2, Asn, N
glutamine
+H3N--CH(COO-)--CH2--CH2--C(NH2)=O, Gln, Q
aromatic ring groups
phenyalanine tyrosine tryptophan
phenylalanine
R groups is large aromatic and nonpolar Phe F
tyrosine
CH?, carbon ring, OH; Aromatic R groups; Try, Y; R-group pKr 10.07;
tryptophan
Trp, W two rings
positively charged R groups
lysine arginine histidine
lysine
CH?, CH?, CH?, CH?, +NH?; Positively charged R groups; Lys, K; R-group pKr 10.53
arginine
CH?, CH?, CH?, NH, C=+NH?, NH?; Positively charged R groups; Arg, R; 12.48
histidine
CH?, C--NH,CH,N, CN (odd); Positively charged R groups; His, H; R-group pKr 6.00
negatively charged R groups
aspartate,glutamate
aspartate
CH?, COO-; Negatively charged R groups; Asp, D; R-group pKr 3.65
glutamate
CH?, CH?, COO-; Negatively charged R groups; Glu, E; R-group pKr 4.25
deprotonated
at high pH
protonated
at low pH
isoelectric point
the pH at which the amino acid forms a zwitterion and is neutral
zwitterion
an amino acid with a protonated amine group and a deprotonated carboxylic group. The amine end is positively charged and the arboxylic end is negatively charged, resulting in a zero net charge overall. This form of ion will not move in an electrical field
L-isomers
All amino acids in proteins are
disrupts a-helix in proteins
proline
Glycine G Gly
not optically active
optically active
A single enantiomer of a mirror image pair is said to be optically active because it can rotate plane polarized light.
enantiomer
one of two compounds that are mirror images of each other.
Methionine
first aa in translation (AUG),
alpha helix
secondary structure formed by intrastrand H-bonds b/w carboxyl Oxygen (CO) and amino hydrogen (NH) of aa 4 residues upstream in pp chain
alpha helix
-right-handed helix
-R groups radiate outward from helix core
beta pleated sheets
secondary structure formed by H-bonding b/w carboxyl oxygen and amino hydrogen of aa residues on adjacent strands
antiparallel
--------run in opposite dirxn; H-bonding connects an aa to one other aa
-Parallel strands' H-bonding connect an aa to two different aa residues on adjacent strand
forces responsible for Quaternary Structure
1. tertiary strx (resulting from primary strx and H2O interactions)
2. H-bonds
3. ionic bonds
4. van der Waals forces
5. disulfide bonds
zwitterion act as an acid or base
both: acid from the NH3+ and base from the O(-): buffers
describe the process of an alpha amino acid neutralizing strong bases
zwitterion (H3N+-CH(R)-C(=O)-O(-)) --OH(-)---> base (H2N-CH(R)-C(=O)-O(-))
describe the process of an alpha amino acid neutralizing strong acids
zwitterion (H3N+-CH(R)-C(=O)-O(-)) --H+---> acid (H3N+-CH(R)-C(=O)-OH
positive, anode
for low pH solutions of amino acids, ___ charges are present, and these will gravitate toward the ____ in an electric field
negative, cathode
for high pH solutions of amino acids, ___ charges are present, and these will gravitate toward the ____ in an electric field
chiral
are proteins achiral or chiral?
secondary structure of a protein
how a polypeptide chain coils or intertwines around itself
tertiary structure of a protein
how different secondary structures coil together
quaternary structure of a protein
how different polypeptide chains glob together to form a protein
describe the process highlighting the primary structure of a protein and its formation
Amino Acid A loses its O- and Amino Acid B loses H2 from NH3+ to stitch them together, releasing a molecule of water in the process and forming a dipeptide
amino, carboxyl
polypeptides are drawn with the ____ group on the left and the _____ group on the right
n-terminus
what is the amino end of a polypeptide called?
c-terminus
what is the carboxyl end of a polypeptide called?
how do you name a polypeptide?
split the molecule at the amide linkage; the n-terminus half is derived from the amino acid's name with the "yl" ending, and the c-terminus have is the regular amino acid's name
no rotation can occur and C, O, H, and N are in a trans-planar arrangement
because of the amide linkage in a peptide bond, _______________
hydrogen bonds
what makes the alpha-helix stable?
hydrogen bonds
what holds beta-sheets together?
those in alpha-helices are within a segment; the ones in beta-sheets are between segments
what's the difference between hydrogen bonds in alpha-helices vs. beta-sheets?
collagen
is formed by a
triple helix chain of left-handed helices
factors that determine the tertiary structure
hydrogen bonds, disulfide bonds between cystine residues, ionic bonds between positive and negative charges, hydrophobic-hydrophobic interactions, hydrophilic-h2o interactions, and prosthetic groups
alpha and beta
the two different types of subunits
hydrolysis
how do we digest proteins?
amino acids
20 different amino acids - typical protein contains 1000 amino acids, large contain 100,000; long chains of organic molecules; 5 components: central carbon atom, hydrogen atom, amino group, carboxylic acid group, a variable group (R group/side chain)
carboxyl
an oxygen atom is double bonded to a carbon atom that is also bonded to an -OH group- carboxylic acid
amino group
A functional group that consists of a nitrogen atom bonded to two hydrogen atoms; can act as a base in solution, accepting a hydrogen ion and acquiring a charge of +1.
D and L
a form of stereochemistry; polarization of light; nearly all biological AA's are in the "L" form when produced, "D" is rare
L form
Do natural amino acids occur in the D or L form?
natural amino acids
L-amino acids, only these occur in proteins
side chain
Another term for R-group; variable group of an amino acid that differs with each amino acid and determines the unique characteristics of a particular AA
chiral
A molecule that is not superimposable on its mirror image. Typically a carbon atom bonded to four different atoms or molecules., Two mirror-image forms, that are not superimposable (enantiomers).
Of the standard ?-amino acids, all but glycine can exist in either of two_____
optical isomers
isomers
One of several organic compounds with the same molecular formula but different structures and therefore different properties. The three types are structural , geometric and enantiomers.
structural isomers
compounds that have the same molecular formula but differ in the covalent arrangements of their atoms.
geometric isomers
have the same covalent partnerships, but they differ in their spatial arrangements (cis isomer and trans isomer)
enantiomers
Mirror image isomers (like your left and right hand), molecules with the same molecular formula but structurally create non-superimposable mirror images of each other/ left-handed (L) and right-handed (R) conformations
optical isomers
A class of chiral stereoisomers that results from two possible arrangements of four different atoms or groups of atoms bonded to the same carbon atom.
L-amino acids
represent all of the amino acids found in proteins during translation in the ribosome,
acid and a base at the same time
Amino acids have both amine and carboxylic acid functional groups and are therefore both what?
D-amino acids
_______ are found in some proteins produced by enzyme posttranslational modification
stereocenter
an atom about which exchange of two groups produces a stereoisomer; chiral centers are one type of this
diastereomers
non mirror image stereoisomers; they have the same configuration at one of more chirality centers but differ at other chirality centers.
aliphatic
having carbon atoms linked in open chains
nonpolar, aliphatic R groups
Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine
polar R groups
Serine, Theronine, Cysteine, Asparagine, Glutamine
aromatic R groups
Phenylalanine, Tyrosine, Tryptophan
Negatively charged R groups
Aspartate, Glutamate
D and L
a form of stereochemistry; polarization of light; nearly all biological AA's are in the "L" form when produced, "D" is rare
dipolar compound
is a chemical compound that exists in at least one stable form
nonionic and zwitterionic
the two states an amino acid exist in
zwitterionic
is a dipolar compound, chemical compound that exists in at least one stable form, with a positive and a negative formal charge on different atoms and a total net charge of zero
zwitterionic
Most amino acids at physiological pH are
ribosome
A cell organelle constructed in the nucleolus and functioning as the site of protein synthesis in the cytoplasm; Consists of rRNA and protein molecules, which make up two subunits.
peptide
A ____________ bond is a link between the amino group [-NH2] of one amino acid and the carboxyl group [-COOH] of the next amino acid in the protein chain. All living things (and even viruses) use various combinations of the same twenty amino acids.
peptide bond
The covalent bond between two amino acid units, formed by a dehydration reaction
dehydration reaction
A chemical process in which two molecules become covalently bonded to each other with the removal of a water molecule. Also called condensation.
peptide bond
Condensation of carboxyl group of one amino acid with and amino group of next amino acid
amide
-nitrogen and carbonyl on end carbon -name ends in "amide
carboxyl end
the end of a protein encoded by the 3' end of the mRNA and is the last part of the protein to be synthesized in translation.
carboxyl end
acts as a slight acid
amino end
the end of a protein having a free amino group
side chains
the parts of the amino acids that are not involved in forming peptide bonds
side chains
unique part of aa projecting off backbone
side chain
the unique substituent attached to the alpha carbon.
aliphatic R Groups
glycine,alanine,proline,valine,leucine,isoleucine,methionine
glycine
Gly, G, nonpolar, only A-chiral amino acid residue, in places where you need a lot of flexiblity,
alanine
Ala, A, CH3, nonpolar, CH?; Nonpolar, aliphatic R group; Ala, A;
proline
An amino acid that causes kinks/bends in protein structures., circles back to link to alpha-carbon
valine
CH, CH?--CH?; Nonpolar, aliphatic R group; Val, V;
leucine
CH2-CH-(CH3)2 (v shape), Hydrophobic, Nonpolar, aliphatic R Groups
isoleucine
CH(CH3)-CH2-CH3 (t-shape)
methionine
CH?, CH?, S, CH?; Nonpolar, aliphatic R group; Met, M; start codon
polar uncharged hydrophilic
serine,threonine,cysteine,asparagine,glutamine
serine
CH?OH; Polar, uncharged R groups; Ser, S
cysteine
CH?, SH; Polar, uncharged R groups; Cys, C; R-group pKr 8.18, disulfide bonds; strongest nucleophile of amino acid residues; two could come together to form a cysteine bridge
asparagine
Polar, uncharged R groups; Asn, N C=O:NH2, Asn, N
glutamine
+H3N--CH(COO-)--CH2--CH2--C(NH2)=O, Gln, Q
aromatic ring groups
phenyalanine tyrosine tryptophan
phenylalanine
R groups is large aromatic and nonpolar Phe F
tyrosine
CH?, carbon ring, OH; Aromatic R groups; Try, Y; R-group pKr 10.07;
tryptophan
Trp, W two rings
positively charged R groups
lysine arginine histidine
lysine
CH?, CH?, CH?, CH?, +NH?; Positively charged R groups; Lys, K; R-group pKr 10.53
arginine
CH?, CH?, CH?, NH, C=+NH?, NH?; Positively charged R groups; Arg, R; 12.48
histidine
CH?, C--NH,CH,N, CN (odd); Positively charged R groups; His, H; R-group pKr 6.00
negatively charged R groups
aspartate,glutamate
aspartate
CH?, COO-; Negatively charged R groups; Asp, D; R-group pKr 3.65
glutamate
CH?, CH?, COO-; Negatively charged R groups; Glu, E; R-group pKr 4.25
deprotonated
at high pH
protonated
at low pH
isoelectric point
the pH at which the amino acid forms a zwitterion and is neutral
zwitterion
an amino acid with a protonated amine group and a deprotonated carboxylic group. The amine end is positively charged and the arboxylic end is negatively charged, resulting in a zero net charge overall. This form of ion will not move in an electrical field
L-isomers
All amino acids in proteins are
disrupts a-helix in proteins
proline
Glycine G Gly
not optically active
optically active
A single enantiomer of a mirror image pair is said to be optically active because it can rotate plane polarized light.
enantiomer
one of two compounds that are mirror images of each other.
Methionine
first aa in translation (AUG),
alpha helix
secondary structure formed by intrastrand H-bonds b/w carboxyl Oxygen (CO) and amino hydrogen (NH) of aa 4 residues upstream in pp chain
alpha helix
-right-handed helix
-R groups radiate outward from helix core
beta pleated sheets
secondary structure formed by H-bonding b/w carboxyl oxygen and amino hydrogen of aa residues on adjacent strands
antiparallel
--------run in opposite dirxn; H-bonding connects an aa to one other aa
-Parallel strands' H-bonding connect an aa to two different aa residues on adjacent strand
forces responsible for Quaternary Structure
1. tertiary strx (resulting from primary strx and H2O interactions)
2. H-bonds
3. ionic bonds
4. van der Waals forces
5. disulfide bonds
zwitterion act as an acid or base
both: acid from the NH3+ and base from the O(-): buffers
describe the process of an alpha amino acid neutralizing strong bases
zwitterion (H3N+-CH(R)-C(=O)-O(-)) --OH(-)---> base (H2N-CH(R)-C(=O)-O(-))
describe the process of an alpha amino acid neutralizing strong acids
zwitterion (H3N+-CH(R)-C(=O)-O(-)) --H+---> acid (H3N+-CH(R)-C(=O)-OH
positive, anode
for low pH solutions of amino acids, ___ charges are present, and these will gravitate toward the ____ in an electric field
negative, cathode
for high pH solutions of amino acids, ___ charges are present, and these will gravitate toward the ____ in an electric field
chiral
are proteins achiral or chiral?
secondary structure of a protein
how a polypeptide chain coils or intertwines around itself
tertiary structure of a protein
how different secondary structures coil together
quaternary structure of a protein
how different polypeptide chains glob together to form a protein
describe the process highlighting the primary structure of a protein and its formation
Amino Acid A loses its O- and Amino Acid B loses H2 from NH3+ to stitch them together, releasing a molecule of water in the process and forming a dipeptide
amino, carboxyl
polypeptides are drawn with the ____ group on the left and the _____ group on the right
n-terminus
what is the amino end of a polypeptide called?
c-terminus
what is the carboxyl end of a polypeptide called?
how do you name a polypeptide?
split the molecule at the amide linkage; the n-terminus half is derived from the amino acid's name with the "yl" ending, and the c-terminus have is the regular amino acid's name
no rotation can occur and C, O, H, and N are in a trans-planar arrangement
because of the amide linkage in a peptide bond, _______________
hydrogen bonds
what makes the alpha-helix stable?
hydrogen bonds
what holds beta-sheets together?
those in alpha-helices are within a segment; the ones in beta-sheets are between segments
what's the difference between hydrogen bonds in alpha-helices vs. beta-sheets?
collagen
is formed by a
triple helix chain of left-handed helices
factors that determine the tertiary structure
hydrogen bonds, disulfide bonds between cystine residues, ionic bonds between positive and negative charges, hydrophobic-hydrophobic interactions, hydrophilic-h2o interactions, and prosthetic groups
alpha and beta
the two different types of subunits
hydrolysis
how do we digest proteins?