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amimoacidos, Apuntes de Bioquímica

Universidad Autónoma de Madrid (UAM)Bioquímica

Asignatura: Bioquímica, Profesor: cualquiera cualquiera, Carrera: Biología, Universidad: UAM

Tipo: Apuntes

2014/2015

Subido el 17/06/2015

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LESSON 5: AMINO ACIDS, PEPTIDES AND PROTEINS

PROTEINS are polymers of amino acids, with each amino acid residue joined to each

other by a peptidic bond.

The 3D structure of a protein is determined by

its amino acid sequence (primary sequence)

The function of the protein

depends on its structure

Protein function often entails an interconversion

between two or more structural forms

Descubre Apuntes de Bioquímica Universidad Autónoma de Madrid (UAM)

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LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS^ PROTEINS^ are polymers of

amino acids, with each amino acid residue joined to each

other by a^ peptidic bond

The 3D structure of a protein is determined byits amino acid sequence (primary sequence)The function of the proteindepends on its structure Protein function often entails an interconversionbetween two or more structural forms

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS^ COMMON AMINO ACIDS^ All 20 of the common amino acids are

L-amino acids.^ They have a common general structure

consisting in a carboxyl group and an amino group bonded to the same carbon atom (α-carbon).Amino acids differ from each other in their side chain or R group.^ GENERAL STRUCTURE^ Each Amino acid:^

Phenylalanine Three letter abbreviation^

Phe One-letter symbol^

Greek lettering and numbering systems helpF to define specific carbon atoms.

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS CLASSIFICATION OF AMINO ACIDS^ Amino acids can be classified based on the properties of their R group, in particular, their^ polarity

Tend to cluster together andstabilize protein structure byhydrophobic interactions^ Reduces^ the^ structural^ flexibility^ of^ polypeptideflexibility^ of^ polypeptide^ regions^ Aromatic aa absorb UV light. Charged amino acids at pH=

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS CLASSIFICATION OF AMINO ACIDS^ Amino acids can be classified based on the properties of their R group, in particular, their^ polarity^ Thioether group^ Ala, Val, Leu and Ile tend to cluster together within proteins, stabilizing protein structure bymean of hydrophobic interactions.^ Pro, the cyclic structure is rigid adn reduces the flexibility of polypeptides regions.^ Phe, Tyr, Trp are aromatic aminoacid

Indol group

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS AROMATIC AMINO ACIDS

SPECTROPHOTOMETER

ABSORPTION SPECTRA

Measurement^ of^ light

absorption^ by^ a spectrophotometer^ is^ used

to^ detect^ and^ identify molecules^ and^ measure

their^ concentration^ in solution.^ The absorbance is directly proportional to theconcentration of the absorbing solute. Aromatic amino acids absorb light

at different^ wavelenght^ with

a^ maximal peak at^ 280 nm. Phe contributes little tothe absortion spectra.

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS CLASSIFICATION OF AMINO ACIDS^ Amino acids can be classified based on the properties of their R group, in particular, their^ polarity^ pH= 7^ -

-^

+^ +^ +^ Guanidiniumgroup

Imidazolegroup NeutralpKa ≈ 7

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS^ AMINO ACIDS ARE AMPHOLYTES, (amphoteric substances)^ Carboxyl and amino groups of amino acids function as weak acids and bases.WHEN AN AMINO ACID, LACKING AN IONIZABLE R GROUP

, IS DISSOLVED IN WATER AT pH≈7, IT EXISTS IN SOLUTION AS THE DIPOLAR ION OR

ZWITTERION^ WHICH CAN ACT AS EITHER AN ACID OR A BASE.^ pH≈ 7 Acting as an acid Acting as a base Zwitterionic^ form^ Zwitterionic^ form pKa 1

pKa^2

ACID^

ACID/BASE^

BASE

(ampholyte) pKa:^ Is a measure of the tendency of a group to give up a proton. Lower the pKa, higher the Ka, higherthe tendency to loss the proton.

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS^ TITRATION CURVES OF AMINO ACIDS

Titration of amino group Titration of carboxyl group

-DIPROTIC: 2 H+, 2 pKa, 2 buf. region.- Carboxyl group is more acidic thanthe ammonium group. Small additions of strong acids or basesgive rise to big changes in the pH Gly has been forced tobe at a very low pH^ Small additions of strong acids orbases give rise to small or nochange in the pH^ BUFFERING REGION

LESSON 5:^ AMNO ACIDS, PEPTIDES AND PROTEINS

Equimolar^ concentrations

TITRATION CURVES OF AMINO ACIDS

-^ charge Equimolar concentrations^ Fully protonated form

Equimolar^ concentrations^ NOT NET CHARGE^ Isoelectric point Zwiterion form^ pI= ½ (pKa1 + pKa2)

-^ charge + charge pH= pI pH< pI CHARGE= 0 CHARGE= +

pH> pI CHARGE= -

LESSON 5:^ AMNO ACIDS, PEPTIDES AND PROTEINS

Equimolar^ concentrations

TITRATION CURVES OF AMINO ACIDS

-^ charge Equimolar concentrations^ Fully protonated form

Equimolar^ concentrations Zwiterion form Titration curves of amino acids give:1.- A quatitative measure of the pKa of each ionizing group

2.- Regions of buffering power (extends 1 pH unit on either side of the pKa).3.- Relationship between its net charge and the pH of the solution.

NOT NET CHARGE Isoelectric point pI= ½ (pKa1 + pKa2) Isoelectric point.

-^ charge + charge

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS^ TITRATION CURVES OF AMINO ACIDS

Tyrosine and Cysteine residue arefrequently found in the catalyticsite of enzymes^ Acid^ Lys (K)^ Arg^ (R)

Base Arg (R) His (H) Cys (C)Tyr (Y) Asp (D)Glu (E) -COOH

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS^ TITRATION CURVES OF AMINO ACIDS^ SIMPLE AMINO ACID (diprotic)

COMPLEX AMINO ACID (with an ionizable group)

pI= 7.

Variations in the pKa values for α-COOH (pKa: 1.8-2.4) and α-NH3 groups (pKa: 8.8-11.0) in aminoacids are due to intramolecular interactions that depends on R side chain.If additional acidic or basic groups are present as side-chain functions…… THE PI IS THE AVERAGE OF THE PKA 'S OF THE TWO MOST SIMILAR ACIDS OR BASES.

pI= 3.

pI= 7.

LESSON 5:^ AMNO ACIDS, PEPTIDES AND PROTEINS^ PEPTIDES AND THE PEPTIDE BOND

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS CLASSIFICATION OF AMINO ACIDS^ Amino acids can be classified based on the properties of their R group, in particular, their^ polarity

amimoacidos, Apuntes de Bioquímica

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LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS^ PROTEINS^ are polymers of

amino acids, with each amino acid residue joined to each

other by a^ peptidic bond

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS^ COMMON AMINO ACIDS^ All 20 of the common amino acids are

consisting in a carboxyl group and an amino group bonded to the same carbon atom (α-carbon).Amino acids differ from each other in their side chain or R group.^ GENERAL STRUCTURE^ Each Amino acid:^

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS CLASSIFICATION OF AMINO ACIDS^ Amino acids can be classified based on the properties of their R group, in particular, their^ polarity

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS AROMATIC AMINO ACIDS

SPECTROPHOTOMETER

ABSORPTION SPECTRA

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS CLASSIFICATION OF AMINO ACIDS^ Amino acids can be classified based on the properties of their R group, in particular, their^ polarity^ pH= 7^ -

-^

+^ +^ +^ Guanidiniumgroup

Imidazolegroup NeutralpKa ≈ 7

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS^ AMINO ACIDS ARE AMPHOLYTES, (amphoteric substances)^ Carboxyl and amino groups of amino acids function as weak acids and bases.WHEN AN AMINO ACID, LACKING AN IONIZABLE R GROUP

ACID^

ACID/BASE^

BASE

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS^ TITRATION CURVES OF AMINO ACIDS

LESSON 5:^ AMNO ACIDS, PEPTIDES AND PROTEINS

TITRATION CURVES OF AMINO ACIDS

Equimolar^ concentrations^ NOT NET CHARGE^ Isoelectric point Zwiterion form^ pI= ½ (pKa1 + pKa2)

pH> pI CHARGE= -

LESSON 5:^ AMNO ACIDS, PEPTIDES AND PROTEINS

TITRATION CURVES OF AMINO ACIDS

NOT NET CHARGE Isoelectric point pI= ½ (pKa1 + pKa2) Isoelectric point.

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS^ TITRATION CURVES OF AMINO ACIDS

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS^ TITRATION CURVES OF AMINO ACIDS^ SIMPLE AMINO ACID (diprotic)

pI= 7.

pI= 3.

pI= 7.

LESSON 5:^ AMNO ACIDS, PEPTIDES AND PROTEINS^ PEPTIDES AND THE PEPTIDE BOND

LESSON 5:^ AMINO ACIDS, PEPTIDES AND PROTEINS CLASSIFICATION OF AMINO ACIDS^ Amino acids can be classified based on the properties of their R group, in particular, their^ polarity

+^ +^ Neutral