chapter 3 (with parts of 4 and 5) bcmb 3100 - chapter 3 (part1)dmohnen/bcmb3100/lecturenotes... ·...

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Chapter 3 (with parts of 4 and 5)

Amino Acids and Primary Structures of Proteins

BCMB 3100 - Chapter 3 (part1)

• Diversity of protein function

• Complete definition of amino acids

• Memorize complete structure of 20 common amino acids!!!

• pKa’s of amino and carboxyl groups

• Amino acids with ionizable side groups

• Titration curve

Pink: make up ~ 97% mass of organismsPurple: five essential ionsLight blue: most common trace elementsDark blue: less common trace elements

PROTEIN STRUCTURE AND FUNCTION

Mulder (1800s):_________________________________________

Berzelius (1838): ____________________from Greek proteios "of first rank"

Proteins recognize and _______ many different types of molecules & ________ most of the chemical ___________ necessary for life.

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Examples of Protein Function

Enzymatic catalysis:enzymes increase reaction rates by__________; nearly all known

enzymes are ____________

Transport & storage:many small molecules and ions aretransported by _________;examples: _____________________

Coordinated motion:examples: myosin and actin (musclemovement)

Examples of Protein Function

Mechanical support: _________(tensile strength to skin and bones)

Immune protection: ____________

Generation & transmission of nerve impulses: example: ____________________

Control of growth and differentiation:___________________ (repressors,activators, transcription factors,hormones, regulation of translation)

Proteins are macromolecules made up of _________________ (20 amino acids)

_______________: consist of an __________, a _______________, a _______________ and a distinctive _________bonded to a carbon atom. This carbon is called the __________ because it is adjacent to the carboxyl group.

WHAT ARE PROTEINS?BCMB 3100 - Lecture 3




• pKa’s of amino and carboxyal groups


• Titration curves & pI

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Amino acids in solution will be in a _____________. The amino group and/or the carboxyl group will be charged depending upon the pH. The R group may also be charged.

At neutral pH amino acids are predominantly _______________________

• Under normal cellular conditions amino acids are _____________ (dipolar ions):

Amino group = -NH3+

Carboxyl group = -COO-

General Structure of the ionized from of an amino acid

COO-

NH3

+ C HR

FischerProjection

COO-: pKa 1.8-2.5

NH+: pKa 8.7-10.7

You MUST know this!!!

COOH → COO-

?

Two representations of an amino acid at neutral pH

(b) Ball-and stick model

(a) Structure

______________________ (asymmetric) due to the tetrahedral array of 4 different groups around the -carbon (glycine is an exception).

Thus all amino acids except glycine can exist as ______________ : two __________ that are nonsuperimposable mirror images of each other.

Enantiomers of amino acids are called D (right-handed) or L (left-handed)

L and D refer to absolute configuration

L-amino acids are the only constituents of _____________

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Mirror-image pairs of amino acids20 different amino acids are found in proteins

___________________ (side chains) that differ in size, shape, charge, hydrogen-bonding capacity & chemical reactivity 20 different amino acids found in proteins of all organisms from bacteria to humans

The amino acid alphabet is at least __________ years old

The diversity of protein structure & function is due to the sequence and number of amino acids found in a protein (__________________)

It is essential that a biochemist commit to memory the structure of the 20 amino acids! Know this!! (structure, & 1 & 3 letter code)

Structures of the 20 Common Amino Acids

• You must learn the one and three letter abbreviations

• You must know the properties of their side chains (R groups)

• Classes: Aliphatic, Aromatic, Sulfur-containing, Alcohols, Bases, Acids and Amides

• You must be able to draw the structure of the 20 amino acids in their correct ionized form at any given pH

Four _________ amino acid structures

-C not chiral

Page 380

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Stereoisomers of Isoleucine

• Ile has 2 chiral carbons, 4 possible stereoisomers

Isoleucine [I] (Ile) Aliphatic amino acid

***

[I](Ile)

Page 38Page 40

Proline has a nitrogen inthe aliphatic ring system

• Proline (Pro, P) - has a three carbon side chain bonded to the -amino nitrogen

• The heterocyclic pyrrolidine ring restricts the geometry of polypeptides

Page 38Page 40

____________ R Groups

• Side chains have aromatic groups

Phenylalanine (Phe, F) - benzene ring (OD 260 nm)

Tyrosine (Tyr, Y) - phenol ring (OD 280 nm)

Tryptophan (Trp, W) - bicyclic indole group (OD 280 nm)

OD at 280 nm is important for identifying proteins during protein purification.

Aromatic amino acid structures

pKa = 10.5

benzene ring

(OD 260 nm)phenol ring

(OD 280 nm)

indole group

(OD 280 nm)

Page 38Page 40

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________________ R Groups

• Methionine (Met, M) - (-CH2CH2SCH3)

• Cysteine (Cys, C) - (-CH2SH)

• Two cysteine side chains can be cross-linked by forming a disulfide bridge (-CH2-S-S-CH2-)

• Disulfide bridges may stabilize the three-dimensional structures of proteins

Methionine and Cysteine

pKa = 8.4

Page 38Page 40

Page 39Page 41

Oxidation: loss of an electron

Two Cys side chains can be cross-linked by forming a disulfide bridge (-CH2-S-S-CH2-); disulfide bridges may stabilize 3D protein structure

Formation of cystineSide Chains with _______________

Serine (Ser, S) and Threonine (Thr, T) have uncharged polar side chains

Page 39Page 41

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________ R Groups

• Histidine (His, H) - imidazole

• Lysine (Lys, K) - alkylamino group

• Arginine (Arg, R) - guanidino group

• Side chains are nitrogenous bases which are

substantially positively charged at pH 7 (true

for K & R)

Structures of histidine, lysine and arginine

imidazolealkylamino

groupguanidino

group

pKa = 6.0

pKa = 10.5 pKa = 12.5

Page 40Page 42

______ R Groups and ______ Derivatives

• Aspartate (Asp, D) and Glutamate (Glu, E)

are dicarboxylic acids, and are negatively

charged at pH 7

• Asparagine (Asn, N) and Glutamine (Gln, Q) are uncharged but highly polar

Structures of aspartate, glutamate, asparagine and glutamine

uncharged but highly polardicarboxylic acids

pKa = 3.9 pKa = 4.1

Page 41Page 43

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_______________ of Amino Acid Side Chains

• ___________ : the relative hydrophobicity of each amino acid

• The larger the __________, the greater the tendency of an amino acid to prefer a hydrophobic environment

• Hydropathy affects protein folding:

*hydrophobic side chains tend to be in the _____

*hydrophilic residues tend to be on the ________

Free-energy change for transfer (kjmol-1)

Aminoacid

Highly hydrophobicIsoleucine 3.1Phenylalanine 2.5Valine 2.3Leucine 2.2Methionine 1.1Less hydrophobicTryptophan 1.5*Alanine 1.0Glycine 0.67Cysteine 0.17Tyrosine 0.08Proline -0.29Threonine -0.75Serine -1.1Highly hydrophilicHistidine -1.7Glutamate -2.6Asparagine -2.7Glutamine -2.9Apartate -3.0Lysine -4.6Arginine -7.5

Hydropathy: the relative hydrophobicity of each amino acid

___________scale for amino acid residues

(Free-energy change for transfer of an amino acid from interior of a lipid bilayer to water)

The larger the hydropathy, the greater the tendency of an amino acid to prefer a hydrophobic environment

BCMB 3100 - Lecture 3







Structures of the 20 Common Amino Acids

• You must learn the one and three letter abbreviations

• You must know the properties of their side chains (R groups)

• Classes: Aliphatic, Aromatic, Sulfur-containing, Alcohols, Bases, Acids and Amides

• You must be able to draw the structure of the 20 amino acids in their correct ionized form at any given pH

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Amino acids in solution will be in a charged state. The -___________ and/or the -___________ will be

charged depending upon the pH. The _________ may also be charged. At neutral pH amino acids are

predominantly dipolar ions (_____________).

COO-

NH3

+ C HR

COO-: pKa 1.8-2.5

NH+: pKa 8.7-10.7

Note:pH dependance

of the ionization state

( COOH ↔ COO- + H+ )

(NH3+ ↔ NH2 + H+ )

Figure 3.2, Page 37/39

Ionization of Amino Acids

• Ionizable groups in amino acids: (1) -carboxyl, (2) -amino, (3) some side chains

• Each ionizable group has a specific pKa

AH B + H+

• For a solution pH below the pKa, the protonated form predominates (AH)

• For a solution pH above the pKa, the unprotonated(conjugate base) form predominates (B)

Titration curve for alanine

• Titration curves are used to determine pKavalues

• pK1 = 2.4

• pK2 = 9.9

• pIAla = isoelectric point

(pI = pH when net charge is zero)

pI = (2.4+9.9) / 2 = 6.15

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pKa values of amino acids

All amino acids contain two ionizable groups:

-carboxyl (pKa 1.8-2.5)

and protonated -amino group (pKa 8.7-10.7)

(Table 3.1, pg 41 gives some specific pKa values)

BUT FOR THIS COURSE use pKa’s from the notes.

The R group of 7 amino acids are also ionizable. The pKa of these R groups can range from 3.9 to 12.5. You must memorize the pKa’s of the side chains of these seven amino acids!

BCMB 3100 - Lecture 3







pKa values of amino acid ionizable groups

α α

Table 3.1

pKa values of amino acid ionizable groups

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Ionization of Histidine

(a) Titration curve of histidine

pK1 = 1.8pK2 = 6.0pK3 = 9.3

To determine the pI: pick the pKa above & below the point where the charge is zero and average those 2 pKa’s

pI = pH at which net charge is zero

Deprotonation of imidazolium ring

pKa=1.8 pKa=9.3

Ionization of Histidine

(a) Titration curve of histidine

pK1 = 1.8pK2 = 6.0pK3 = 9.3

To determine the pI: pick the pKa above & below point where charge is zero and average those 2 pKa’s

pI = pH at which net charge is zero

pI = (6 + 9.3)/2 =7.65

Ionization of the protonated -carboxyl of glutamate

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Deprotonation of the guanidinium group of Arg

BCMB 3100 – Chapter 3 (part 2)

• Summary of amino acids

• Polypeptides: definition, structure, and direction

• Peptide bond

• Disulfide bonds

• Protein purification

• Methods to determine amino acid composition, cleavage of proteins, protein sequencing

• Diversity of proteins

The 20 amino acid are divided into 7 groups

•_________: Gly, Ala, Val, Leu, Ile, Pro (G A V L I P)

•_________: Phe, Tyr, Trp (F Y W)

• ____________________: Met, Cys (M C)

• __________: Ser, Thr (S T)

• ________: His, Lys, Arg (H K R)

• ________: Asp, Glu (D E)

•_________: Asn, Gln (N Q)

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Amino acids are linked by ___________ to form polypeptide chains

carboxyl of one amino acid is joined to -amino group of another amino acid by a peptide bond (amide bond) with concomitant loss of H2O

Many amino acids are joined by peptide bonds to form an ____________ polypeptide

_________ : amino acid unit in a polypeptide

By convention the direction of a polypeptide is written starting with amino end

aa + aa + aa + aa NH3+-aa-aa-aa-aa-COO-

H2OH2OH2O

H O

NH3+ C C O-

R

+

H O

NH3+ C C O-

R

H O H O

NH3+ C C N C C O-

R H R

H2O

Formation of a dipeptide

Figure 4.1

Most polypeptides contain between 50 and 2000 amino acids

Average M.W. for an amino acid is 110 daltons so M.W. of most proteins is 5500 to __________ daltons. (One dalton equals one atomic mass unit; kilodalton = 1000 daltons). Most proteins have M.W. of 5.5-220 kd.

Some proteins contain disulfide bonds that cross-link between cysteine residues by the oxidation of cysteine.

Intracellular proteins often lack disulfides while extracellular proteins often have them.

Peptide bond between two amino acids

Formation of peptide bonds eliminates the ionizable-carboxyl and -amino groups of the free amino acids except for those at the amino and carboxy termini

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Figure 4.2 Challenge of the Weekto be given out on 8-25-08

Work with your group of 4 people and find at least oneexample of a mutation in humans, or in industry-relevant plants, animals or microbes. Present, on a single,one-side, typed page, the amino acid mutated, the phenotype ofthe effect on the organism, the molecular reason that themutation causes the effect(s), and the effect that this mutationhas on/for humans.

Hand in a single, one-sided, typed sheet of paper with ALLgroup members names (first and last name correctly spelled) aswell as a single sentence behind each name describing theircontribution to the answer. These will be collected ONLY atthe Breakout Session on September 1.

Aspartame, an artificial sweetener

• Aspartame is a dipeptide methyl ester (aspartylphenylalanine methyl ester)

• About 200 times sweeter than table sugar

• Used in diet drinks

Aspartame, an artificial sweetener

• Aspartame is a dipeptide methyl ester (aspartylphenylalanine methyl ester)

• About 200 times sweeter than table sugar

• Used in diet drinks

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Cleaving, blocking disulfide bonds-mercapto-

ethanol

See also Figure 4.4

Figure 4.5

Figure 4.5 Amino acid sequence of bovine insulin.This mature processed form of insulin exemplifies intra-peptide disulfide bonds (within the same chain) and inter-peptide disulfide bonds (between chains)

PROTEIN PURIFICATIONGeneral strategyTissue disrupt crude fractionation selected fractionation

Proteins can be separated by:_____________ : gel electrophoresis, gel filtration

chromatography, dialysis, centrifugation ____________: salting out _________: ion-exchange chromatography, isoelectric focusing_________________: hydrophobic interaction chromatography,

reverse phase chromatography_______________: affinity chromatography, antibodies

Purified proteins can be analyzed by:____________: Edman degradation, (proteolysis), Mass Spectrometry

____________: X-ray crystallography, NMR___________: automated solid phase

To purify large amounts of proteins one requires:

1. An _______ for the protein (enzyme, antibody, etc.)

2. A __________to separate desired protein from "all" other proteins and to keep the protein "active“ during the process

3. Example strategy:

Salting-out: the "specific" precipitation of a given protein at a specific high-salt concentration

Ion exchange Gel-filtration Affinity chromatography

Dialysis often used to remove salts: separation of protein from small molecules through a semipermeable membrane (cellulose)

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Figure 5.3

Different types of chromatography (1)

_____________________: proteins passed over a column filled with a hydrated porous beads made of a carbohydrate or polyacrylamide polymer (large molecules exit (elute) first)

Fig 5.4Gel-filtration chromatographyDifferent types of chromatography (2)

__________________: separation of proteins over a column filled with charged polymer beads (+ charged beads = anion-exchange chromatography; - charged beads = cation exchange chromatography.) Positively charged proteins bind to beads of negative charge & vice versa. Bound proteins are eluted with salt. Non-charged proteins and proteins of similar charge to resin will elute first.

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Fig 5.5Ion-exchange chromatography:


_________________________: proteins are passed through a column of beads containing a covalently bound high affinity group for the protein of interest. Bound protein is eluted by free high affinity group.

Affinity chromatography: Fig 5.6


______________________________________of protein:

hydrophobic interaction chromatography (HIC) and reverse-

phase chromatography (RPC) are both based on interactions

between hydrophobic patches on the surface of a protein and

hydrophobicity of ligands (e.g. alkyl groups) covalently

attached to a gel matrix. In RPC, proteins can bind very

strongly to the gel and require non-polar solvents for their

elution. In HIC protein binding is promoted by inclusion of

salt in the solvent and elution of proteins is caused by

decreasing or removing salt from the solvent.

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Column Chromatography

(a) Separation of a protein mixture

(b) Detection of eluting protein peaks

_________________: movement of charged solutes through a gel in response to an electric field

_____________________________________________:chemically inert; polymerized acrylamide matrix of

controlled pore size; allows separation of proteins based on mass and charge

_______________: (sodium dodecyl sulfate, page 73): anionic detergent used for polyacrylamide gel electrophoresis. It complexes with proteins (1 SDS/2 amino acids) denatured protein of negative charge proportional to protein mass. Note: reducing agents (mercaptoethanol, dithiothreitol) are also added to reduce disulfide bonds. Mobility of many proteins under these conditions is linearly proportional to the log of their mass. Smaller proteins migrate faster.

Polyacrylamide gel electrophoresis (PAGE): Fig 5.8(a) SDS-PAGE Electrophoresis

(b) Protein banding pattern after run

Comassie Blueor

Silver staining

SDS

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Proteins can also be separated by electrophoresis based on their native charge.

_______ (isoelectric point): pH at which net protein charge is zero

__________________: electrophoresis of proteins (w/o SDS) in a pH gradient to a position in the gel at which pH = pI. pH gradient formed by polyampholytes (small multi-charged polymers of many pIs).

Isoelectric focusing: Fig 5.10

Combined SDS-PAGE andIsoelectric focusing: 2D-PAGE

Fig 5.11

Purification Table

Fig 5.13(see also Fig. 5.9)

In western blotting or immunoblotting, proteins are separated in an SDS‐PAGE gel, transferred to a polymer, and then stained with a fluorescent antibody.

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Fig 5.23Amino Acid Composition (1)

1. Determine amino acid composition

hydrolysisa. Peptide free amino acids

6 N HCl100°C, 24 hr

b. Amino acid composition of hydrolysates determined by automated cation-exchange chromatography (amino acid analyzer). Column contains solid granules of sulfonated polystyrene. Amino acids reacted with ninhydrin (yields colored product) & detected by O.D.

Acid-catalyzed hydrolysis of a peptide

Problem: Asn → Asp; Asn + Asp = Asx or BGln → Glu; Gln + Glu = Glx or Z

Loose some: Ser, Thr, Tyr; Loose most Trp

Amino Acid Composition (2)

c. Another method for aa composition analysis is to treat protein hydrolysate with phenylisothiocyanate (PITC) at pH 9.0 to yield PITC-aa derivatives, separate by HPLC via hydrophobic attraction of aa side chains to hydrocarbon matrix of column and quantitate by OD 254 nm (due to PTC moiety).

(The first pure protein analyzed for a.a. composition was -lactoglobulin. It took several years of work. Today amino acid analyzers allows composition analysis within 2-4 hours with samples as small as 1 pmole!!!)

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Amino acid treated with PITC

phenylisothiocyanate

Chromatogram from HPLC-separated PTC-amino acids

Note: acid treatment converts Asn→Asp; Gln→Glu; Trp is destroyed, some loss of Ser, Thr, Tyr.

B = (Asn→Asp) + Asp; Z = (Gln→Glu) + Glu

Fig 5.252. Determine amino-terminal residue

_________ devised the first method to label N-terminal residue by reacting 2,4-dinitrophenylbenzene with -amino group yellow derivative. Subsequent hydrolysis (6N HCl) hydrolyzes away all other amino acids. N-terminal residue derivative identified by chromatography

Today Dabsyl chloride (colored derivative) or Dansyl chloride ( fluorescent derivative) are used.

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3. Determination of amino acid sequence by Edman Degradation (________________) (1950)

Edman Degradation is now done on sequenators (automated, liquid phase sequenator analysis by HPLC (one cycle 2 hr)

Gas-phase sequenator: detection of pmole amounts (single SDS-PAGE band)

Frederick Sanger determined the first complete sequence of a protein (insulin) in 1953 (51 amino acid long)

Note: Amino acid sequence of small proteins and peptides is now commonly determined by mass spectrometry(e.g. electrospray MS, MALDI MS).

Edman degradation procedure

Phenylisothiocyanate(Edman reagent)

pH = 9.0

Phenylthiocarbamoyl-peptide

F3CCOOH

Edman degradation procedure (cont)

Aqueous acid

Polypeptide chain with n-1 amino acids

Returned to alkaline conditionsfor reaction with additional phenylisothiocyanate in the next cycle of Edman degradation

Edman degradation procedure (cont)

Aqueous acid

Polypeptide chain with n-1 amino acids

Returned to alkaline conditionsfor reaction with additional phenylisothiocyanate in the next cycle of Edman degradation

Submit remaining polypeptide to another

round of Edman DegradationPTH-

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Fig 5.26Edman Degradation Summarized

Protein Cleavage

Edman degradation limited to polypeptides of 50 a.a.

____________________:Cyanogen bromide (CNBr): splits on carbonyl side of Met

_____________________:

________: protease cleaves on carbonyl side of Arg and Lys

_____________: protease cleaves on carbonyl side of bulky hydrophobic and aromatic amino acids

Protein cleavage by BrCN

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Cleavage, sequencing an oligopeptide

See also Fig 5.27

______________must be removed from proteins by reduction & alkylation before sequencing.

(iodoacetate)DTT ICH2COO-

R-S-S-R R-SH HS-R R-S-CH2-COO-

DNA recombinant technology DNA sequence of nascent protein

Limitation of the amino acid sequence only from DNA code: it is only the sequence of the nascent protein.

_______________: direct polypeptide product of translation (no modification)

Reducing agent

Cleaving, blocking disulfide bonds

Phylogenetic tree for Cytochrome c

•Protein amino acid sequences can be deduced from the sequenceof nucleotides in the corresponding gene

•Closely related species contain proteins with very similar amino acid sequences

•Differences reflect evolutionary change from a common ancestral protein sequence

human & chimp Cyt c are identical

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Polypeptide chain nomenclature

• Amino acid “residues” compose peptide chains

• Peptide chains are numbered from the N (amino) terminus to the C (carboxyl) terminus

• Example: (N) Gly-Arg-Phe-Ala-Lys (C) (or GRFAK)

• Formation of peptide bonds eliminates the ionizable -carboxyl and -amino groups of the free amino acids

chapter 3 (with parts of 4 and 5) bcmb 3100 - chapter 3 (part1)dmohnen/bcmb3100/lecturenotes... ·...

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