Protein Structure & Function

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In principle: Proteins are polymers of amino acids

[sometimes NH₃⁺ & COO^- : depends on pH]  [iGen3-06-01] [iG1 7.02]

R = radical group:
asymmetric (Homework); levo (L)-rotatory  [cf. dextro (D)-rotatory]

determines biological properties: 20 types (note 1- & 3-letter codes) [iGen3-06-02] [iG1 7.Table 1] [iG1 7.03]

Group properties	Three- & Single-letter codes
neutral, non-polar  (hydrophobic]	gly,ala, val, leu, ile, pro, met, phe, trp
	G    A    V    L    I    P    M     F    W
neutral, polar (hydrophilic)	gly, ser, thr, cys, tyr, asn, gln
	S    T    C    Y    N    Q
polar basic  (positive charge)	lys, arg, his
	K    R    H
polar acidic (negative charge)	asp, glu
	D    E

[Memorization of the abbreviations is not required for exams, but will make your lives as biologists easier!]

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Dehydration of carboxy & amino termini forms peptide bond [iGen3-06-03] [iG1 7.05]

Peptidyl Transferase catalyzes analogous reaction
carboxyl (C) terminus of growing polypeptide in P site
            cleaved from the tRNA &
joined to amino (N) terminus of new amino acid in A site [iGen3-06-18]

                => carboxyl end "grows": in the last example,

NH₂ - fmet - phe - gly - pro - COOH   +   NH₂ - lys - COOH

NH₂ - fmet - phe - gly - pro -  lys - COOH

Recall that amino acid in A site is linked to tRNA through COOH terminus
    Repeating, remnant backbone subunit [N - C(R) - C ] is an amino acid residue

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Proteins have four levels of structure  [iGen3-06-04]

Primary Structure - order of amino acid residues in polypeptide
                20^N possible, where N is number of residues
                Potential for enormous variety:
                    e.g., 20⁵ = 3.2 x 10⁶  possible pentapeptides

Secondary Structure - configuration of [-N-C(R)-C-] backbone [iG1 6.06]
        alpha helix: a right-handed helix
beta-pleated-sheet: parallel / antiparallel chains
both stabilized by H-bonds

Tertiary Structure - 3-Dimensional folding of backbone [iG1 7.07]
cys + cys pairs form disulfide bridges ( - S - S -) [iG1 7.08]
        pro residues form hydrophobic "corners"
        hydrophilic residues occur on exterior,
                participate in reactions in aqueous environments
         hydrophobic residues occur in interior,
                interact with membrane lipid bi-layer
gly fits in both hydrophobic & hydrophilic environments

Quaternary Structure - assembly of multiple subunits [iG1 7.11]
            monomers / dimers / oligomers
               e.g., hemoglobin is a tetramer: two alpha + two beta chains
           charged residues (asp, glu, lys, arg, his) form ionic bonds bx subunits

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Post-translational processing (IG1 Table 8.6)
Chemical modification of amino acids
          addition of formyl group to met  fmet
   Addition of carbohydrate side chains (glycoproteins) (IG1 8.21)
ABO blood group proteins
   Amino acids may be cleaved out of primary structure (IG1 8.22,23,25)
e.g., biologically active insulin is less than half the primary  sequence (IG1 8.24)

preproinsulin proinsulin insulin
        (110 aa's)            (86 aa's)        (51 aa's)

signal peptide (24 aa's) clipped from amino terminus
C peptide (31 aa's) excised from center
Tertiary (active) structure of insulin is
A chain (30 aa's) & B chain (21 aa's) held together by 3 disulfide bridges

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Detection of genetically-based variation in Proteins

allelic variation translates to proteins with minor changes in electric charge
allozymes arise from different alleles of the same protein gene locus
          substitution of alternatively charged amino acids changes overall charge
             [cf: Isozymes are homologous proteins encoded by different gene loci]

Ex.: Sickle-cell hemoglobin (HbS) is a variant of standard HbA beta globin protein
glu  val  in sixth residue of beta chain
             because GAG  GUG in sixth codon of beta-chain mRNA
HOMEWORK: What is the corresponding mutation in the DNA?
             "minus"  "neutral" charge net negative charge decreased
val stabilizes crystalline form of hemoglobin    'sickling' of rbc's

Homework: Critique the following statement:
           "Electrophoresis of hemoglobin shows two alleles, F and S, for the Hb gene."

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Overview of protein function

Enzymatic catalysis of biological reactions

Substrates are bound in active sites: the Induced-Fit Model
        Lowered energy of activation
            biological reactions occur at body temperature
                                                          with lower energy input
Anabolic - synthesis of complex molecules from simpler components
Ex., transferases synthesize peptide bonds
synthetases attach tRNA to amino acid
Catabolic - break-down of complex molecules into simpler components
Ex., dehydrogenases remove protons (H⁺)
proteases split peptide bonds

Structural motifs recur in proteins with similar functions

        Identification of motifs allows inferences about function (IG1 Res Briefing 9.1, pp. 170-171)
Helix - turn - helix motifs binds Ca⁺⁺ (IG1 RB9.1)
Zinc - finger motifs binds major & minor DNA grooves (IG1 RB9.2) (cf. iG1 7.12]
Leucine Zipper motif binds DNA and forms 'zippable' dimer (IG1 RB9.3)

    Other protein functions
Structural
Collagen constitutes 25% of human protein
Histones are the major components of chromosomes
                [online MGA animation of DNA packing into chromosomes]

Nucleic Acid binding proteins
Polymerases, nucleases, helicases, ligases, etc.

    Transport
    Hemoglobin in blood & myoglobin in muscle bind O₂

Miscellaneous
            immunoglobulins, hormones , etc.
    Major Histocompatibility Complex (MHC) determines transplant success

Drosophila Genome Project has cataloged >11,000 genes with protein products
> 1/2 have unknown functions

Human Genome comprises ~20,500 protein coding genes: why so few?

Protein-coding regions may be transcribed in different ways from different promoters
mRNAs may be spliced in different wasy to combine different exons

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All text material ©2012 by Steven M. Carr

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