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| Aspartate (Aspartic Acid) |
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| Glutamate (Glutamic Acid) |
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Positively charged, Aromatic
His
H |
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Ingesting These Little Molecules Has Value When Knowledge Fails
(Lys, Thr, Leu, Met, Ile, His, Phe, Val, Trp) |
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| Protein-Energy Malnutrition (PEM) associated with emaciation, muscle-wasting, loss of adipose |
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| Protein-Energy Malnutrition (PEM) associated with Feet edema, distended abdomen, enlarged liver, dermatosis, tooth loss. Also associated with alfatoxin poisoning |
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| Conversion of Phe->Tyr by Phe-hydroxylase is deficient. Accumulation of Phe and its breakdown products in the blood result in mental retardation. Effects can be prevented. Treatment is low protein supplemented with AA mix low in Phe. Aspartame contains an ester of the Asp-Phe dipeptide. |
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| Characteristics of Polar R Groups |
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• Hydroxyl, sulfhydryl, or carboxylamide
• H-bonding
• Cys in disulfide bonding
• Pro has circular side chain, fixed dihedral angle provides rigidity (not polar in structure, but behaves as such in protein)
• Asn (N) was first AA to be isolated |
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| Characteristics of Aliphatic, Nonpolar R Groups |
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• Hydrocarbon R groups
• Gly has no side chain (H) (non-chiral)
• Hydrophobic contacts
• Not exposed in large numbers on the surface, except in proteins interacting with lipids
• Ala used in mutagenesis studies bc of small inert side chain |
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| Characteristics of Aromatic R Groups |
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• Phe, Tyr, Trp absorb UV light at 280 nm. Used for protein detection and quantification. Allows each protein to be assigned an extinction coefficient.
• Trp (W) has only one codon, largest AA, less frequent in protein |
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| Characteristics of Charged R Groups |
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• Often protein surface
• Intra- and inter- chain interactions
• Salt bridges
• Many enzymatic sites (bc can change ionization states) |
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Signaling domain
Interaction domain |
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Transmembrane
Signal peptide
Interaction domain |
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Nuclear localization signal
Nucleic acid binding region
Interaction domain with glycosamioglycans |
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Right handed coil
3.6 residues per turn
Pitch is 5.4 angstrom
Stabilized by hydrogen bonds
Amino acid side faces out |
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| Hydrophobic AA line up on one side, hydrophilic on the other side. Often seen in membrane proteins |
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| Aliphatic residue such as Leu or Ile repeated every 7 residues on helix. Acts as dimerization domain. Sequence: L(X6)I(X6)L(X6)L(X6). 7 residues ~ 2 turns of helix. |
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Post Translational Mods:
Permanent |
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| Partial proteolysis – zymogens, insulin |
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Post Translational Mods:
Relatively permanent (covalent additions) |
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Glycosylation - Ser/Thr (O-linked) and Asn (N-linked oligosaccharides)
Hydroxylation - collagens
Acylation, prenylation, methylation, addition of glycosyl-phosphatidyl-Inositol anchor
ADP-ribosylation.
Covalent prosthetic groups (e.g. biotin and phosphopanthetein for lipid synthesis) |
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Post Translational Mods:
Reversible (covalent additions) |
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Phosphorylation of proteins via protein kinases: occurs on Ser/Thr or Tyr residues.
Methylation of Lys and Arg of histones in regulation of gene transcription |
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N-Glycosylation
Glycosylation General |
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The sequence Ser/Thr-X-Asn is the motif of the primary structure where N gets glycosylated. (X not a Proline)
• during or immediately after protein synthesis.
• occurs in the lumen of the endoplasmic reticulum
• Glycoproteins are destined to be secreted or exposed on the cell surface. |
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| Glycosyl-phosphatidyl inositol anchor (GPI anchor) |
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Addition of lipid
• Added in lumen of the ER to a synthesized protein
• Signal near the C-terminus of the protein. Precursor protein is cleaved before two small residues (w+1 and w+2) and transferred to the GPI
• GPI anchored proteins:
o - have more mobility on lipid membranes than transmembrane proteins.
o - often accumulate in cholesterol-rich microdomains (membrane rafts). |
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| The affinity of oxygen binding to hemoglobin is decreased by decreasing pH or increasing CO2 concentration (Bohr effect). |
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| Mutation of the B-globin gene. Mutated hemoglobin tends to crystallize. |
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| Vancomycin and B-Lactam Antibiotics |
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| Interfere with synthesis of cell wall |
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| Erythromycin and tetracycline |
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| Disrupt ribosomes that make proteins |
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| Inhibit enzymes involved in replicating DNA |
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| Interfere with DNA synthesis |
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| Reversibly inhibit the transpeptidase that catalyzes the crosslinking of a bacterial cell wall. Penicillin type drugs are B-lactam antibiotics. In the presence of B-lactamase (hydrolyzes B-lactams) bacteria are penicillin resistant. |
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| Combo drug of amoxicillin (B-lactam) and clavulinate (reversible inhibitor of B-lactamase) |
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| transcribing protein-coding genes |
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| Basal Transcription Factors (TFIIs) |
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Locate TATA Box, define transcription start
recruit RNA polymerase II
provide low level of transcription
present in all cell nuclei |
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| Regulatory Transcription Factors ( |
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control the rate of transcription
function either as activators or repressors
are often tissue-specific |
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