Amino Acids and Peptides
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| only source of nitrogen in our bodies | amino acids
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| a metabolic energy source | amino acids; last resource for metabolic energy
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| amino acids are classified based on | R groups
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| the carbon in the center of the amino acid; has an amine, R group,H, and acid group attached | alpha Carbon
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| contains BOTH positive and negative charges at pH 7.4 | zwitterionic
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| Amino Acids are asymmetric, except for | glycine; all others have 4 different things on chiral carbon
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| CORN | L- amino acid; COOH, R group, and NH2; COUNTING CLOCKWISE. If not in this order they are "D"
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| All 20 standard amino acids are "L" true/ false? | true; the D forms are plants and bacteria
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| antibiotics derived from bacteria with D- amino acids degrade more slowly | true
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| amino acids are broken into charged and uncharged; the 5 subclasses are? | negative and positive (charged) and polar, aromatic, and non-polar (neutral)
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| negative amino acids (2) | Aspartic; Glutamic
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| Positive Amino Acids (3) | Arginine, Histidine, and Lysine
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| Polar amino acids (5) STAGC | Serine, Threonine, Asparagine, Glutamine, Cysteine
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| Aromatic Amino acids (3) PTT | Phenylalanine, Tyrosine, Tryptophan
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| Non- polar amino acids (7) V A L G I M P | Valine, Alanine, Leucine, Glycine, Isoleucine, Methionine, Proline
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| Which amino acid is neither L or D? | Glycine; R group is a Hydrogen; no chiral structure so cannot determine CORN
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| Size/ shape of R- groups determine protein topology, form hydrophobic faces | Neutral, non-polar aliphatic amino acids
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| WHent he R group of an amino acid is attached to the amine group what happens? | It causes a kink in the protein
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| UV absorbed by this type of amino acid | Neutral aromatic; planar shape and stacking
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| Which amino acid R group is an SH | Cysteine; can be sulfur breach protein linkage
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| MUST know charged amino acids by name and structure | check PPT notes
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| an oxidized derivative of cysteine | Cystine; the disulfide S-S bond makes Cystine; free cysteine molecules bond to form cystine in the extracellular space. Once transported intot he cell cystine is reduced back to cysteine
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| The solubility of cystine decreases when pH is? | Low
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| Cystine causes disease under what conditions? | pH imbalance, precipitates in kidney
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| Characteristics of CHARGED amino acids | hydrophilic surfaces in proteins; salt bridges in proteins; acid/ base and covalent protein chemistry
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| Glucose is utilized by every cell in the body | Fat not utilized by brain or RBC's
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| NOT biosynthesized by humans, required in the diet | Essential Amino Acids
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| Tyrosine is biosynthesized from | Phenylalanine
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| Bulky Aliphatics and aromatics (except Tyrosine) | Esential amino acids
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| Short aliphatics, negative charges, amides | Non-essential; also Tyrosine
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| Semi-essential amino acids required by children and pregnant women | Histidine and Arginine
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| amino acids that are biosynthesized by humans | non-essential
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| If no Phenylalinine there is also no | Tyrosine
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| Cysteine is biosynthesized from | Methionine
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| Essential Amino Acids (8) | Iso; Leu; Lys; Meth; Phenyl; Threo; Trypto; Val
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| Recommended Daily Allowance of protein | 0.8g "high quality"; contains all the essential amino acids (animal sources) milk, eggs, meat
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| Low quality protein | deficient in one or more essential amino acid (vegetable proteins)
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| High Lysine and low Arginine is used to deter | herpes outbreaks; lysine disrupts functioning of herpes because it uses high Arginine and Lysine inhibits ARginine utilization; viral replication disrupted
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| molecule that generates a second molecule | precursor
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| If asked the precursor to Epinephrine we would answer | Tyrosine; L- dopa; and Dopamine
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| Amino Acic; CNS neurotransmitter found in spinal fliud | Glycine
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| Non- standard amino acids | Hydroxylysine; HYdroxyproline: Ornithine; Citrulline; Carnitine; Creatine; Taurine; Homocysteine; NME- amino acids
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| Non-standard amino acid important for maintaining collagen structures | Hydroylysine and Hydroxyproline
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| Non- standard amino acid found in natural products from microorganisms; stabilize peptide against degradation | NMe amino acids (N-Methyl Glycine is sarcosine)
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| Non- standard amino acid; intermediates in the urea cycle | Ornithine and Citrulline
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| Non-standard amino acid; Lys derivative; fatty acid transport | Carnitine
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| Non- standard amino acid; Arg+ Gly derivative; accepts and donates phosphate group that can supply ATP in active muscle | Creatine
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| Non- standard amino acid; Cys derivative; Bile salt conjugate | Taurine
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| Non- standard; Met derivative; associated with heart disease | Homocysteine
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| Aspartic acid and Phenyl alanine= | Aspartame
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| Genetic defect of the lys-arg-orn-cystine transport protein in intestine and kidney; (1 in 2500-15000) | Cystinuria; Cysteine is not soluble; causes kidney stones. Treatment= basifying urine (acitozolamide penicillin); conjugating the cystine with drugs and lots of water
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| Genetic defect of the lysosomal cystine transport system | Cystinosis; Cystine accumulates in lysosomes causing increased cell death rates and organ failure (1 in 100,000- 200,000)
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| Genetic defect of a neutral amino acid transport protein in intestines and kidney | Hartnup disease; (1 in 24,000) Prevents proper absorption/reabsorption of these amino acids including Tryptophan (precursor of Vit B6); results in niacin deficiency and PELLAGRA
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| Genetic defect of a homocysteine- metabolizing enzyme, cystathionine synthase. | accumulation of homocysteine causes long, thin bones, lens dislocation, mental deficiencies, and HEART DISEASE. 50% respond to treatment with B6 or B12 and folic acid
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| Phenylketonuria | PKU; 1 in 15,000; inability to breakdown phenylalanine- it builds up and is toxic to brain
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| Symptoms of PKU | intellectual disability; seizures; nausea; vomiting; eczema- like rash; mousy body odor
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| what diet restriction allows normal growth for PKU? | Phenylalanine; BH4 oral can also reduce blood levels of this amino acid
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| amino acids cause the urine to smell like maple syrup; lack of amino acid metabolizing enzymes | maple syrup urine disease;Mennonite families; treatment = dialysis B1 (thiamin) injections; diet low in leucine, isoleucine, valine
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| lack of enzyme needed to metabolize tyrosine | Tyrosonemia; dysfunctional liver and kidney
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| B6, B12, and Folic acid have been shown to prevent atheroschlerotic plaque in what amino acid based disorder | Hyperhomocysteinemia; elevated blood homocysteine- not currently true that B vitamins help and hyperhomocysteinemia is not correlated to heart disease
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| pKa = -log (Ka) | no answer
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| the point of NO net charge | isoelectric point; when pH= pI there is no net charge
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| pH > pI means | negative charge
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| pH < pI means | positive charge
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| calculating pI | pK1 + pK2 divided by 2 = pI
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| how to calculate pI when 3 pKa values given | there will be 4 forms; ex: A-, A, A+, A--; the 4th form will either be 2+ or 2-
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| To determine what 4th form will be we need to know what? | If we are told the amino acid we will know whether it is positive or negative
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| Ex of 4th form with Histidine | A++__A+__A__A- ; fill in the blanks with the given pKa and use the 2 values to the right because they include a neutral A; p31 of notes
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| Low pKa= molecule likes to | release H+; requires high concentration of H+ to populate molecule with H+
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| the pKa's surrounding the neutral species are used to calculate pI | no answer p.36
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| amino acids react to form | peptide (amide) bonds
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| amino acids that make up a polymer are called | residues
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| The 1st amino's COO- binds to the 2nd amino's NH3+ | H2O molecule created; H2 from amino, O from the carboxylic acid
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| Direction of free ends in naming a peptide always | N-terminal to C-terminal; -yl replaces -ine or -ate except the C terminal(last) amino acid in the sequence
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| 2/3 residues | dipeptide/ tripeptide
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| A few residues | Oligo
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| many residues | polypeptide
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| a few residues with 2D or 3D shape, usually 40+ | protein
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| naming example: H3N+-Gly-Asp-His-Leu-Val-Coo- | glycyl-aspartyl-hitidyl-leucyl-valine; start with the H3N side and leave the last amino acid in whole name
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| Isoelectric points are used to determine | electrophoretic mobility of amino acids, peptides, proteins, and manipulating protein solubility
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| When protein's pI= pH of solution, a protein is | least soluble
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| Ligands for opioid receptors; signal for pleasant feelings that counteract pain | Enkephalins and Endorphins; physiological peptides
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| peptide hormone; 9 amino acids (nonapeptide); released from pituitary after hypothalamus detection of lack of water | Vasopressin, or ADH; promotes water retention by kidneys and induces vasoconstriction to maintain blood pressure
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| Lack of the physiological peptide Vasopressin can lead to | diabetes Insipidus; excessive thirst and urination
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| Physiological peptide; doesn't cross blood- brain barrier; secreted from pituitary; uterine contractions | oxytocin
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| advantages of peptide drugs | specific, active,minimal drug interactions, less accumulation in other tissues, less toxicity, potent, diverse
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| disadvantages of peptide drugs | low absorption (injection often required); difficult membrane transport, costly, immunological risk, cleared from body quickly
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