Chapter 1 Amino Acids

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A buffer is a solution that RESISTS change in pH following the addition of an acid or base. A buffer can be created by mixing a weak acid (HA) with its conjugate base (A). If an acid such as HCl is added to such a solution, A- can neutralize it, in the process being converted to HA. If a base is added, HA can neutralize it, in the process being converted to A-. Maximum buffering capacity occurs at a pH equal to the pKa but a conjugate acid/base pair can still serve as an effective buffer when the pH of a solution is what? A zwitterion is the isoelectric form of a molecule having an overall charge of zero, what else is this called? (form) All amino acids found in proteins are of the L-configuration. So where would the Damino acids be found? All of the amino acids with uncharged POLAR side chains are hydrophilic except which one? All of the NONpolar amino acids are hydrophobic except? Amino acids are classified by their side chains (R-groups). If the amino acid has an even distribution of electrons, is it polar or nonpolar?

within approximately 1 pH unit of the pKa - (example) - solution containing acetic acid (HA = CH3COOH) and acetate (A- = CH3COO-) with a pKa of 4.8 resists a change in pH from pH 3.8 to 5.8, with maximum buffering at pH = 4.8. [Note: At pH values less than the pKa the protonated acid form (CH3-COOH) is the predominant species. At pH values greater than the pKa the deprotonated base form (CH3-COO-) is the predominant species in solution.]

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Amino acids are classified by their side chains (R-groups). If the amino acid has an uneven distribution of electrons, is it polar or nonpolar? Amino acids in aqueous solution contain weakly acidic -carboxyl groups and weakly basic -amino groups and each of the acidic and basic amino acids contains an ionizable group in its side chain. Thus, both free amino acids and some amino acids combined in peptide linkages can act as what? Amino acids that have an asymmetric center at the -carbon can exist in two forms, designated D and L, that are mirror images of each other. What are the 2 forms called? Are ketogenic amino acids basic or acidic? What are the ketogenic amino acids? Concept question: Which amino acid will increase your respirations or increase your potassium levels? Concept question: Which hormones have a lot of cysteine?

Polar - ie Acids or Bases

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Buffers

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Stereoisomers, optical isomers, or enantiomers Acidic 1. Leucine 2. Lysine Leucine, Lysine If they have cysteine - they have dissulfide bonds (Insulin, inhibin, growth hormone, prolactin) Serine

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Dipolar form

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Some antibiotics and in bacterial cell walls.

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Tyrosine

Cysteine's side chain has a -SH group which is an important component of the active site of many enzymes, which other amino acid has a side chain that is an important component of the active site of many enzymes?

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Methionine - hydrophillic contains SULFUR Nonpolar

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Define dissociated vs soluble vs. bioavailable in reference to acid/base?

Dissociated is loss of H+ (removal of hydrogens) Bioavailable is neutral, can cross a fat soluble membrane Soluble (POLAR) has a charge and will attract H2O (can not cross BBB) CHARGED at physiologic pH Amino group is protonated (NH2 to NH3+) Carboxyl Group is dissociated (COOH to COO-)

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Most enzymes have serine, threonine or tyrosine in their active sites, what is important about this? N-linked glycosylation of proteins - post translational modification of proteins associated with what cell organelle? O-linked glycosylation of proteins - post translational modification associated with which cell organelle? Proteins located in a hydrophobic environment, such as a membrane, where are the nonpolar amino acids found? Substances that can act as either an acid or a base are defined as what and are referred to as what? The alpha carbon of each amino acid is attached to four different chemical groups and is therefore considered to be a chiral carbon or optically active carbon. What protein is the exception? The alpha carbon of each amino acid is attached to four different chemical groups and is therefore considered to be what type of carbon atom? The amino acids (with acidic side chains) aspartic and glutamic acid: are they proton donors or proton acceptors?

These amino acids have an OH group that is used to make bonds

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Endoplasmic Reticulum

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Describe the amino group and carboxyl group of an amino acid at physiologic pH. Explain the equation: Ka = [H+] [A-] ----------------[HA]

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Golgi Apparatus

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Dissociation constant: The larger the Ka, the stronger the acid, because most of the HA has been converted into H+ and A+. Conversely, the smaller the Ka, the less acid has dissociated and, therefore, the weaker the acid. pH = pKa - 1 = 10% dissociated (10% bioavailable)

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For a base w/ pH = 7 and pKa = 8, how much is dissociated and how much is bioavailable? For and acid w/pH = 5 and pKa = 4, how much is dissociated and how much is bioavailable? If your body is acidic, what effect does this have on your potassium? In proteins found in aqueous solutions, where are the nonpolar acids found? In proteins, the -SH groups of two cysteines can become oxidized forming a covalent cross-link called a dissulfide bond, this is called what? Ketones are broken down and made from Acetyl-CoA, so what is the building block for ketones?

Nonpolar R-groups are found on the outside surface of the protein, interacting w/the lipid environment - they function to stabilize the protein structure 1. Amphoteric 2. Ampholytes (amphoteric electrolytes) Glycine - its alpha carbon has 2 hydrogens attached

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pH = pKa - 1 = 10% dissociated (90% bioavailable)

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Acidic = Hyperkalemic

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Nonpolar (oily) - are found clustered together in the interior of the protein = hydrophobicity of the R-groups - help give it, its 3-D shape. Cystine (a dimer)

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Chiral Carbon or Optically active carbon atom

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Acetyl-CoA

Proton Donors - side chains are fully ionized at neutral pH containing a negatively charged carboxylate group (COO) so called Aspartate and Glutamate to emphasize that these amino acids are negatively charged at physiologic pH Proton Acceptors - side chains are fully ionized at physiologic pH being positively charged

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The amino acids (with basic side chains) Lysine and arginine: are they proton donors or proton acceptors?

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The amino acids w/uncharged polar side chains have a zero net charge at neutral pH, but the side chains of which 2 amino acids can lose a proton at an alkaline pH? The amino acids with nonpolar side chains do not bind or give off protons, do not participate in hydrogen or ionic bonds. They can be characterized as "oily" or lipid like, this is a property that promotes what kind of interactions? The quantitative relationship between the concentration of a weak acid (HA) and its conjugate base is described by what equation? The side chains of Serine, threonine and rarely, Tyrosine contain a polar hydroxyl group that participate in hydrogen bonds, these side chains also have what other function? The side chains of which 2 amino acids contain a carbonyl group and an amide group that can participate in hydrogen bonds? This protein's side chain forms a ring structure and contains an IMINO group (making it different from the other amino acids), what protein is it?

Cysteine and Tyrosine

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What are the branched chain amino acids? What are the NONpolar amino acids?

1. Leucine 2. Isoleucine 3. Valine 1. Gly 2. Ala 3. Val 4. Leu 5. Iso 6. Phe 7. Trp 8. Met 9. Pro The side chain b/c the amino and carboxyl groups are not available for chemical rxn except for hydrogen bonding to other N- or C- Terminals pH will be acidic - you will hyperventilate (increase respirations - to blow off CO2 (acidic) to return body to homeostasis pH = pKa + log [A-] ------------log[HA] pH = pka = 50% dissociated and 50% bioavailable (uncharged - metabolized by the liver) pH = pKa + 2 = 99% dissociated (1% bioavailable) pH = pKa + 1 = 90% dissociated (10% bioavailable) pH = pKa = 50% dissociated (50% bioavailable) pH = pKa - 1 = 10% dissociated (90% bioavailable) pH = pKa - 2 = 1% dissociated (99% bioavailable) Phenylalanine and Tyrosine

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Hydrophobic Interactions

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HendersonHasselbalch equation Serve as a site of attachment for other compounds, such as phosphate groups 1. Asparagine 2. Glutamine

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What dictates the role of an amino acid in a protein?

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What effect would ketogenic amino acids have on your respirations? What is the HendersonHasselbach equation? When the pH = pka what are the percentages of dissociated vs. available?

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Proline contributes to the formation of the FIBROUS structure of collagen and INTERUPTS the helices found in globular proteins Below (gets protonated below its pKa COO- to COOH) Above

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To make an acid more bioavailable, do you stay above or below its pKa?

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To make an base more bioavailable, do you stay above or below its pKa? What are the 2 acidic amino acids?

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1. Asp 2. Glu Neg Charge at physiologic pH 1. His 2. Lys 3. Arg Pos Charge at physiologic pH 1. Insulin 2. Inhibin 3. Growth Hormone 4. Prolactin They have cysteine

Which 2 amino acids are precursors for catecholamines? Which 2 amino acids have a site for N-linked Glycosylation of Proteins? Which 3 amino acids have a site for O-linked glycosylation of proteins? Which amino acid has a sulfhydryl group (-SH) which is an important component of the active site of many enzymes?

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What are the 3 basic amino acids?

1. Asn 2. Gln 1. Ser 2. Thr 3. Tyr Cysteine

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What are the 4 hormones w/dissulfide bonds?

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Which amino acid has an Inole group? Which amino acids are glucogenic and Ketogenic?

Tryptophan the "Largest" amino acid 1. Phe 2. Iso 3. Thr 4. Trp Mr. PITT 1. Ser 2. Thr 3. Tyr 4. Asn 5. Cys 6. Glu Histidine Tryptophan Histidine 1. Serine 2. Threonine 3. Tyrosine 1. Asparagine - amide group 2. Serine or Threonine hydroxyl group

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Which amino acids have uncharged POLAR side chains?

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Which free amino acid is weakly basic and largely uncharged at physiologic pH? Which NONpolar amino acid can form Serotonin & niacin? Which protein is the best buffer in the body? Which three amino acids have a polar hydroxyl group that can participate in hydrogen bond formation? Which three amino acids have side chains that can serve as a site of attachment for oligosaccharide chains in glycoproteins?

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