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146 Cards in this Set
- Front
- Back
The principal classes of biomolecules are:
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proteins, carbohydrates, lipids, and nucleic acids
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Proteins are polymers of:
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amino acids
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Every amino acid contains:
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an amine group (-NH₂), a carboxyl group (-COOH), and an R group called a side chain all bonded to the same carbon atom.
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The carbon that the amine group (-NH₂), a carboxyl group (-COOH), and an R group called a side chain are all bonded to is called:
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the alpha carbon (α-carbon)
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A large biological molecule made of many amino acids linked together through amide (peptide) bonds.
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Protein
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A molecule that contains both an amino group and a carboxylic acid functional group.
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Amino acid
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The variable group bonded to the central carbon atom in an amino acid; different in different amino acids.
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Side chain (amino acid)
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An amino acid in which the amino group is bonded to the carbon atom next to the -COOH group.
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α-amino acid
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The α-carbon is:
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the central carbon in an amino acid to which the amine, carboxyl, and side-chain R groups attach.
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An amide bond that links two amino acids together.
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Peptide bond
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Two amino acids, three amino acids, and many amino acids are called:
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a dipeptide, tripeptide, and a polypeptide respectively
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What reaction forms a peptide bond? What groups react?
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The amine group of one amino acid replaces the hydroxyl group of the carboxylic group on another. An H from the amine and -OH from carboxylic acid form water.
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The sequence of amino acids in a protein chain.
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Primary structure
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The regular and repeating spatial organization of neighboring segments of single protein chains.
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Secondary Structure
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The overall shape of a protein molecule produced by regions of secondary structure combined with the overall bending and folding of the protein chain.
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Tertiary structure
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The overall structure of proteins composed of more than one polypeptide chain.
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Quaternary structure
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What distinguishes one amino acid from another?
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their different side chains
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What are some different functions of proteins in the body?
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-structure and support
-hormones and enzymes -storage and transport -protection (immunity) |
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All of the proteins in living organisms are made from _____ amino acids.
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20 α-amino acids
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19 of the amino acids differ in _______, but one of the them, _______ differs in:
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19 of the amino acids differ in the side chain, but one of the them, proline differs in that it is a secondary amine whose N and α-carbon atoms are joined in a five-membered ring.
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The 20 α-amino acids that make up proteins are classified as:
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neutral, acidic, or basic, depending on the nature of their side chains.
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Neutral amino acids are further divided into:
How many of the amino acids are neutral? |
those with polar or non-polar side chains
15 are neutral |
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What is of central importance in determining the shapes and functions of proteins?
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Intermolecular forces
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Non-polar side chains are described as:
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hydrophobic
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Polar, acidic, and basic side chains are described as:
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hydrophilic
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Forces of attraction other than covalent bonds that can act between molecules or within molecules.
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Noncovalent forces
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"Water-fearing"; does not dissolve in water:
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hydrophobic
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"Water-loving"; dissolves in water.
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hydrophilic
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Amino acids contain both an acidic group (carboxyl group) and a basic group (amine group), can they undergo an intramolecular acid-base reaction?
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yes, the result is a transfer of the hydrogen from the hydroxyl group of the carboxylic acid to the amine group.
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The intramolecular acid base reaction of an amino acid forms a:
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dipolar ion, an ion that has one positive charge (ammonium ion) and one negative charge (carboxylic acid anion).
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Dipolar ions are known as:
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zwitterions
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What is the charge of zwitterions?
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neutral
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A neutral dipolar ion that has one positive charge and one negative charge.
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zwitterion
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Because they are zwitterions, amino acids have many of the physical properties of:
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salts
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What are the properties of amino acids?
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-can form crystals
-high melting points -soluble in water, not soluble in hydrocarbons solvents |
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In acidic solutions, zwitterions:
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ACCEPT protons on the carboxylic acid anion, leaving only the positively charged amine group.
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In basic solutions, zwitterions:
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LOSE protons on the amine cation, leaving only the negatively charged carboxylic acid anion group.
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Draw the reaction of a NH₃⁺CH(R)COO⁻ + H⁺
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NH₃⁺CH(R)COO⁻ + H⁺ → NH₃⁺CH(R)COOH
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Draw the reaction of a NH₃⁺CH(R)COO⁻ + OH⁻
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NH₃⁺CH(R)COO⁻ + OH⁻ → NH₂CH(R)COO⁻ + HOH
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Do amino acids ever exist in a completely un-ionized form in either the solid state or in aqueous solution?
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No
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THe charge of an amino acid molecule at any given moment depends on:
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the particular amino acid and the pH of the solution.
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Define the isoelectric point (pl)
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The pH at which the net positive and negative charges are evenly balanced for a particular amino acid.
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The point at which the net charge of all the molecules of a particular amino acid in a pure sample is zero.
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isoelectric point (pl)
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Is the (pl) the same for all amino acids?
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No, the (pl) is different for each amino acid, due to differences in their side chains.
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Pl influences:
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protein stability and determines which amino acids in an enzyme participate.
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The acidic and basic side chains are particularly important because:
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at physiological pH, these groups are fully charged and can participate not only in ionic bonds within a protein chain but can also transfer H⁺ from one molecule to another during reactions.
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Which amino acids are hydrophilic and which are hydrophobic?
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The polar, acidic, and basic side chains are hydrophilic since they can interact with water.
The non-polar side chains are hydrophobic since they cannot interact with water. |
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Describe hydrolysis:
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A reaction in which a bond or bonds are broken and the H- and -OH of water add to the atoms of the broken bond or bonds.
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What reaction is involved in the formation of peptide bonds?
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amide formation where: an H from the amine is added to the carboxyl group -OH forming water as the N-chain is added to the carbonyl group C.
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Alanine
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Ala
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Glycine
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Gly
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Isoleucine
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Ile
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Leucine
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Leu
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Methionine
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Met
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Phenylalanine
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Phe
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Proline
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Pro
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Tryptophan
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Trp
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Valine
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Val
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Asparagine
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Asn
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Cysteine
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Cys
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Glutamine
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Gln
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Serine
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Ser
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Threonine
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Thr
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Tyrosine
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Tyr
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Aspartic acid
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Asp
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Glutamic acid
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Glu
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Arginine
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Arg
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Histidine
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His
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Lysine
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Lys
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Having right or left-handedness with two different mirror image forms that cannot be superimposed.
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chiral
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The opposite of chiral; having superimposable mirror images and thus no right or left-handedness.
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achiral
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Define a chiral carbon atom aka chiral center:
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A carbon atom bonded to four different groups.
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The two mirror image forms of a chiral molecule.
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Enantiomers (optical isomers).
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Define stereoisomers:
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Isomers that have the same molecular and structural formulas but different spatial arrangements of their atoms.
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Does the presence of a chiral atom always produce a chiral molecule?
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yes
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Pairs of enantiomers always differ in:
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their affects on polarized light and in how they react with other molecules that are chiral.
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Pairs of enantiomers often differ in:
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their biological activity, odors, tastes or activity as drugs.
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Of the 20 alpha amino acids, how many are chiral?
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19 of them; only glycine is achiral.
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Even though the 19 chiral α-amino acids can exist as either D- or L- enantiomers, nature exclusively uses only:
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L-amino acids for making proteins
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Which amino acids have abbreviations that are not the first 3 letters?
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G.A.I.T.
Glutamine Gln Asparagine Asn Isoleucine Ile Tryptophan Trp |
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How do you determine if a molecule is chiral?
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Make a list of the different carbon atoms and the groups bonded to them. If a carbon has 4 different groups, it is chiral.
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Define primary protein structure:
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The sequence in which amino acids are linked by peptide bonds in a protein.
ie.. Alanine + Serine → Alanylserine but, Serine + Alanine → Serylalanine |
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In the primary structure, the electrons of each carbonyl group double bond are shared to a considerable extent with:
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the adjacent C-N bond (the α-carbon-nitrogen bond).
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Does the C-N unit that shares electrons with the carbonyl group double bond carbons rotate?
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No, this sharing of bonds makes it sufficiently rigid that there is no rotation.
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One planar unit consists of:
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the carbonyl carbon, -NH group bonded to it, and the two adjacent α-carbons.
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Are the side chains on the same or opposite side of the backbone of the primary structure?
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On opposite sides.
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The amino acid with the free -NH₃⁺ group at the end of a protein.
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Amino-terminal (N-terminal) amino acid.
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The amino acid with the free -COO⁻ group at the end of a protein.
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Carboxyl-terminal (C-terminal) amino acid
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An amino acid unit in a polypeptide.
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Residue
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By convention, peptides and proteins are always written with the amino-terminal amino acid on the ______ and the carboxyl-terminal amino acid on the _______.
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left; right
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The individual amino acids joined in the chain are called:
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residues
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How are peptides named?
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Starting at the N-terminal amino acid and ending at the C-terminal amino acid, all residues are named in order. The residue name endings are changed from -ine to -yl for all except the C-terminal amino acid.
They can also be named by listing their 3-letter abbreviation in order, separated by hyphens. ie... serine + tyrosine + glycine = seryltyrosylglycine or Ser-Tyr-Gly. |
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In L-forms of amino acids, the amino group is on the:
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left
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When drawing the 3-D primary protein structure of a L-hand form, the H atoms on the top are on the ____ side and point:
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left side; away from you
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When drawing the 3-D primary protein structure of a L-hand form, the H atoms on the bottom are on the ____ side and point:
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right side; toward you
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The planar unit square connects:
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The α-carbon, carboxyl O, -NH group H, and second α-carbon.
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Where there are ionized acidic and basic side chains, the attraction between their positive and negative charges creates:
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salt bridges
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Where there are interactions between hydrocarbon side chains, the attraction is from:
These interactions are called: |
london-dispersion forces; hydrophobic
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What is the one type of covalent bond in the formation of protein structure?
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covalent sulfur-sulfur bonds.
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covalent sulfur-sulfur bonds are formed between these residues:
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between the thiol-containing side chains of two cysteine amino acids which form a sulfide bond.
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What are the different types of bonds that determine protein structure?
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-H bonds
-Salt bridges -Hydrophobic interactions -Sulfur-Sulfur bonds |
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An S-S bond formed between two cysteine side chains; can join two separate peptide chains together or cause a loop in a single peptide chain.
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Disulfide bond
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Describe the reaction of a disulfide bond:
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-SH + -SH [O]⟶ S-S + HOH
Sulfide + Sulfide (with oxidizer) ⟶ Disulfide + HOH (two H's from each S add to an O from the oxidizer to form the HOH) |
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In the covalent disulfide bond between two cysteine residues, if they are in different protein chains, then:
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the chains become linked together
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In the covalent disulfide bond between two cysteine residues, if they are in the same protein chain, then:
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a loop is formed in the chain
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The regular and repeating structural patterns (ie.. α-helix, β-sheet) created by hydrogen bonding between backbone atoms in neighboring segments of protein chains.
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Secondary protein structure
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Secondary protein structure in which a protein chain forms a right-handed coil stabilized by hydrogen bonds between peptide groups along its backbone.
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Alpha helix (α-helix)
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Secondary protein structure in which adjacent protein chains either in the same molecule or in different molecules are held together by hydrogen bonds along the backbones, forming a flat sheet-like structure.
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Beta-sheet (β-sheet
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A tough, insoluble protein whose protein chains form fibers or sheets.
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Fibrous protein
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A water-soluble protein whose chain is folded in a compact shape with hydrophilic groups on the outside.
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Globular protein
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Define secondary protein structure:
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The spatial arrangement of the polypeptide backbones of proteins.
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The secondary structure includes two kinds of repeating patterns known as:
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α-helix and β-sheet
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In both α-helix and β-sheet patterns, what holds the polypeptide in place?
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H bonding between backbone atoms
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In both α-helix and β-sheet patterns, the H bonds connect:
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the carbonyl oxygen atom of one peptide unit to the amide H atom of another.
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an α-helix is:
and resembles: |
A single protein chain coiled in a spiral with a right-handed (clockwise) twist. It resembles a coiled telephone cord.
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What is the spatial arrangement of the H bonds and amino acid R-groups in the α-helix?
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The H-bonds lie vertically along the helix and the amino acid R groups extend to the outside of the coil.
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What is the spatial arrangement of the H bonds and amino acid R-groups in the β-sheet?
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H-bonds connect different protein chains, which are fully extended, with their R-groups extending above and below the sheet.
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Proteins are classified in several ways, one of which is to identify them as either:
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fibrous or globular proteins.
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How are the N-terminals and C-terminals arranged among the protein chains in a β-sheet?
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They run in an antiparallel arrangement
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Which structure is primarily responsible for the nature of fibrous proteins?
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secondary protein structure
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The way in which an entire protein chain is coiled and folded into its specific 3-dimentional shape.
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Tertiary protein structure
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A protein with the shape (secondary, tertiary, and quaternary structure) in which it exists naturally in living organisms.
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Native protein
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Secondary structure depends mainly on attraction between ___________, where tertiary structure depends mainly on attraction between ____________.
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Secondary structure depends mainly on attraction between BACKBONE ATOMS, where tertiary structure depends mainly on attraction between AMINO ACID SIDE CHAINS THAT ARE FAR APART ALONG THE SAME BACKBONE.
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Define a Simple protein:
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A protein composed of only amino acid residues.
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Define a Conjugated protein:
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A protein that incorporates one or more non-amino acid units in its structure.
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Which structure determines the overall shape of fibrous proteins? Which structure determines the overall shape of globular proteins?
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Secondary structure determines the shape of fibrous proteins. Tertiary structure determines the overall shape of globular proteins.
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A simple protein is made of nothing but __________, while a conjugated protein has:
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A simple protein is made of nothing but amino acid residues, while a conjugated protein has something else in its structure, i.e... myoglobin which has a heme group in its structure.
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The way in which two or more protein chains aggregate to form large, ordered structures.
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Quaternary protein structure
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Collagen and Hemoglobin both have this structure:
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quaternary protein structure
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The most abundant of all proteins in mammals is:
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collagen; making up 30% or more of the total.
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Define primary structure:
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the sequence of amino acids connected by polypeptide bonds.
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Define secondary structure:
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the arrangement in space of the polypeptide chain (α-helix and β-sheet)
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Define tertiary structure:
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the folding of a protein into a specific 3-D shape
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Define quaternary structure:
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two or more protein chains assembled in a large 3-D structure.
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Describe the bonds involved in each structure.
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Primary = peptide bonds
Secondary = H-bonds between backbone carbonyl oxygen and amine hydrogens. Tertiary = interactions between amino acid side chains, (in some cases disulfide bonds), that can be quite far apart along the backbone. Quaternary = noncovalent interactions. |
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The reverse of protein synthesis is:
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protein hydrolysis
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Describe the reaction of protein hydrolysis:
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Protein reacts with H³O⁺ or enzyme which breaks peptide bonds and adds an -OH group to the carboxyl carbon and an H⁺ to the amine.
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The loss of secondary, tertiary, or quaternary protein structure due to disruption of non covalent interactions and/or disulfide bonds that leaves peptide bonds and primary structure intact.
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Denaturation
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Denaturation is accompanied by changes in:
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physical, chemical, and biological properties.
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Is solubility usually increased or decreased by denaturation?
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decreased
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What agents cause denaturation?
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heat, mechanical agitation, detergents, organic solvents, extremely acidic or basic pH, and inorganic salts.
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How does heat denature proteins?
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It breaks side-chain interactions in globular proteins.
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How does Mechanical agitation denature proteins?
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stiffens the proteins
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How do Detergents denature proteins?
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disrupts hydrophobic side chains
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How do Organic polar solvents denature proteins?
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Polar solvents such as acetone and ethanol interfere with H bonding by competing for bonding sites.
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How do Inorganic salts denature proteins?
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by disrupting salt bridges
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