Proteins and Amino Acids

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Structural proteins are:
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tendons, cartilage, hair, nails
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Contractile proteins are:
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muscles
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Transport proteins are :
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hemoglobin
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Storage Proteins are :
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milk
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Hormonal Proteins are:
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insulin and growth hormone
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What do enzyme proteins do?
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catalyze reactions in cells
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What do protection proteins do?
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immune response
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What is the basic structure of an AA?
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alpha carbon, amino group, carboxy group, and R side chain
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What determines the properties of amino acids?
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its side chain
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How many naturally occurring AA are there?
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20
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Nonpolar is when the R group is what?
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Nonpolar: R = H, CH3, alkyl groups,
aromatic
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What are your polar R groups?
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O
R = –CH2OH, –CH2SH, –CH2C–NH2,
(polar groups with –O-, -SH, -N-)
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A positive ion has a low/high pH?
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low
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A negative ion has a low/high pH?
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high
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A neutral ion is called what?
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zwitterion
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H3N–CH2–COOH
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Positive ion
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H3N–CH2–COO–
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Zwitterion
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H2N–CH2–COO–
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negative ion
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Zwitterion has both a ?
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positive and negative charge
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H3N–CH2–COO–
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zwitterion of glycine
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NH2–CH2–COOH
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glycine
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What are proteins?
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long polypeptide chains
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What is a polypeptide chain?
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less than 40-50 amino acids or residues
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Polypeptides larger than 40-50 amino acid chains or residues are called what?
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proteins
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The structure, function and general properties of a
protein are all determined by the ?
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sequence of amino acids that make up its primary sequence
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To make a protein, these amino acids are joined together in a polypeptide chain through the formation of a ________ bond
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peptide
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____ is strongly favored over ____.
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trans; cis
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What is the hierarchal nature of protein structure?
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1. Primary Structure-amino acid sequence
2. Secondary Structure- alpha helix or beta sheet
3. Tertiary Structure- formed by assembly of secondary structures
4. Quaternary Structure- assembly of more than one polypeptide chain
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What is the primary structure of protein?
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the sequence of amino acids along the polypeptide chain
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What terminus do you begin and end with when reading or making proteins?
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begin with the N, end with the C (right to left)
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The primary sequence or main chain of the protein must organize itself to form a ______ structure. This is done in an elegant fashion by forming __________ structure elements
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compact; secondary
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The two most common secondary structure elements are _______ _______ and ______ _______, formed by repeating amino acids with the same angles
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alpha helices and beta sheets
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turns, coils, triple helix, etc., are _________ structures?
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secondary
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Alpha helices and beta sheets have regular _________ bonding patterns.
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hydrogen
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Three-dimensional arrangement of amino acids with the polypeptide chain in a corkscrew shape
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secondary structure- alpha helix
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Held by __ bonds between the __ of –N-H group and the __ of C=O of the _______ amino acid along the chain
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hydrogen; H; O; 4th
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High tensile strength
fibrillary proteins due to residues extending outward
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alpha helices
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Polypeptide chains are arranged side by side
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secondary beta sheet structure
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Hydrogen bonds form _________ chains
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between
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R groups of extend above and below
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Beta sheets
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Typical of fibrous proteins such as silk.
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beta sheets- secondary structure
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Beta sheets can be _______ or __________.
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parallel or antiparallel
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What is a triple helix?
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secondary structure- three polypeptide chains woven together
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Glycine, proline, hydroxyproline and hydroxylysine
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triple helix
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H bonding between –OH groups gives a strong structure
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triple helix
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Typical of collagen, connective tissue, skin, tendons, and cartilage
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Triple helix
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To make the protein look like a protein, the
secondary structure elements come together to
form the tertiary structure-the _________ _______ of the ________.
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the overall shape of the protein
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Cross links between R groups of amino acids in chain
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tertiary structure
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disulfide
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-S-S-
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ionic
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–COO– H3N–
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Hydrogen bonds
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HO-
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–CH3 H3C–
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hydrophobic
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________ proteins then bind together to form dimer, trimers, or higher order structures
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folded; quaternary structures
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The functional form of hemoglobin is a __________.
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tetramer
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The backbone and side chain bonds are all
_______ bonds, but _________ bonds are required to maintain _________, ________, and ________ structures.
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covalent; non-covalent; secondary, tertiary, and quaternary
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Bond types include:
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– Hydrogen bonds (H-bonds)
– Electrostatic (ionic)
– van der Waals
– disulfide bonds
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__________ interactions also predict 3D shape
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hydrophobic
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Pairs of ________ can form _______ bonds between different parts of the main chain.This adds stability
and is common in __________ proteins
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cysteines; disulfide; extracellular
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Hydrophobic interactions are not attractive interactions but results from the inability of water to form __ bonds with certain _____ _______.
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Hydrogen; side chains
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Hydrophobic a.a. residues cluster in _______ of globular proteins
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interior
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Hydrophilic a.a are usually ____________.
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towards the surface
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Some proteins get help from __________ that deal with ________ structure formation.
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chaperones; tertiary structure
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Chaperones assist in protein ________.
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folding
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Chaperones create a _________ environment for the protein.
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hydrophilic
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Protein degradation
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ubiquitin-proteasomal pathway
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Steps in ubiquitin-proteasomal pathway.
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1. Ubiquitin (globular protein) attaches to protein to be degraded
2. Polyubiquitinated proteins recognized by
proteasome (proteolytic complex)
3. Proteasome degrades proteins into peptides, then into amino acid precursors for disposal by immune system
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Disruption of secondary, tertiary and quaternary protein structure.
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denaturation
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Forms of protein degradation:
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ubiquitin-proteasomal pathway and denaturation
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What causes denaturation?
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1.heat/organics- Break apart H bonds and disrupt hydrophobic attractions
2. acids/ bases- Break H bonds between polar R groups and ionic bonds
3. heavy metal ions- React with S-S bonds to form solids
4. agitation- Stretches chains until bonds break
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heat/organics- Break apart __ bonds and disrupt _________ attractions
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Break apart H bonds and disrupt hydrophobic attractions
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-acids/ bases- Break H bonds between _________ and _____ bonds
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polar R groups; ionic bonds
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heavy metal ions- React with ____ bonds to form ______.
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-S-S-; solids
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Agitation- _________ chains until they break.
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stretches
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Hard boiling an egg
1. Cooking food to destroy E. coli
2. Heat used to cauterize blood vessels
3. Autoclave sterilizes instruments
4. Milk heated to make yogurt
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Denaturation
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misfolded proteins can aggregate to form beta- pleated fibrils
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Amyloidopathies
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Accumulation of misfolded proteins in tissues causes:
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amyloids
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Example of Amyloidopathies?
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Alzheimers disease
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_______ can change the conformation of other proteins.
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prions
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example of prion disease:
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mad cow disease

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