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168 Cards in this Set
- Front
- Back
sulfydryl groups are a defining feature of:
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thiol compounds, R-SH
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Hydroxyl groups are a defining feature of:
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alcohols
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Amino groups are a defining feature of:
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Amines. eg: putrecine
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Amido groups are a defining feature of:
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Amides. eg: pepties
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Carbonyl groups are a defining feature of:
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a variety of compounds
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Acyl groups are a defining feature of:
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a variety of compounds
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What are the four major classes of biomolecules?
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amino acids, carbohydrates, lipids, and nucleotides
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Characteristics of amino acids?
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amphoteric, exist as zwitterions (at neutral pH), and polymerize to form polypeptides
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amphoteric
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has both acidic and basic groups
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zwitterions
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have both positive and negative charges
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Characteristics of carbohydrates:
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1. are polyhydroxylated aldehydes or ketones (or derived thereof)
2. may be simple or polymeric |
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glycosidic bond
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bond connecting 2 saccharides into a disaccharide
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oxidation
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loss of electrons
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reduction
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gain of electrons
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Order of electronegativity most to least
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O-N-S-C-H
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log10 x =
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10^? = x
the power to which 10 is raised to get x |
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antilog10 y =
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10^y
10 raised to the yth power |
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pH =
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-log[H+]
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What is an acid by the bronsted definition?
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H+ donor
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Bronsted base?
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H+ acceptor
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A reaction is at equilibrium when...
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...the rate of the forward reaction equals the rate of the reverse reaction. NO net change in product or reactant concentration.
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how would you deteremine the equilibrium constant?
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concentration of the products at eq. divided by the concentration of the reactants at eq.
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What does Keq tell you?
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how likely the reaction is to proceed in the forward or reverse direction
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Keq>1 will proceed in which direction
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foreward
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Keq less than 1 will proceed in which direciton?
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reverse
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Dissociation constant of an acid Ka=?
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[A-][H+]/[HA]
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pka=?
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-logKa
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smaller ka = ?
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weaker acid
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smaller pka=?
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stronger acid
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henderson hasselach equation?
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ph = pka + log([A-]/[HA])
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the pKa of most alpha amino acids is about?
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9.3
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pKa of alpha-carboxylic acid group of most amino acids is about?
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2.2
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What is a buffer?
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a solution that resits changes in pH when either acid or base is added
composed of a weak acid and its conjugate salt |
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What are the most important intracellular buffers?
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phosphate and proteins
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for every mmHg the partial pressure of CO2 increases, the mM dissolved CO2 increases by how much?
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.0301 mM dissolved CO2
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The pKa of blood is?
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6.1
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hydroxyl suffix
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-ol
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carboxyl ending
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acid
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amino suffix
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-ine
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amido suffix
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-ide
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acid anhydride ending
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anyhydride
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ketone suffix
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-one
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aldehyde suffix
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-al
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Characteristics of Lipids:
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1. Diverse
2. poorly soluble in water 3. composed primerily but not exclusively, of C and H 4. Often amphipathic |
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Characteristics of Nucleotides:
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1. compsed of at least on phospate, a sugar(ribose/deoxyribose) and a nitrogenous ring
2. polymerize to form biologically essential molecules (RNA/DNA) 3. in monomeric form are often important as energy currency and components of coenzymes |
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avagodro's number
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6.02x10^23, #C's in 12 grams of carbon
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amphipathic
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both hydrophyllic and hydrophobic components
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salt of organic acid suffix:
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-ate
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normal blood plasma pH=
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7.4
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normal blood plasma pH above what? and below what? will cause death?
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7.6 and 7.2
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Functions of Protiens:
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enzymatic catalysis (hexokinase)
mechanical support (collagen) transport and storage (hemoglobin) movement (actin) transmission of never impulses (opsin) regulation (insulin) protection (immunoglobulins) |
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-ase often indicates?
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catalytic function
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-in often indicates?
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non-enzymatic function
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only achiral aa at alpha carbon?
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glycine
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normal aa's are L or D?
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L
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Abbreviations of glycine
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Gly, G
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Abbreviations of alanine
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Ala, A
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Abbreviations of valine
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Val, V
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Abbreviations of leucine
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Leu, L
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Abbreviations of isoleucine
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Ile, I
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Abbreviations of phenylalanine
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Phe, F
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Abbreviations tryptophan
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Trp, W
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Abbreviations methionine
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Met, M
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Abbreviations proline
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Pro, P
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Abbreviations serine
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Ser, S
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Abbreviations cysteine
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Cys, C
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Abbreviations threonine
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Thr, T
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Abbreviations tyrosine
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Tyr, Y
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Abbreviations asparagine
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Asn, N
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Abbreviations glutamine
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Gln, Q
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Abbreviations Aspartate
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Asp D
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Abbreviations glutamate
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Glu, E
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Abbreviations Lysine
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Lys, K
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Abbreviations arginine
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Arg, R
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Abbreviations histidine
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His, H
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Does the pKa of an aa change or remain the same when an aa is incorporated into a protein? Why?
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pka changes because interactions between nearby amino acid side chains can affect the ability of a given side chain to donate or accept H+s.
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pka aspartate
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3.9
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pka glutamate
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4.3
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pka lysine
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10.5
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pka arginine
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12.5
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pka histidine
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6.0
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the peptide bond has ______-_______-_______ character
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partial double bond
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Does the C and N of a peptide bond rotate with respect to one another?
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no
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the N terminus of a peptide is always depicted on the________ side?
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left
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Common modifications to to aa's of polypeptide chains
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phosphorylation
gylcosylation hydroxylation carboxylation others |
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phosphorlyation
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occurs on aa side chains with free hydroxyl groups
done to many proteins can increase or decrease activity |
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glycosylation
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carbohydrate groups may be added to protein via N or O linkages
done to many proteins carbohydrate groups often act as destination tags |
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hydroxylation
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of prolyl or lysyl residues
done to a few proteins |
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carboxylation
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of glutamyl groups
done to a few proteins especially ones for blood clotting |
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aa's that undergo o-linked glycosylation:
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ser, tyr, thr
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aa's that undergo n-linked glycosylation
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asn
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lysyl residues are hydroxylated at which carbon
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delta
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lysyl residue reacts with ________ and _____ via the enzyme __________ to form _____ and ____.
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alpha ketoglutarate, oxygen, lysyl hydroxylase, hydroxylysyl residue and succinate
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What role does vitamin C play in hydroxylation?
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reduces the enzyme if it becomes inappropriately oxidized
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prolyl residue reacts with ____ and____ in hydroxylation via enzyme ____ to form _____ and _____
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alpha ketoglutarate, oxygen, prolyl hydroxylase, hydroxylprolyl residue, and succinate
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What is oxidized in hydroxylation?
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lysyl residue and alpha ketoglutarate
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What is reduced in hydroxylation?
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oxygen
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What is oxidized in carboxylation? what is reduced?
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oxidized; glutamyl and vitamin K dihydroquinone
reduced: CO2 and O2 |
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Which carbon in glutamyl undergoes carboxylation?
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gamma
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What types of bonds/interactions orchestrate folding or proteins into 3D shape?
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disulfide bonds
ionic interactions hydrogen bonds hydrophobic interactions |
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What energy investment is required to disrupt disulfide bonds?
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100 kcal/mol
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What energy investment is required to disrupt ionic interactions
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10 kcal/mol
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What energy investment is required to disrupt hydrogen bonding
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5 kcal/mol
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What energy investment is required to disrupt hydrophobic interactions?
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3kcal/mol
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which bonds/interactions are most important in protien 3D shape?
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hydrogen bonding and hydrophobic interactions
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Describe disulfide bridges
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covalent bonds
formed by oxidation of cysteinyl residues intra or inter chain |
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What's a hydrogen bond?
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bond between O,N,S and hydrogen covalently bonded to another electronegative atom
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What's hydrophobic interaction?
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occurs between nonpolar R groups
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primary structure of a protein is maintained by...
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covalent peptide bonds
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secondary structure is maintained by...
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hydrogen bonds
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What's tertiary structure of a proteins? maintained by?
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overall 3D shape
h bonds, hydrophobic interactions, ion interactions, disulfide bridges |
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Quaternary protein structure?
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more than one polypeptide and their spatial arrangement
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alpha helix is stabalized from h bonds how many residues apart
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4
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alpha helix is destabled by...
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large numbers of charged R groups
bulky R groups prolyl residues |
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parallel beta sheet
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run in same direction
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anti parallel beta sheets
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run in opposite directions
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Same chain vs. independents chain...
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involve segments of same protein/different porteins
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Tertiary structure is maintained by which structure?
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secondary
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Gross classification of tertiary structure...
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Fibrous or Gobular
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Fibrous
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(rod like)
keretin silk collagen |
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Globular
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(spherical)
hemoglobin immunoglobulins alcohol dehydrogenase |
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keratin's secondary structure
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alpha helical
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silk's (fibroin) secondary structure
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beta sheet
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collagen's secondary structure
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neither alpha helix or beta sheet, unique
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hemoglobulin
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mostly alpha helical
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immunoglobuin secondary structure
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mostly beta sheet
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alcohol dehydrogenase's secondary structure
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both aphla helix and beta sheet
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oligomeric protein
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more than one protein
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dimer
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2 polypeptide chains
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homodimer
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both chains are identical
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heterodimer
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the 2 chains are different
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trimer
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3 protein subunits
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tetramer
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4 protein subunits
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Changes in what environmental factors cause a protein to lose activity? why?
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pH, salt concentration, temperature
destroys weak interactions that maintain protein's shape |
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Denaturations?
loss of primary structure? reversible? |
breaking of weak bonds maintaining protein's conformation
no usually not |
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endothermic
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heat is consumed
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exothermic
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heat is released
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endergonic
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useful energy is consumed
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exergonic
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useful energy is released
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Gibbs free energy (G)
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the amount of energy available to do useful work
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change in G measures
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how endergonic or exergonic a reaction is
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exergonic reactions spontaneous or non spontaneous?
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spontaneous
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Can you determine if a reaction is endo/exothermic from knowing exer/endergonic?
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no
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enthalpy
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heat content
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enzymes
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catalysts, undergo no net change
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Do enzymes change the keq of a rxn?
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no
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Can enzymes alter the ability of a reaction to proceed spontaneously?
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no
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Do enzymes increase the rate of reaction equally in the forward and reverse direction?
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Yes, as to not change keq
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cofactor
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non protein molecule required for enzyme activity
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examples of cofactors
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metal ions (Fe++, Mg++, Zn++, Ca++)
organic molecules (called coenzymes) |
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apoenzyme
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enzyme without cofactor, usually inactive
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holoenzyme
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apoenzyme and cofactor together
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How are cofactors bound to enzymes?
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covalently or non covalently
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Enzymes stabilize what?
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transition states
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induced fit model
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substrate binding cuases conformational change in the enzymes that make sit easier to attain the transition state
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classifications of enzymes
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oxidoreductases
transferases hydrolases lyases ligases isomerases |
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oxidoreductases
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catalyze oxidation-reduction reactions
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transferases
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catalyze transfer of groups such as amino, carboxyl, methyl, carbonyl, tec.
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hydrolases
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catalyze hydrolytic cleavages
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lyases
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catalyze cleaveage of c-c, c-n, c-o, or c-s bonds without hydrolysis or redox
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ligases
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catalyze the formation of new c-c, c-n,c-s or c-o bonds, in a reaction coupled to hydrolysis of ATP or other high energy compound
|
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isomerase
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catalyze intra molecular rearrangements
|
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enzymes increase rxn rate ____ fold
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10^5 to 10^11 times
|
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allosteric effectors
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bind to enzyme noncovalently
reversible sometimes substrate, often not often products of metabolic pathway |
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product inhibition
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at high product concentration, may compete with substrate for binding in the active
|
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inducible enzymes
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rate of enzymes sythesis increases in response to increased substrate concentration or related metabolite
|
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repressible enzymes
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rate of enzyme synthesis decreases in response to increased [product] or related metabolite
|
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constitutive enzyme
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rate of enzyme synthesis remains virtually constant for the life of the cell
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