BCMB 3100: Test 1
90 Cards in this Set
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genome
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heritable information
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replication
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process of copying the genome
catalyzed by DNA polymerase
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transcription
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DNA is transformed into RNA
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plasma membrane
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lipid bilayer
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fibrous proteins
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water insoluble
provide mechanical support "tough"
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globular proteins
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compact/ spherical
hydrophobic interrior
hydrophillic exterrior
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allosteric enzymes
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regulate biochemicals through metabolic pathways
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vitalism theory
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1800's- animate world obeys different laws than inanimate world
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Friedrich Wohler
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1828-showed urea could be synthesized from inorganic materials
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Edward/ Hans Buchner
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1897-death of vitalism
fermented sucrose into alcohol w/ yeast extract
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Emil Fischer
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1890- lock and key model
-4 substarte enzyme
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Max perutz
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hemoglobin 3D structure
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John kendrew
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myoglobin 3D structure
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watson/ crick
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determined 3D structure of DNA
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biochemical generalizations
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life requires life
reactions require catalyst
info of life is transmitted through genome
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proteins
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constructed of amino acids linked by peptide bond- forms unbranched polymer
fold into 3D structure
act as catalyst- enzyme
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nucleic acid
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information molecules of cell
-store/ transfer info
constructed of nucleotides
-5-carbon sugar, deoxy/ribose w/ base and phosphate
ex: DNA/ RNA
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DNA
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deoxyribose
nucleotides linked by phosphodiester links
double stranded
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RNA
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ribose
single stranded
mRNA= template for protein synthesis
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lipids
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storage for of fuel/ barrier
much smaller than proteins/ nucleic acids
part hydrophilic/ hydrophobic= allowed to form barriers
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carbs
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fuel- glucose stored as glycogen
linked in chains- branched
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Eukaryote
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membrane bound compartments:
- nucleus/ ER/ golgi/ mitochondria/ lysosomes/ peroxisomes/ chloroplasts
cell= inside is chemically differnt than envio
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nucleus
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info center of cell
double bounde- contains pores
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mitochondria
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2 membranes
fuel molecules undergo combustion into co2/ H2o - generating ATP
produces 90% of cells energy
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ER
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smooth= processes exergonous chemicals
rough= ribosomes attached- synthesize proteins that will secrete from the cell
-transported into lumen during translation- then folds into proper shape w/ help from chaperones
-leave through transport vesicles
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golgi complex
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recieves TV from rough ER
differnt set of carbs attach
sorts proteins
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endosome
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endocytosis
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lysosome
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digestive enzymes
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H2O
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solvent of life
polar
bound covalently
H-bond= partial + H binds w/ partial - O
- common weak bond
non-polar/ hydrophobic cannot dissolve in water
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weak interactions
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ionic bonds= opposite charged- 2.8A-- 40-200 kj/mol
-maximized in uncharged envio
-weakend by H2O= competes for attraction/ solvation around shell
h-bonds= arise when H is cov bounded to EN atom- 2.6-3.1A--2-20kj/mol
-weaker than cov
stronger in absence of water
van der waals-depend…
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hydrophobic effect
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non-polar molecules cluster together in H2O
-b/c water binds strongly to itself
- clusters- not b/c of high affinity for each other but because when they dissociate they release h2O molecules
--entropy driven
--spontaneous- no energy required
membrane formation/ protein folding= powe…
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amphipathic
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both hydrophilic/ hydrophobic
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Kw
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1.0 x 10^-14 at 25 deg c
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pH= -log10(H+)
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...
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Ka
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acid= proton donor/ base acceptor
Ka= [H][A]/[HA]
pKa= log(1/Ka)
- pH at which the acid is 1/2 dissociated
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henderson hasselbach
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pH= pKa + log(A/HA)
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Amino Acids
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contain: carbon linked to amino group/ carboxylic acid group/ H+/ R-group
neutral pH= exist as zwitterions (dipolar)= NH3+/ COO-
low pH= NH3/ COOH
high pH(9)= NH2/ COO
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4 AA classification groups
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1. hydrophobic aa w/ non polar r-groups
- only H/ C side chains
-Gly/ Ala/ Leu/ Ile/ Met/ Pro
2. polar aa w/ neutral r groups
-r group contains EN atom- hydrophillic
-Asp/ Glutamine
3. positive aa w/ r groups at pH=7.4
-highly hydrophilic
-Arg/ Lys/ His
4. negative aa= have acidi…
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essential aa
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must be obtained from diet
-His/ Ile/ Leu/ Cys/ Met/ Tyr/ Val/ Phy/ Thr
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hydropathy
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relative hydrophobicity of each aa
- larger it is- more it prefers a hydrophobic environment
--- effects folding
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proteomics
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study of large sets of proteins
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primary structure
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3D structure depends on primary backbone
linear polymer- alpha amino group linked to alpha C
- has directionality
crosslinked peptide chains contain disulfide bonds
-formed through oxidation of cysteine residues
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Sanger
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determined aa sequence of insulin
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secondary structure
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residue by residue conformation backbone of a polymer
a-helix= coiled structure- stabalized by H-bonds between Carbonyl O--- N amnio group
-- right handed
--- rise= .15nm pitch= .54 3.6 residue per turn
B-sheets= 2+ peptide chains (b-strands) not coiled
-- stabalized by H bonds bet…
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conformation
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arrangement of sub groups that are free to change positions without breaking any bonds
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configuration
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arrangement of atoms that cannot be changed without breaking bonds
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turns/ loops
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allow chain to change direction
loops- on protein surface/ interact w/ other proteins/ envio
turns= loops containing less than or equal to 5 residues
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tertiary structure
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3D conformation in native folded state
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motifs
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recurring protein structures
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domains
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independently folded/ compact distinct structural units in protein
- connected by flexible segment
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Quaternary structure
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3D structure of multi-subunit
- multiple chains can assemble in single protein
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dimer
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2 identical subunits
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denature
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unfolding of native conformation
due to chaotropic agents= denature proteins
- ex: urea
- dont cleave bonds- disrupt 2, 3, 4 structures
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reducing agents
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B-mercaptoethanol
dithiothreital
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christian Anifinsen
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showed aa determined 3D structure
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cooperativity folding
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formation of one part of structure leads to formation of remaining part
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current theory of protein folding:
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not random
cooperative/ sequential
dependent on primary structure
some require help folding= chaperones/ enzymes
rapid < 1s
most have single native 3D shape
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chaperones
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proteins that bind newly synthesized polypeptides/ assist folding
- increase folding rate
- prevent incorrect folding
- most are heat shock proteins
- requires ATP
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collagen
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fibrous protein w/ triple helix
most abundant vertebrate protein
- bone/ tendons/ cartilage/ skin/ vessels/ glue
3 left hand helices
- 3 aa per turn pitch= .94nm rise= 3.1
- high % of Pro/ Gly/ Hyp
- Hyp allows more interchain H-bonding/ stabalization of helix
- Pro/ Hyp prevent …
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scruvy
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vitamin c deficiency
weakness in blood vessels/ skin
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cofactor
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small non protein required for enzyme activity
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prosthetic
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metal ion/ non amino acid tightly bound to protein- essential for activity
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holoprotein
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complete= protein w/ all its cofactors
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apoprotein
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w/ out cofactors
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myoglobin
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bond O2- stores/ transports O2 in muscle
prosthetic group= heme= Fe-protoporphyin IX
globular protein w/ 8 a-helices
all polar residues on surface
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hemoglobin
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allosteric protein= changes shape when bound to a particular molecule
transports O2 in blood
prosthetic group= heme= Fe-protoporphyrin IX
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conservative substitutions
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do not affect conformation
- aa in same family
--- ex: Val-- Ile
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nonconservative subs
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effect conformation
ex: Glu-- Val
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bohr effect
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increase of CO2 in blood-results in lower pH- decreases hemoglobins affinity for O2
-p50
- graph shifts right
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globular proteins
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compact shape- many reversible turns w/ a-helix/ b-structure
- 2-16 aa in loops
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4 protein domains
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1. all a-helices/ loops
2. all B sheets and non-repetitive structures that link b-strands
3. mixed a/ B= supersecondary structures
--a-helix/ b-strands alternate
4. a+ B= clusters of a helices/ b sheets in seperate regions of chain
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7 amino acid groups
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1. aliphatic= Gly/ Ala/ Val/ Leu/ Ile/ Pro
2. aromatic= Phe/ Tyr/ Trp
3. sulfur-containing= Met/ His
4. alcohols= Ser/ Thr
5. Basic= His/ Lys/ Arg
6. acidic= Asp/ Glu
7. amides= Asn/ Gln
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gel filtration chromatography
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proteins pass over column filled w/ hydrated porous beads filled w/ carbs
- large molecules exit first
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ion exchange chromatography
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separates proteins over column filled w/ charged polymer beads
-opposite charges attract
- bound proteins elute w/ salt
- non charged elute first
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affinity chromatography
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proteins pass through column of veads containing covalently bound high affinity group for desired protein
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hydrophobic-interaction chromatography (HIC)/ Reverse phase chroma (RPC)
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based on hydrophobic interactions on surface of protein
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polyacrylimide gel electrophoreisis (PAGE)
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chemically inert
polymerized acrylamide matrix of controlled pore size
- allows seperation of proteins based on size/ mass
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SDS-PAGE
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sodium dodecyl sulfate
an ionic detergent used for PAGE
must also add B-mercaptoethanol or dithiothreitol to reduce disulfide bonds
smaller proteins migrate faster
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pI (isoelectric point)
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pH at which net protein charge= 0
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isoelectric focusing
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electrophoreisis of proteins w/o SDS in a pH gradient
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assay
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measure of enzyme activity
disappearance of substrate or appearance of product
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gradient centrifugation
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separates extremely small molecules
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western plot
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permits detection of proteins separated by gel electrophoreisis (imunoblotting)
separated in SDS-PAGE gel
transferred to polymer-- then stained w/ fluorescent antibody
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How to determine primary structure
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1st hydrolyze into aa using heat and strong acid
individual aa can be separated by ion exchange chromatography
-visualized w/ flourorescamine
sequenced determined using edman degradation (limited to 50 aa)
- removes 1 residue at a time from the amino end of the peptide
phenyl isoth…
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Cyanogen Bromide
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CnBr
splits on C=O side of Met
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enzymatic cleavage
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trypsin= cleaves on C=O side of Arg/ Lys
chymotrypsin= cleaves on C=O of bulky hydrophibic and aromatic aa
dissulfide bonds must be removed
-- reduction-- alkylation
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nascant protein
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direct polypeptide product of translation
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6 major groups of enzymes
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1. oxidorecductases= catalyze oxi-redox reactions
-transfer electrons
2. transferases= transfer functional groups
- prominant in aa synthesis/ degradation
3. hydrolazses= cleaves molecules by adding H2O
-Ex: trypsin
4. lyases= adds atoms/ func. groups to a double bond/ reduces to f…
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haloenzyme
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complete= w/ cofactors- catalytic ready
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apoenzyme
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w/ out cofactors
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BCMB 3100: Test 1