Exam 1 Study Guide
Exam 1 Study Guide BCH 4603
Popular in General Biochemistry
Popular in Biochemistry
This 10 page Study Guide was uploaded by Carly Miller on Sunday September 13, 2015. The Study Guide belongs to BCH 4603 at Mississippi State University taught by Florencia Meyer in Spring 2015. Since its upload, it has received 171 views. For similar materials see General Biochemistry in Biochemistry at Mississippi State University.
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Date Created: 09/13/15
Macromolecules assume their shape in response to most metabolic machinery operates where the useful properties of water arise from its what forces do H bonds provide why does water have a higher melting and boiling point are H bonds weak or strong how many dipoles in a water molecule in ice form how do water molecules arrange in liquid form room temp ice melts and water evaporates spontaneously these processes increase if you increase entropy then G will be why H can form a bond with what must the donor and acceptor atoms be for an H bond to take place if something can H bond it will have a higherlower bp H bonds are strongest when donor and acceptor atoms are solubility of organic molecules depends on 2 things why can water dissolve polar substances why is solvation favorable water in water structure cohesive forces between water molecules extensive H bonding individually weak but a water molecule can form up to 4 H bonds 2 form H bonds with exactly 4 others regular lattiace molecules are disorganized and in continuous motion bond ratio 1 to 34 randomness or entropy negative because H is positive it is the increase in S entropy that makes G negative OandN electronegative higher in a straight line polarity and ability to form H bonds with water it can form salvation spheres around the electrolytes preventing the solute molecules from interacting it increases the entropy the system negative G why do gases have poor solubitlity which gases are not soluble in water and which are how do water molecules arrange around hydrophobic molecules what does this do to the order of the system larger hydrophobic surfaces have largersmaller effects non polar regions react how what forces keep them together amphipatic bioligical membranes and 3d structures of proteins are held together by hydrophobic interactions intended to achieve what what causes van der waalslondon forces a transient dipole in one atom will cause what in another these two dipoles do what as they become closer what is a van der waals radius the net attraction between the nuclei is maxmin four types of non covalent interactions the cumulative affect of many weak interactions maintains they are non polar decreases their entropy not nitrogen oxygen carbon dioxide are ammonia hydrogen sulfide bc they are polar they form a cage like structure and are constrained in their possible orientations increases order of the molecules larger cluster together to minimize area exposed to water hydrophobic interactions combination of polar and non polar regions on same molecule hydrophobic interactions no actual interaction takes place to achieve greatest thermodynamic stability and decrease ordering of water around hydrophobic surfaces electron clouds around atoms influencing close by atoms causes transient electric dipole in another atom attract each other the electron clouds repel each other how close an atom will allow another atom to approach maximal hydrogen bonds ionic interactions hydrophobic interactions van der waals the structure of many biomolecules what hydrogen bonds ionic interactions hydrophobic interactions van der waals the movement of water from hi to low concentration produces what is osmotic pressure osmotic pressure depends on what is osmolarity osmolarity depends on osmosis what does water mostly move through isotonic hypertonic hypotonic why do water molecules move very fast in solution Keq of water Kw of water product of HOH in solution is always in pure water in equilibrium the concentration is what is the basis of the ph scale pH low pH and high H acid is a proton base is a proton between neutra groups O HO between peptide bonds O HN attraction or repulsion water quotcagingquot around hydrophobic molecules two atoms in close proximity osmotic pressure the force needed to resist flow of water osmolarity the extent to which the solute dissociates into two or more ionic species ONLY the NUMBER of dissolved particles water movement across biological membranes aquaponns iso same inside and out hyper osmolarity outside cell is greater water moves out into solution hypo osmolarity is greater inside cell water moves in quotproton hoppingquot 18E 16 1x 10A14 1 X 10quot14 Mquot2 the same H OH 1x10 A 7 Kw log H acidic donor acceptor the stronger the acid what is its tendency to donate its proton do weak acids dissociate in solution stronger acid what kind of pKa titration what is a buffer what does a buffer consist of where do buffers best work at ionizable groups in proteins contain their own what is an example of a buffer system in this system if H increases pH falls H falls pH increase with henderson hasselbach equation a buffer works best when the oxygen in water acts as a weak what is a nucleophile in condensation reactions greater tendency to donate not completely stronger acid lower pKa add base to acid solution the base provides OH to bond with free H H20 is formed at mid point half the acid has been dissociated so concentration is equal at this point the pH is equal to the pKa a solution that prevents changes in pH when base or acid is added a weak acid and its conjugate base plus or minus 1 pH unit from the pKA maximal buffering capacity pKa and thus at a particular pH they will be charged or not have an H or not blood plasma carbon dioxide carbonic acidbicarbonate buffer system increase in carbonic acid and equation shifts to left the excess COZ expired increased respiration ex hypovolemia diabetes cardiac arrest becomes more basic decrease in canonic acid and equation shifts right fall in 002 levels in blood breathing slows ex vomiting hypoventilation respiratory depression A HA1 log 1 0 so PH would equal pKA nucleophile negatively charged and attack electrophiles during sub or addition reactions a water molecule is formed use ATP and exlude water in hydrolysis proteins are polymers of what gives a protein its three D structure and function the carbon of an amino acid is amino acids exist as DandF amino acids in nature are in what configuration what make each amino acid different aliphatic AAs glycine alanine proline valine leucine isoleucine methionine aromatic AAs water is used to break a bond alpha amino acids combination of amino acids in a particular order chiral except glycine stereoisomers same formula different configuration D right F left side chains or residues R groups R groups consist of Carbon and Hydrogen glycine alanine proline valine leucine isoleucine methionine smallest with no chiral center next smallest with methyl side chain cyclic structure with secondary amino group kinks and rigidity in proteins 3 carbons w double methyl at the end protein folding 4 carbons with double methyl group at end 2 chiral centers contains thio eter group in an internal position R groups have phenyl ring phenylalainine tyrosine tryptophan phenylalanine tyrosine tryptophan aromatic AAs absorb Uv light at polar uncharged AAs senne threonine cysteine aspargine glutamine positively charged AAs lysine arginine histidine negatively charged AAs aspartic acid glutamic acid the 21st amino acid at physiological pH 72 74 all amino acids have a charge of zwitterion what determines overall charge each amino acid has how many pKa values very hydrophobic w phenyl group contains a terminal alcohol group contains a N in the indole ring 280 NM used to estimate protein conc senne threonine cysteine aspargine glutamine hydroxyl group hydroxyl group and a methyl terminal sulfhydrylthiol grop highly reactive can act as a weak acid and form disulfide bond with another cysteine forms cystine hydrophobic contain terminal amide groups have a net positive charge at neutral pH lysine arginine histidine terminal amino group terminal guanidinium group aromatic imidazole group in side chain pKa is 60 so can be or uncharged at neutral pH aspartic acid glutamic acid aspartic carboxyl group negative charges on proteins glutamic carboxy group selenocysteine ZGI39O amino group protonated and carboxyl group ionized number of amino and carboxyl groups 2 does the nonionic form of an amino acid exist how many deprotonation events in each amino acid isoelectric point or pl if the amino acid has no ionizable side chain the pi is what happens to the net charge as you get further away from the isoelectric point iprgtp pHltp how many amino acids have ionizable side chains what happens to the titration curve because of this what are the polymers of amino acids oligopeptide polypeptide protein what kind of bond is the peptide bond polypeptides have characteristic titration curves depending on what charge does the polypeptide have at characteristic pl conjugated proteins no zwitterion H is always on the amino not the carboxyl at least 2 pH at which the amino acid has a net charge of zero zwitterion state the mean of the two pKa values the greater the net charge negative charge no charge positive charge 7 3 inflection points pK1 pK2 and pKr polypeptides few aminioacids many amino acids thousands of amino acids planar with no rotation around CN axis trans form R groups pKa of different R groups affected by new environment no net charge proteins that have an extra chemical component needed for function this extra chemical is called a prosthetic group and it is permanently associated like glycoproteins and lipoproteins primary structure of a protein secondary structure tertiary structure quarternary structure what does primary structure determine what is polymorphism what percentage of proteins in humans are polymorphic conserved regions what did sanger do this made scientists realize chemical protein sequencing can be used to determine wht what did sanger develop to label the amino terminal residue hydrolysis in GM urea yields what you can only unveil what with sanger sequencing human insulin has how many polypeptides labels and removes the N terminal residue leaving all other bonds intact what happens in the process of edman degradation what is the result what is crucial and what would happen otherwise two ways to break disulfide bonds linear sequence of amino acids in the polypeptide chain stable local arrangement of amino acid that forms characteristic 3D patterns describes all aspects of the 3d folding when there are 2 or more polypeptides to a protein folding arrangement function and properties different sequences in different individuals 20 30 regions in the protein responsible for function worked out the polypeptide sequence of the amino acid residues in Insulin DNA and amino acid sequences are related primary sequence of a polypeptide 1fouro24dinitrobenzene FDNB individual amino acids the amino terminal residue 2 heterodimer edman degradation phenylisothyocianate reacts with n terminal residue then the peptide bond is cleaved in anhydrous triflouroacetic acid a labeled amino acid plus the rest of the polypeptide which has a new N terminus residue maximum efficiency is crucial otherwise you end up with mixtures 1 oxidation of the cysteine residue to 2 cyseic acid residues 2 reduction by DTT or mercaptoethanol to produce 2 cys residues two ways to cleave polypeptide chains how do you determine where the 8 8 bonds are how are resulting fragments separated for each disulfide bond there will be what is the easiest way to determine sequence of a protein differences in what are used to separate proteins what is salting out what does dialysis allow for chromatography what comes out first cation exchange chromatography anion exchange chromatography what are the implications of anion cation chromatography affinity chromatography SDS polyacrylamide gel electrophoresis SDSPAGE 2D electrophoresis mass spectormetry followed by acetylation 1 proteases that cleave the protein at predictable and reproducible sites trypsin chemotrypsin pepsin etc 2 using diff enzymes on the same protein to yield partially overlapping fragments that can be assembled together cleave the protein with a known protease without reducing the 8 8 bond gel electrophoresis 2 bands missing and a new larger one appearing in the gel look at the dna sequence and translate it to the corresponding amino acid sequence solubility adding a salt so that solubility of proteins decreases and they precipitate in the tube removal of salts and exchange of buffers from protein sample larger molecules cannot get into the pores and are eluted first smaller molecules get caught in the pores molecules interact with beads molecules don39t and are eluted first matrix in the column is charged negative ions are retained postive elute first net charge of a protein changes with ph beads have ligands for a specific protein protein is retained in column because it interacts with ligand all other molecules don39t interact and are eluted mixture moves through 3D network of polyacrylmide gel proteins are pre incubated with SDS and have a negative charge SDS partially unfolds them so all proteins are rod shaped proteins separated regarding mass combines isoelectrofocusing and SDS PAGE determines composition of a protein mixture mixture ionized mass spectrometer analyzes each charged species assigning a mass to charge ratio
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