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185 Cards in this Set
- Front
- Back
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What is the grading rubric for PBS 513 Biochem
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Open Book Quiz 1 - 2%, Open Book Quiz 2&3 - 4% each, Exam 1, 2, and 3 - 30% each
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What are the characteristics of the 20 amino acids?
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The charges shown are those at ph =7. The carboxylic acid group has a pKa ~ 2 so it is in its carboxylate form. The alpha-amino group has a pKa of ~9 so its in its ammonium ion form.
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What is a protein?
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Proteins are polymers of amino acids (aas). It is >50 aas.
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What is a peptide?
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A polymer of <= 50 aas is called a peptide
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What is a a peptide bond?
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The C to N bond formed between two amino acids
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What is a cis peptide?
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Cis peptide is the configuration that is higher energy and less stable due to steric clashes between the two side chains. It is found in some enzymes used to provide energy for catalysis.
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What is a trans peptide bond?
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The c-alpha of two neighboring residues found on opposite sides of each other on the peptide bond. Trans configuration is lower energy and more stable than cis.
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What is primary structure?
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The covalent bonds between the aas are called the proteins primary structure. THIS IS NOT CALLED THE PRIMARY SEQUENCE!!!!!!!!!!!
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What are characteristics of how the primary structure can fold?
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Single bonds can rotate, steric constraints limit the possible positions thus partially determing the folding pattern, hydrophobicity partially determines the folding pattern, charges partially determine the folding pattern
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What is secondary structure?
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Secondary structure is the local folding of the backbone. SIDE CHAINS ARE NOT CONSIDERED IN THE SECONDARY STRUCTURE. Beta sheets and helixs are characteristic shapes of secondary structure
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What residues do cis-trans-prolyl isomerases interconvert the cis and trans peptide bond?
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proline residues
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What protein catalyzes the breakage and formation of disulfide cystine bonds in order to form the proper cystines?
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Disulfide isomerases
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What do HSP60 and HSP10 bind on misfolded proteins?
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They form a cavity which binds exposed hydrophobic patches of misfolded proteins
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What powers HSP complex?
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ATP powers the HSP complex to unfold and refold misfolded proteins
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When does glycosolation occur?
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during the secretory pathway
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Where does N-linked glycosylation occur?
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At Asn-X-Thr/Ser (x is any aa except Pro or Asp)
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An oligosaccharide is linked through the amide nitrogen of Asn contranslationally in what process?
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N-linked glycosylation
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Where does o-linked glycosylation occur?
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in the golgi
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What aminos have o-linked glycosylation occur to them?
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Ser or Thr
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How can Lys be glycosylated?
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By hydroxylation adding an O that allows glycosylation to occur
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What does a mannose 6-phosphate signal when appended to a protein?
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That the protein is to be transported to the lysosomes
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When can proteolysis occur to a protein?
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Either cotranslationally (with Signal recognition particle) or posttranslationally (insulin)
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Where is preproinsulin produced?
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Islets of Langerhangs.
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How is preproinsulin converted into insulin?
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Proteolysis in the ER removes the 24 aa N-terminal signa peptide giving proinsulin. The enzyme caboxypeptidase E cleaves proinsulin between the T30 - R31 and also between R65 - G66 that releases the connecting peptide (c-peptide) forming insulin (with A and B chains held together by disulfide bonds)
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What are the differences between porcine, bovine, and human insulin?
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Human and pig differ by the B30 amino - pigs have Ala and humans have Thr. Cows are different than humans at A8, A10, and B30 and therefore more likely to cause an immune reaction
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Where does the o-linked glycosylation in procollagens occur?
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at the 5-hydroxylysine that is formed cotranslationally by the hydroxylation of lysine
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What protein is desmosine crosslinked formed in?
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Elastin
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What is the composition of the desmosine crosslink?
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Three allysines and one lysine (ring that rotates)
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What are the three factors involved in protein lifespan determination?
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1. Protein halflife is determined in part by their n-terminal aa 2. PEST proteins (rich in P, E, S, and T) are also rapidly degraded 3. The enzyme ubiquitin-protein ligase (E3) identifies a protein to be condemned and binds to it, thus tagging the protein for intracellular digestion
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What protei have a halflife of greater than 20 hrs?
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M, S, A, T, V, G
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What proteins have a half life of 2 mins?
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Proteins with K or R at the N terminal
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What bond does ubiquitin protein ligase (E3) form to the condemned protein?
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isopeptide bond
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What amino acid does E3 attach ubiquitin?
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Lys
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What are the intracellular digestion paths?
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1. Extracellular proteins can be imported and digested in the lysosomes 2. Apoptosis can activate cysteine aspartyl proteases (capspases) which digest the cell 3. Calcium dependent thiol proteases (calpains) can also perform limited proteolysis
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What is the number of antibodies that a human can make?
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100 million variations
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What is the structure of an antibody in terms of chains?
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Four polypeptide chains (2 heavy and 2 light)
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How are the chains of Ig connected to eachother?
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Disulfide bonds
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What are the regions that complement and bind he topology of the antigen using noncovalent interactions called? Where in the Ig chain are these located?
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They are called complementarity determining regions (CDRs) and are locaed in the V (variable) regions of the chains
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What are the functions of the heavy chain (Ch) constant region?
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Determine antibody class, bind complement proteins to lyse invading cells, and contain the binding site necessary to cross the placental membrane
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What is the dominant secondary structure motif in Ig and how many of these are there?
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B-strands and there are generally 7 to 9 in two antiparallel sheets
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What is used in the catalytic mechanism of Ser proteases?
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serine
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How can serine proteases be identified?
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They have irreversible reactions at their active site of Ser with diisopropylfluorophosphate (DFP). DFP does NOT react with all Ser side chains, only the catalytic Ser (ie Ser 195)
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What is the catalytic triad?
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His57, Ser 195, and Asp102 - active aminos in Ser proteases
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What is the inactive form that serine proteases are in to be activated by limited proteolysis?
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Zymogens - all serine proteases are in this state to start
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How can you tell a word refers to a zymogen?
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It has the suffix -ogen (chymotrypsinogen) or the prefix pro- (prothrombin)
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What are the names of the zymogens chymotrypsinogen and prothrombin when they are active?
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Chymotrypsin and thrombin
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What is the bond in a polypeptide to be cut by a protease called?
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scissile bond
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How is the scissile bond determined by the protease?
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Binding of the protease to the amino acid used noncovalent interactions
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What is Factor II?
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A serine protease that forms soft blood clots
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What is Factor IX?
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a serine protease that deficiency causes hemophilia B
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What is Factor X?
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a serine protease that activates thrombin
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What is tPA?
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tissue plasminogen activator - a serine protease; a thrombolytic agent (clot buster) activates plasminogen, given to remove a blood clot causing a heart attack or a stroke
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What is plasmin?
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a serine protease that lyses fibrin blood clot
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What is trypsin?
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a serine protease that cleaves on carboxyl side of Arg and Lys in digestion
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What is Chymotrypsin?
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a serine protease the cleaves on carboxyl side of tyr, trp, and phe in digestion
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What are natural inhibitors that are used to stop further proteolysis that bind very tightly to the protease so that other molecules cannot be cut?
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Serpins (serine protease inhibitors)
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What is Antithrombin III?
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serpin; inhibits Factor II (thrombin)
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What is Plasminogen activator inhibitor?
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serpin; inhibits plasminogen activators
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What is alpha2-antiplasmin?
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serpin; inhibits plasmin
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What is the composition of adult hemoglobin?
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two alpha chains and two beta chains
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What is the composition of fetal hemoglobin?
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two alpha chains and two gamma chains
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How many oxygen molecules can each HB chain carry?
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One 02 per chain
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How many oxygen molecules can Mb (myoglobin) carry?
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One 02 per chain, but only has one chain unlike hb which has four
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What is a nonpolypeptide moiety that forms a functional part of a protein?
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prosthetic group
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What is a protein without a prosthetic group?
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apoprotein
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What is a protein with a prosthetic group?
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holoprotein
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What are the two domains of each Hb chain?
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a globin fold and a heme prosthetic group
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What are the structural motifs of a heme group?
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4 pyrrole rings with side chains of methyl (4), proprionate (2), and vinyl (2)
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Is the heme portion of Hb hydrophobic or hydrophilic?
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hydrophobic
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What is the state of iron when it is bond by 02?
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ferrous state
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What is a hyperbola (very steep) saturation response curve of myoglobin mean in relation to hemoglobin?
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It means that myoglobin becomes saturated much faster than hemoglobin
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What does the sigmoidal (very diagonal) saturation response curve in hemoglobin mean in relation to myoglobin?
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It means that hemoglobin takes much longer to saturate with oxygen than myoglobin. This is due to the multiple chains of hemoglobin and the singular chain of a myoglobin molecule
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What is meant by the T state of Hb?
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The tension state of hemoglobin is from the steric hindrance between the proximal His and the prophyrin ring (leads to Fe being pulled out of porphyrin plane by 0.5A)
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What causes the R state of Hb?
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Binding of 02 relaxes the structure a little and continues as more 02 binds
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What is the alkaline Bohr effect?
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Hb binds 02 more tightly when at pH 7.4 compared to a slightly more acidic environment
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What is the term for the conversion of c02 in the blood by carbonic anyhdrase to form carbonic acid which spontaneously dissociates into bicarnbonate and Hydrogen atoms?
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isohydric transport (enzymatic transport that accounts for 80% of the transport of c02)
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What is the term for the transport that c02 bind nonenzymatically to the n-terminus of oh Hb?
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carbamino-hemoglobin
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What is the biological function of NO (nitrous oxide)?
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Vasodilator
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What state is hemoglobin in when it binds NO?
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T conformation
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Where does NO initially bind?
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Fe2+ of the alpha chain
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What blocks NO being bound to B-cys-93 while in the t conformation?
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the b-asp-94 to b-his-146 bond
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What breaks the b-asp-94 bond to b-his-146 in Hb to allow NO to bind b-cys-93?
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The binding of O2 (b-cys-93 binds to the N of NO)
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What is bound to NO during the protected conformation of Hb?
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the S of b-cys-93 is bound to the N of NO during the relaxed conformation of Hb
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What causes the release of the bound NO from the r state of Hb?
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Low oxygen levels in tissues cause the 02 to be released which causes the b-cys-93-NO to draw the NO away from the porphyrin ring and allows the NO to be picked up by glutathione
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What is the result of the release of NO?
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dialated capillaries; increased transfer of O2 and CO2; lower blood pressure and thus more blood flow
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What is a specialized protein that catalyzes a biological reactiojn?
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an enzyme
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What is something that lowers the energy of activation at the transition state?
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catalyst
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What tells if a reaction can occur?
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thermodynamics
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What tells how fast a reaction occurs?
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kinetics
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What is the state that is between the substrate and the product?
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transition state
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What is the term for when a substrate and an enzyme both change shape to fit eachother?
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induced fit
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What is a common way to form a carbon-carbon double bond?
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Have a carbanion attack a carbonyl (found in gluconeogenesis)
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What is a carbonyl?
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C double bonded to O and single bonded to two other random groups
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What is a carbanion?
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carbon which has an unshare pair of electrons
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The ability of enzymes being able to tell the difference between maltose (alpha linkage) and cellobiose (beta linkage) is an example of what?
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high specificity of enzymes
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Can enzymes differentiate between optical isomers?
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yes
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Why is enzyme specificity important to pharmacists?
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Racemic mixtures are often made in pharmaceutical production
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Does the stereochemistry of enzyme catalyzed reactions vary?
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NO
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Does the binding of substrate to the enzyme in term of orientation ever vary?
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NO
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What are small organic molecules that are often dereivatives of vitamins?
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coenzymes
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What is the term for when a substrate and an enzyme both change shape to fit eachother?
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induced fit
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What is a common way to form a carbon-carbon double bond?
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Have a carbanion attack a carbonyl (found in gluconeogenesis)
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What is a carbonyl?
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C double bonded to O and single bonded to two other random groups
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What is a carbanion?
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carbon which has an unshare pair of electrons
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The ability of enzymes being able to tell the difference between maltose (alpha linkage) and cellobiose (beta linkage) is an example of what?
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high specificity of enzymes
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Can enzymes differentiate between optical isomers?
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yes
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Why is enzyme specificity important to pharmacists?
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Racemic mixtures are often made in pharmaceutical production
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Does the stereochemistry of enzyme catalyzed reactions vary?
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NO
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Does the binding of substrate to the enzyme in term of orientation ever vary?
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NO
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What are small organic molecules that are often dereivatives of vitamins?
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coenzymes
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What are coenzymes that are altered by the reaction called?
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co-substrates
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What are metal ions required for enzyme reactions called?
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co-factors
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What is the vitamin and reaction mediated by coenzyme of biotin?
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biotin / carboxylation
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What is the vitamin and reaction mediated by the coenzyme of cobalamin?
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cobalamin / alkylation
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What is the vitamin and reaction mediated by the coenzyme of coenzyme A?
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pantorhenate / acyl transfer
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What is the vitamin and reaction mediated by the coenzyme of flavin coenzymes?
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riboflavin / oxudation-reduction
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What is the vitamin and reaction mediated by the coenzyme of lipoic acid?
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none / acyl transfer
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What is the vitamin and reaction mediated by the coenzyme of nicotinamide enzymes?
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nicotinamide / oxidation - reduction
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What is the vitamin and reaction mediated by the coenzyme of pyridoxal phosphate?
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pyridoxine amino group transfer
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What is the vitamin and reaction mediated by the coenzyme of tetrahydrofolate?
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folic acid / one-carbon group transfer
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What is the vitamin and reaction mediated by the coenzyme of thiamine pyrophosphate?
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thiamine / carbonyl transfer
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What is the the study of rates of chemical reactions?
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kinetics
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What affects the rate of chemical reactions?
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enzymes
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What is the slope of a first order reaction?
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negative (down from top left to bottom right)
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What is the term for the maximum velocity that a reaction can achieve?
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vmax
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What is the term for the initial velocity of a reaction?
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Vo
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What is the term for the overall catalytic rate when the enzyme is working at maximum efficiency?
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Kcat (catalytic constant)
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What value of velocity is when the graph of the product vs time will plateau?
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when velocity equals zero (equilibrium)
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What affect does doubling the enzyme concentration have upon the initial velocity?
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doubles the initial velocity
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What is the substrate concentration that yeilds half the vmax?
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Michaelis-menten constant or Km
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What does a larger Km indicate about the enzyme and the substrate?
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that the enzyme and the substrate dissociate more readily; NOT that they bind to each other tightly
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What are inhibitors that bind to the enzyme substrate binding site called?
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competitive inhibitors (velocity decreases with increasing inhibitors. km varies)
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What are inhibitors that bind to the ES complex rather than free enzyme called?
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uncompetitive inhibitors (think unconnected lines)
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What are inhibitors that bind to both the enzyme and the enzyme substrate complex called?
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noncompetitive inhibitors (Km is constant between all but velocity decreases with increasing inhibitors)
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What are ligands that change the enzymatic activity but are not changed themselves?
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Effectors, modifiers, or modulators
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Do modulators increase or decrease enzymatic activity?
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both
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where do modulators bind?
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allosteric sites
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If binding of the modulator increases the enzymatic activity, what is the allosteric site called?
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activator site
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If binding of the modulator decreases the enzymatic activity, what is the allosteric site called?
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inhibitory site
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What is a compound that binds a modulator to keep it inactive?
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separable regulatory subunit
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What general reaction does cytochrome p450 perform?
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family of heme proteins that insert one atom of O to a substrate
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What paths do the P450s participate in?
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1. Production of steroid hormones 2. metabolism of fatty acids&prostaglandins&leukotrienes&retinoids 3. inactivation or activation of therapeutic agents 4. conversion of chemicals to highly reactive molecules that may produce unwanted cellular damage 5. enzyme inhibition or induction resulting in drug-drug interactions and adverse effects
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Where are the p450s located?
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they are integral membrane proteins
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What is the function group of p450?
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single iron protoporphrin IX prosthetic group
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What is the shape of p450?
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triangular shape
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What is an easily identifiable characteristic of p450?
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i-helix
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Why are p450 named as such?
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due to the pigment absorbance peak at 450 nm
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What is the general equation for p450 reaction?
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NADPH + H + O2 +SubstrateH ----P450---> Nadp+ + H20 + SubstrateOH
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What is NADPH?
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Reduced nicotinamide adenine dinucleotide phosphate
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What is the function of FMN in cytochrome p450 reactions?
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It is able to transfer one electron at a time to the heme reducing it to ferrous 2+ heme
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What cyp450 converts cholesterol to pregnenolone?
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cyp11A1 (steroid biosynthesis - not a reversible reaction)
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What are foreign to life molecules called?
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xenobiotics
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What are the two pathways that xenobiotics are metabolized in?
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phase I and phase II
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What is the phase that p450 introduces oxidative functional groups?
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phase I
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What is the phase that p450 connect function groups to endogenous species like glutathione?
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phase II
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What is the purpose of phase I or phase II reactions of p450?
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to facilitate the interaction with water of the compound to help it get excreted in the kidneys
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What is cyp450 enzyme that metabolizes diazepam and is responsible for 50% of all metabolizing rxns?
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cyp3a4
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What is the cyp450 enzyme that metabolizes APAP by converting it to NAPQI (toxic)?
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cyp2E1
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Why does alcohol consumption increase apap toxicity?
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Either increasing cyp2E1 activity or depleting GSH (glutathione) which is normally used to inactivate the toxic metabolite of NAPQI
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What is the substrate for NOS?
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Arg
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What is Arg converted to by NOS?
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NO and Citrulline
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If arg is not present, what can NOS do?
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Make ROS
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What is neuronal NOS?
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nNOS or NOS I
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What is inducible NOS?
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iNOS or NOS II
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What is endothelial NOS?
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eNOS or NOS III
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What is sGC?
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Soluble guanylate cyclase (heterodimer heme-containing protein)
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What does sGC do?
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converts GTP to cGMP
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What relationship does sGC have to NO?
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Binding of NO to sGC activates sGC to produce cGMP
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What activates nNOS?
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Ca influx (at neurons)
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Where is iNOS found?
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immune cells (iNOS = immune nos)
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Does iNOS require calcium?
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NO
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How does iNOS compare to nNOS or eNOS?
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Produces 1000 times more NO
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What is the purpose of NO in macrophages?
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causes DNA damage to pathogen, inhibits pathogens p450
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Where is eNOS found?
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epithelial cells (eNOS = epithelial)
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What activates eNOS?
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stress, insulin, histamine, actylcholine, bradykinin
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What are the three major components of membranes?
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glycerophospholipids, spingolipids, cholesterol
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What are the functions of myristic acid and palmitic acid?
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anchor peripheral proteinsq
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Do transporters bind the molecule being transported?
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yes
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What are the four steps of transport across the membrane?
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recognition, transport, release, recovery
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What glut transporter (passive transporters) transports in erythrocytes and brain cells?
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glut1
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What glut transporter (passive transporters) transports in intestines and pancreas cells?
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glut2
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What glut transporter (passive transporters) transports in brain, kidney, and placenta cells?
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glut3
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What glut transporter (passive transporters) transports in adipose, muscle, heart cells?
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glut4
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What glut transporter (passive transporters) transports in sarcolemmal membranes of skeletal muscle?
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glut5
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What active transport system used approx 65% of the ATP energy synthesized in nerve and muscle cells?
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Na/K pump (K pumped, Na pumped out)
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