Biochemistry Chapters 1-4 4th edition Fundamentals of Biochemistry – Flashcards
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1. What is the most abundant element in the human body (dry weight)? ???????????????
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oxygen????????????????????????
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2. Be able to identify the functional groups important in biochemistry. What's a thiol? Whats a sulfyhydryl group? Ester has two types of linkage what are they?
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RSH(thiol) SH( sulfylhydryl group) ester ( rcoor linkage and rco- linkage)
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3. What are the main function(s) of the following cell's organelles : nucleus, nucleoulus, peroxisome, golgi apparatus, smooth and rough E.R.
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Nucleus- directs the synthesis of protein cell components nucleoulus- major role in the synthesis of ribosomal RNA peroxisome- protects cells from disease by ROS, such as hydrogen peroxide Golgi apparatus- secretion and shuffling of proteins, Smooth ER- lipid syntheis, and biotransformation Rough ER- synthesis of membrane proteins and exported proteins
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4. Be able to identify amino acids, nucleosides or nucleotides, lipids, and carbohydrates.
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nucleosides do not have a phosphate group nucleotides do carbohydrate- ring with several oh groups nucleotide- base, sugar, and phosphate group amino acid - small chain with carboxylic acid lipid- can have rings with long saturated carbon chain
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5. Be able to state the first two laws of thermodynamics.
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first law of thermo- total E of the system and the surrounding is a constant system 2nd law of thermo- the total entropy of a system plus that of its surroundings always increases
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6. Be able to define entropy and enthalpy.
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entropy- degree of randonmess or disorder in a system enthalpy- heat content of a reacting system
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7. Be able to calculate the change in Gibbs free energy for a reaction and predict whether the reaction is spontaneous under specified conditions. whats are the gibbs equations
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S is positive G is negative H- negative , G= g(knot) + RT ln(k) R=8.314 j/k x mol g(knot)= -rt ln keq keq= e ^ - g(knot) /RT
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8. What is the standard state for biochemical reactions? M? temperature? ph? Pressure?
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solution is 1M 25 degrees C= 298 K 7 pH P 1 bar close to 1atm
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9. Be able to calculate the equilibrium constant for a given reaction and use it to calculate the standard Gibbs free energy. whats the gibbs equations ?
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G= g(knot) + RT ln(k) R=8.314 j/k x mol g(knot)= -rt ln keq keq= e ^ - g(knot) /RT
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10. Be able to discuss the structure of water. what shape is water? why is it asymetric?
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h20 is a bent molecule polar, asymetric due to electronegativity
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11. What is a hydrogen bond?
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bond between two molecules resulting from an electrostatic attraction between a proton in one molecule and an electronegative atom in the other.
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12. Be familiar with the unusual properties of water such as its high boiling point, high specific heat, high heat of vaporization and drop in density as it freezes. What structural feature of water is responsible for these properties?
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its asymetric due to electronegativity differences, and extremely polar , also hydrogen bonds are strong
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13. Be able to describe and rank in order of strength the noncovalent interactions that are important in biological systems. in order , dipersion forces, ionic , dipole-dipole, hydrogen bond
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ion-ion>hydrogen>dipole>london
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14. What happens when a water-soluble molecule is added to water?
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Ion becomes surrounded by water molecules
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15. What happens when a water-insoluble molecule is added to water?
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they colease into droplets because hydrogen bonding interactions in h20 are stronger than h20 non polar interactions
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16. What happens when an amphiphilic or amphipathic molecule is added to water? What is the driving force in the formation of micelles and bilayers?
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they congregate to form micelles , polar head towards water, non polar inside
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17. What is the difference between osmosis and dialysis?
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osmosis low to high, dialsyis is by diffusion high to low
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18. Be able to calculate osmotic pressure. what is the formula and the units? of the formula and osmotic pressure
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Pi= iMRT osmotic pressure measured in atm M-mol/L , T - Kelvin , R - 0.0821 mol/L i( vant hoff's factor ( neglible mostly )
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19. Be able to explain why intravenous solutions contain salts or glucose.
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its so that your cells remain in an isotonic solution and wont shrink from dehydration or lyse from swelling
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20. Know the definition of acid, base, and pH.
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acid- substance that donates a proton - base- substance that accepts proton or yields oh- group when dissolved in h20
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21. Be able to calculate the pH of a buffer solution using the Henderson-Hasselbalch equation and the new pH given the addition of acid or base. Whats the equation? what is pk?
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ph=Pk+ log { A-/HA} pk point in ph where {A-}= {HA}
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22. Be able to describe the bicarbonate buffering system for blood. What are the other physiological buffering systems?
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designed to maintain blood ph around 7.4 , 0.6 drop or rise in ph can result in death the concentrations of carbon dioxide and bicarbonate can be regulated by breathing and the kidneys when blood ph decreases , carbonic acid is released , then breaks down into c02 in the lungs, and expelled , and vice versa
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23. Be able to identify uracil, cytosine, thymine, hypoxanthine, guanine, and adenine and their corresponding nucleosides. You should also be familiar with the numbering systems of purines and pyrimidines.
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CUT pyridine - cytosine , uradine, and thymine do not have pyridine ring thymine- ch2 group , uracil HN group , cytosine NH2 group on rings adenine-regular with nh2 group. guanine h2n adenosine nh2 at 1 carbon guanosine nh2 at 3 carbon
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24. Know the difference between ribose and deoxyribose and nucleosides and nucleotides. what group is on the 2 carbon in deoxyribose? and ribose? what do nucleosides not have?
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2-deoxyribose - has H at 2 carbon, ribose - has oh at 2 carbon nucelosides, dont have phosphate
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25. Be able to describe the common features of DNA structure - double helix, complementary, antiparallel, phosphodiester bond, location of bases. How does the 5' end of DNA differ from the 3' end of DNA? How do we write DNA? Where are the bases in relation to the helix ? how would you describe the backbone? Phosphate groups acidic or basic? what charge is on nucleic acids ? How are bases bonded to complentary base on opposite strand?
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we write dna 5-3 end bases are inside the helix backbone alternating phosphate and dexoydribose units phosphate groups are acidic nucleic acids are (-) charged they are hydrogen bonded phosphodiester bonds link 3 and 5 positions of neighboring deoxyribose units
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26. Be able to identify the tautomeric forms (keto-enol and amino-imino) of the major bases of DNA. what is a tautomer ? which is dominant amino or imino?
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keto form will have an H and will be in carbonyl form constitutional isomers that differ in the location of H and a double bond relative to 0, S, or N amino form - has nh2 group
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27. Be familiar with the hydrogen bonding patterns in the bases of DNA. what part of A and C are hydrogen bond donors? which ring nitrogen atoms in A and C are hydrogen bond acceptors? where is C hydrogen acceptor? where is G hydrogen acceptor, and its donors (two) T where are the acceptors (2) and the donor?
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amino groups of A, and C are hydrogen bond donors ring nitrogen atoms N1 in A and N3 in cytosine are hydrogen bond acceptors C has hydrogen bond acceptor at C2 G hydrogen bond acceptor at C6 , and N1 and C2 are hydrogen donors T groups C4 and C2 are hydrogen bond acceptors and N3 is hydrogen bond donor
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28. Know the biological functions of nucleotides. there is four think HENM
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hormones, metabolic intermediates, enzyme components, neurotransmitters,
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29. What are the three types of RNA ? their functions?
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rRNA-major constiuent of organelles(protein synthesis ) MRNA- carries genetic info from DNA TRNA- carries amino acid and ribosomes for incorporation into amino chain
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30. Be able to describe the dideoxy sequencing method for DNA. Given a gel generated during dideoxy sequencing be able to determine the sequence of the template DNA.
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Dideoxy , stops growth of DNA, it terminates the sequence, and the sequence is visualized and read by gel electrophoresis sequence from jel complentary to orginal
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31. Describe how gel electrophoresis works.
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charged molecule moveves under the influence of field smaller molecules move faster than bigger ones distance it moves is function of its size
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32. Describe the three common types of cloning vectors and the limitations on the size of the insert with which they can be used. think PBB
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three vectors are Plasmid-10KB ( can clone upto that much ) Bacteriophages- 16kb Bacterial artificial chromosomes- 100kb-300kb
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33. Describe the process by which a gene is cloned. there is four steps , what are they?
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1. Fragment of appropriate size is generated by either, R.E. , PCR, or chemical synthesis 2. fragment is incorporated into one of the vectors , which contain the sequences 3. the vector containing fragments is introduced into the cells 4.cells with dna thats wanted are identified.
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34. Describe the process by which a library can be screened for a particular insert.
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can use one of three ways, autoradioagraphy, a probe, or replica plating, to scan for the piece of DNA
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35. How does the PCR process work? for each cycle how much dna is produced?
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It doubles. Uses heat stabled form of DNA polymerase 1. primers are chemically synthesized that are complentary to the 3 ends of DNA segment to be amplified 2. assemble reaction mixture consisting of template dna, primers, taq polymerase, and 4 dNTP's , put in thermal cycler cycle 1 - seperates template dna strands by heating , cool, and anneal primers, to template DNA then makes new copy of each template dn2 strand using taq polymerase cycle 2 repeat cycle 3- 3-20
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36. Be able to describe how DNA fingerprinting works. Be able to calculate the probability of having a particular arrangement of short tandem repeats.
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STR- each individual has different ones region of DNA containing STR is amplified , products seperated by electrophoresis number of str's determined at each loci to calculate percentage for multiple loci multiply percentages times each other then divide by 1/ #
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37. What is CODIS?
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name for FBI fingerprinting data base,
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38. What are some of the applications of recombinant DNA technology?
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production of large amounts of proteins,( insulin , clotting factors ) analyis of protein function , transgenic plans treatment of genetic disorders
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39. What was the first disease treated by gene therapy? Be able to describe some of the problems associated with gene therapy.
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SCID, delivery of the gene therapy through a vector such as retrovirus with the gene rejection response(leukimia like)
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40. Be able to describe the general structure of an amino acid. what are the four groups around the carbon ? draw it
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r at the top , cooh to right, h at bottom, h2n at left
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41. Be able to classify an amino acid as neutral nonpolar, neutral polar, acidic or basic given the structure of the amino acid.
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ASN, MEt, CYS, SER , GLu, Thr- neutral polar GLu, and ASP-acidic - two cooh groups on side chain basic - nh2group next to cooh group LYS, HIS, and ARg
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42. What structural feature makes 19 of the 20 standard amino acids optically active? Be able to identify all of the chiral centers in an amino acid given its structure. Which amino acid is not optically active?
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chiral carbon proline-imino acid
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43. Be able to calculate the isoelectric point of an amino acid or peptide given pK values.
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pI=pk1+ pK2/2
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44. Why is it usually safe for drugs to be sold as the racemic mixture? Give an example when this practice had disastrous consequences.
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drugs exists as a preferred isomer, thalidomide sold as sedative for women who were pregnant, caused birth defects
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45. Why do some bacteria incorporate D-amino acids into their cell walls? How do bacteria synthesize the D-amino acids?
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helps protect their cell wall from attack by peptidases and proteases they have enzymes known as racemaces that convert l to d amino acids
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46. What is the function of glutathione? How does it carry out this function? What is an isopeptide bond
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protects against oxidation amide bond not present on the main chain of a protein , forms between the carboxyl terminus of an l 1 protein and amino group of a hygine residue
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47. Be able to give examples of biologically active amino acids and their associated functions.
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l-glyceraldehyde, l-a amino acid
