1. Bohr Effect chart (low pH) C- High CO2 H- High H+ A- Acidic R-Release of O2(rt. Shift) T- tense state (in tissues) 2. Primary structure Sequence of
... [Show More] amino acids that make up a pro- tein 3. Secondary Structure Sequence of amino acids fold. 4. Tertiary Structure -more folding in a 3D shape. -R groups (side chains) 5. Quaternary Structure Protein has more than 1 polypeptide chain. 6. Chemical reaction -absorb and release energy -activation energy -energy is released (heat & light) when bonds are broken. 7. Exothermic reaction Exo=to release Thermo=heat -chemical reaction that releases more energy than it absorbs (as heat & light) 8. Example of exothermic re- action Cellular respiration- breaks down glucose to make cellular energy 9. Endothermic reaction Endo=absorb Thermos=heat -absorbs more energy than it releases 10. Example of endothermic reaction Photosynthesis- takes in light to break down to create glucose 11. Catalyst Substance that will decrease the activation en- ergy needed to start a chemical reaction 12. Enzymes -catalysts used by cells -increase the rate of chemical reaction -specific to substrates 13. Enzyme structure -they are proteins -twist, fold, bend to final shape -shape attracts specific molecules 14. Substrate Molecules that bind to the enzyme 15. Active site -location on enzyme where substrate binds 16. Function of DNA poly- -increase expression merase in process of PCR. -2 genes -SIRT1 & SIRT2 17. Function of a molecule Structural component of the lipid bilayer 18. How would lipid produc- tion in a cell change in order to maintain fluidity of its cell membrane as it adapts to lower tempera- tures? Produce lipids with shorter fatty acid chains 19. Function of cholesterol Maintains membrane fluidity 20. Lipid (fat) soluble vitamins A, D, E, K 21. What stimulates beta-oxi- dation of fatty acids? 22. What occurs in an oth- erwise healthy person whose diet has very few carbs and high levels of fats? 23. Amino acids An increase in NAD+ concentration in the mito- chondrial matrix Acetone is produced in the blood 24. Which type of mammalian DNA damage repair re- quires the presence of the chromosome that is ho- mologous to the damaged chromosome? 25. Xeroxerma Pigmentosum (XP) 26. Why do XP patients have a much higher incidence of skin cancer than the gen- eral population? 27. Assuming 100% reaction efficiency, how many DNA copies are created after the completion of 4 com- plete PCR cycles? 28. What is the function of DNA polymerase in the process of PCR? 29. What difference in the re- gions of the SIRT1 & SIRT2 genes in people addicted to cocaine increases their expression? 30. What occurs during the process of alternative splicing of RNA? -Non-polar (hydrophobic) -Polar charged -Polar uncharged Recombination A recessive genetic disease that occurs when one or more of the genes that perform nu- cleotide excision repair are nonfunctional The mutation of all other genes is higher due to failure to repair. 16 It recognizes the primers and uses the avail- able dNTPs to replicate the template DNA se- quence. The nucleosomes become more widely spaced. Alternate combinations of Exons within the same gene are linked together. 31. Polypeptides -functional proteins -made of folded up polymers 32. Elements Substance that cannot be broken down into another substance by chemical reaction. 33. Ionic bond Actions share + & - charge 34. Covalent bond When atoms share electrons 35. Hydrogen bond Forms when portion of a polar molecule that is partially positive interacts with portion of a polar molecule that is partially negative 36. Van der Waals interactions Occur due to random, transient movements of electrons that at any given instant, give mole- cules regions of + & - charges. 37. Amino acid -has amino group (-NH2) -& a carbonyl group (-COOH) -cx. Based on side chains 38. Elevated levels of AST & ALT 39. Which level of protein structure is disrupted through the hydrolysis of peptide bonds? -indicates liver damage (When damaged, their protein contents can spill into blood stream) Primary 40. Sickle cell disease Caused by mutation in the Hgb-beta gene. (Causes cells to become rigid, sticky, mis- shapen.) 41. Which force is most influ- ential in determining the secondary structure of a protein? Hydrogen bonding 42. Hydrophobic effect Tendency of non polar substances to aggregate in an aqueous solution & exclude water mole- cules. 43. Hydrophobic interaction Mutation of gene for protein that leads to sub- stitution of no polar amino acid with charged amino acid 44. Dopamine -neurotransmitter -variety of functions (including motor control) Parkinson's = decreases dopamine. Sinemet helps by increasing dopamine levels. 45. Lactose breaks down into : Glucose and galactose 46. Frameshift mutation -insertion or deletion of 1 or 2 nucleotides 47. Missense mutation -substitution of one amino acid for another -results in 10 different amino acids or 10 mis- sense mutations 48. Nonsense mutation -premature stop codon incorporated into the sequence -leads to a shorter protein 49. Carbohydrates -linear -CH2O formula -energy=glucose -structure=cellulose 50. Lipids -energy storage -signaling -high amount of C 51. DNA -twisted ladder -double helix -in nucleus -deoxyribose -bases= Anine, Thymine, Cytosine, Guarine -in all molecules -have nucleotides 52. RNA -plays "messenger" -in & outside nucleus -ribose -Adenine, Uracil, Guarine, Cytosine -mRNA=messenger (takes message to ribo- some) -rRNA=ribosomal RNA -tRNA=transfers amino acids 53. Transcription -comes first! Transcribes DNA into message. (RNA polymerase will connect complementary bases. mRNA can go out of nucleus to attach to ribosome of rRNA) 54. How do rising blood CO2 levels promote the deoxy- genated confirmation of hemoglobin? 55. How does hemoglobin keep blood pH neutral dur- ing exercise? 56. What is occurring in sur- rounding tissues as the amount of hemoglobin saturated with oxygen in- creases? CO2 reacts with H2O in the blood & decreases pH, which promotes the dome confirmation of the heme group. Deoxygenated hemoglobin binds to excess H+ The concentration of hydrogen ions decreases. 57. Translation -2nd step -builds protein (tRNA leaves behind its amino acid, built chain of amino acids) 58. Factors that favor the oxy- genated form of hemoglo- bin: -increased pH -decreased CO2 59. Which metal ion is bound to the porphyrin ring in he- moglobin? 60. Which feature of hemoglo- bin makes it an effective O2 transport molecule? 61. What is a temporary mod- ification to protein struc- ture by kinases that alters enzyme function? 62. Which type of inhibition occurs when a particular drug binds to the allosteric site of an enzyme and sub- sequently changes the en- zyme's structure? Iron It's affinity for O2 is regulated by pH. Phosphorylation Noncompetitive 63. Proteases -a class of enzymes -hydrolyze protein strands into smaller units -increase pH= significant decrease in protease activity 64. How do the rates of en- zyme catalyzed reactions compare to those of corre- sponding uncatalyzed re- actions? 65. Which change will likely increase the activity of an enzyme currently at opti- mal conditions? 66. What occurs immediately after the appropriate mole- They are 10^6 to 10^12 times faster. Significantly increasing substrate concentra- tions The enzyme binds to the molecule to form an enzyme molecule complex. cule enters the active site of the enzyme? 67. Are enzymes specific? Yes 68. What process is disrupted after a patient invests ex- cessive antacid that neu- tralizes the pH of the stom- ach? 69. In Alzheimer's patients, which biochemical event is responsible for their be- havior? 70. In which situation would altering a protein structure lead to a disease state? 71. Which force is most influ- ential in determining the tertiary structure of a pro- tein? Protein catabolism Protein aggregation A mutation aconitase blocks essential step in aerobic metabolism Hydrophobic effect 72. Quaternary structure Large, functional protein structure composed or smaller proteins with multiple subunits. 73. Primary Level of protein structure established through the dehydration synthesis of peptide bonds 74. Describe the protein gradi- ent of the proton that dur- ing aerobic metabolism. 75. Which complex polysac- charide acts as an energy storing molecule in the liv- er? There is a higher H+ concentration in the inter membrane space than in the matrix. Glycogen 76. How does insulin im- pact carbohydrate metab- olism? 77. What occurs during the biochemical process of glucation? 78. Which metabolic path- way involves coenzyme A, NAD, & FAD? 79. Which cellular condition prompts the cell to per- form fermentation rather than the citric acid cycle? 80. What causes the symp- toms of NIDDM type 2? 81. Which molecule is pyru- vate directly converted to under aerobic conditions? 82. Which cellular organelle required for the citric acid cycle and electron trans- port chain is not present in RBCs? 83. Which molecule is replen- ished by fermentation? 84. Which pathway is trig- gered by the intake of carbs during exercise? 85. How many ATP molecules are used in the conversion of pyruvate to glucose? It stimulates the uptake of glucose from the blood by cells in the body. A covalent bond forms between a sugar and a protein or liquid. Beta oxidation Lack of O2 There are not enough GluT4 transporters on plasma membranes. Acetyl CoA Mitochondria NAD+ Glycolysis 6 86. Increased expression Make proteins 87. Decreased expression Not making proteins 88. Promoter Start line 89. Methylation -methyl (CH3) -mRNA added to DNA or nuclosomes - causes decreased expression 90. Base excision repair -only 1 nucleotide damaged - remove and replace 91. Nucleotide excision repair -more than 1 nucleotide damaged -cut a sequence & replace that section 92. Mismatch repair -happens in mistakes with DNA replication -DNA polymerase proofreads to see if make a right choice, but makes a mistake. -remove big section of damage and replace all of it 93. Homologous recombina- tion 94. Non-homologous end-joining -use 2nd copy of the DNA to copy back the correct info - double strand (cut DNA in 2), break -happens before DNA replication -trim the ends-stuck back together 95. PCR -DNA replication in a test tube -Denature, Anneal, Elongation, Repeat 96. Denature -step 1 of PCR -increase heat to separate the DNA 97. Anneal -step 2 of PCR -use DNA primers that match the gene to find only the gene we want (ex: to find BRCA gene) 98. Elongation -step 3 of PCR -use DNA polymerase to make copies of our genes 99. Which ingredients/mole- cules are required to set up a PCR? 100. DNA polymerase always makes strands : -DNA polymerase (elongation) -DNA nucleotides (dNTPs) -primers (annealing) -template DNA (patient DNA) 5'-3' 101. What breaks ionic bonds? -pH changes -salt changes 102. What breaks hydrogen bonds? 103. What breaks hydrophobic bonds? 104. Types of bonds from strongest to weakest 105. Which bond is weakest, but have most influence on protein structure be- cause of how many there are? -pH and salt changes (Disulfide bonds broken by reducing agent) Heat -disulfide bond -ionic bond -hydrogen bond -hydrophobic bond Hydrophobic bond 106. Quaternary Structure -only some proteins will get here -2 or more subunits -proteins -Polypeptides (Example= myoglobin and hemoglobin) 107. Hydrolysis Broken peptide bonds 108. Chaperones Help fold proteins 109. Denature -have an environmental change that causes a protein to misfold or unfold. -breaking side change & secondary structure bonds -disulfide=reducing agent -ionic=pH or salt change -hydrophobic=heat change 110. Degradation Break peptide bonds (Hydrolysis) 111. Aggregation -proteins clump together in abnormal way (d/t hydrophobic interactions) 112. Enzymes -functional proteins -catalysts -reusable (can be recycled!) -specific -induced fit -work like assembly line (enzyme pathway) 113. Feedback inhibition -stop the enzyme "assembly line" because we have too much "product" -happens naturally to maintain homeostasis 114. Competitive inhibition -medicine/drugs -competitive inhibitor will bind to active site to prevent substrate from binding -(overcome inhibition by adding more sub- strate) 115. Non-competitive inhibi- tion -more effective -bind to allosteric site of enzyme -changes the shape of the protein 116. DNA -phosphate + deoxyribose sugar + A/T/C/G -contains 2 strands -the strands are anti-parallel (opposite each other) : 5'-3' 3'-5' 117. RNA -phosphate + ribose sugar + A/U/C/G -single strand (can fold back onto itself & form pairs between itself (stem-loop) 118. Nucleotides -contain one or more phosphates -a 5 carbon sugar and a nitrogen base -always in the 5' to 3' direction 119. DNA organization DNA is wrapped around proteins called his- tones -~nucleosomes-~chromatin fiber-~ chro- mosomes 120. Pairing DNA= A—T RNA= A—U 121. Steps of DNA replication -DNA is separated, creating a replication fork (by helicase) -primase attaches on RNA primer, where the replication starts -DNA polymerase adds bases to remaining of the strand until it reaches a stop codon. (This is done in fragments-"ozaki fragments" -DNA ligase seals the 2 strands forming a dou- ble helix 122. Epigenetics -involves packaging of DNA (packages are called nucleosomes. How tightly packed they are determines whether or not the gene is on or off) -loosely packed=transcription possible -tightly packed=transcription impeded 123. Point mutations When one of the DNA bases (nucleotides) are replaced with another, results in a different pro- tein. 124. Myoglobin - 1 subunit - tertiary - used for O2 storage - in muscles -high affinity (how tightly it holds onto some- thing) 125. Hemoglobin - 4 subunits -quaternary -for O2 transport -moving through blood from lungs to tissues -low affinity (because it gives O2 up) 126. Heme -special molecule inside the protein -iron (Fe) -where O2 binds -in myoglobin, carries 1 O2 -in hemoglobin carries 4 O2 127. CO -carbon monoxide (1 O2) -poison! -binds to hgb on the heme & blocks O2 from binding -has 200 x higher affinity -a competitive inhibitor -puts hgb into the R state (makes hgb want to bind hgb even more) -this is why it is so dangerous, our hgb picks it up instead of O2) 128. 2, 3, BPG -produced in our body naturally -similar function to H+ (stabilizes the T state) -produced in 2 cases (high altitudes & pregnan- cy) 129. Hemoglobins role I'm CO poisoning Hgb binds to CO with a higher affinity than O2 & stabilizes the R state 130. An increase in the concentration of H+ What facilitates the tran- sition of hgb from the R state to the T state? 131. Carbohydrate metabolism 1. Glycolysis 2. Citric acid cycle (aerobic) 3. Electron transport chain (aerobic) 4. Firmentation (anaerobic) 5. Gluconeogenesis (anaerobic) 132. What occurs during aero- bic respiration? 133. What directly provides the energy necessary for the conversion of ADP to ATP by ATP synthase? NADH & FADH2 are produced from NAD & FAD during citric acid cycles. -NADH & FADH2 donate electrons to the ETC, re-engineering NAD & FAD. -O2 accepts electrons, producing water Protons moving down a concentration gradient from the intermembrane space to the mitochon- drial matrix. 134. Cori Cycle -muscle cells produce lactate which is then con- verted to glucose in the liver 135. Exonuclease During DNA replication, if an error is detected, DNA polymerase removes the nucleotides and replaces them with correct ones. 136. Glyco/ gluco Glucose 137. Genesis Make 138. Lysis Break 139. Neo New 140. Insulin -increase glucose in blood -fed state(after we eat, increase glucose=pan- creas releases insulin) -lets glucose into cells -signals for GluT4 to go to cell membrane 141. Glycolysis -break glucose -make ATP (useable energy) 142. Glycogenesis -store glucose as glycogen (short term storage) -in liver 143. Fatty acid synthesis - make fat from acetyl CoA -fats stored in triglycerides (3 fatty acids) -adipose tissue (long term storage) 144. Glycogenolysis Break glucose out of glycogen 145. Gluconeogenesis -make new glucose(from lactate) -acetyl CoA~pyruvate~glucose -glycerol (from triglycerides) -amino acids(last resort!) 146. Beta oxidation Break fats into acetyl CoA 147. Fatty acid structures -made up of carbonyl groups 148. Saturated fatty acids -no double bonds -maximum Hs 149. Unsaturated fatty acid -(not saturated with Hs) -at least 1 double bond -lose 2 Hs per double bond 150. Essential -we have to eat it (our bodies cannot make it) -omega 3 -omega 6 - essential for building other types of lipids 151. Unsaturated fats -natural (veg oils) -1 double bond 152. Trans-unsaturated -treat saturated with chemicals to switch hydro- gen to other side -not natural! Build up in our body d/t doesn't recognize them. 153. Fluidity -more double bonds=always more fluid! -if same # double bonds, but shorter chain, will be MORE fluid! 154. Poly unsaturated -more than one double bond 155. Acetyl CoA -2 carbons -attached to coenzyme A (to make sticky we need biotin) 156. Beta oxidation -breakdown of fats -occurs when we eat fats, or exercise -break beta bonds 157. Oxidative damage to DNA can often result in the al- teration of a single nu- cleotide. Which DNA repair mechanism would repair this type of damage? 158. Which structural level is impacted by denaturing a protein containing a single polypeptide? 159. Frying an egg changes the egg white from a clear liq- uid to an opaque solid. Which molecular change in the albumin protein causes this change in ap- pearance? Base excision repair Tertiary Hydrophobic interactions form between dena- tured egg white proteins. 160. Three dimensional structure Which features of a pro- tein made of a single polypeptide chain is most directly responsible for its function? 161. Which reaction is respon- sible for the formation of polypeptides? 162. How can alteration in pro- tein structure lead to a dis- ease state? 163. Steps of DNA replication: Dehydration A mutation replaces an isoleucine with an as- partic acid in a transcription factor protein, which blocks the normal folding of the protein & its function in the expression of certain genes. [Show Less]