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CHEM 301 BIOCHEM STUDY NOTES
1. UNIT 1 Define "biochemistry.": the study of the building blocks, or molecules, of life and how these interact in the
processes that occur in living organisms.
2. Name the major classes of biomolecules, and identify the atoms most com- monly found
in each class.: - proteins (amino acids)
- carbohydrates or polysaccharides (monosaccharides or simple sugars)
- lipids (fatty acids)
- nucleic acids (nucleotides).
3. Define "metabolic pathway.": linked series of chemical reactions occurring within a cellular processes
4. List the 6 elements that make up 99% of living cells: CHNO CP
carbon, hydrogen, nitrogen, oxygen, calcium, and phosphorus.
5. Identify some applications of biochemistry.: medicine (causes and cures of diseases) nutrition
(maintain health and wellness, nutritional deficiencies) agriculture (soil and fertilizers)
6. What are the four elements most commonly found in biomolecules?: carbon (C), oxygen (O),
hydrogen (H) and nitrogen (N)
7. Describe the organization of Eukaryotic Cells and Prokaryotic C
8. How does the composition of the earth's crust and living cells differ?: The earth's crust is mostly
composed of Oxygen, Aluminum, Silicon, and Iron. Living cells are mostly composed of C, H N, O. Two elements found in the earth's crust, Si and Al, are not found in living matter.
9. What is the function of the following organelles?
Golgi apparatus, lysosome, ribosomes, mitochondria, cytoskeleton: Golgi apparatus
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n a
hydrogen
ith a lone
- protein assembly and secretion lysosomes - digestion of proteins ribosomes - synthesize proteins mitochondria - synthesize ATP cytoskeleton - provides support and structure to the cell.
10. Where are sugars and fats digested in the cell?: Sugars and fats are partially digested in the
cytoplasm. They are then transported into the mitochondria, where they are converted into ATP.
11. List the differences between prokaryotic and eukaryotic cells in terms of the
following: nucleus internal structures cytoskeleton DNA organization Reproduction:
12. Explain DNA difference of prokaryotic and eukaryotic: eukaryotic DNA: linear and
packaged with histones prokaryotic DNA is circular and negatively supercoiled and is not associated with histones.
13. Explain how the chemical properties of water make it the ideal biological solvent.:
Water is a universal solvent, Mosaic structure, Hydrogen bonds, Surface tension it is capable of dissolving more substances than any other liquid. It is polar
14. Describe hydrogen bonds (H-bonds).: Dipole-dipole attraction which occurs whe atom
bonded to a strongly electronegative atom exists in the vicinity of another electronegative atom w of electrons
15. Using the concept of H-bonding, explain how small items that are denser than
water (e.g., a fine needle or a water bug) can remain on the surface instead of sinking.: hydrogen bonds btwn water molecules, form a lattice of water molecules, which is strong and flexible. Creates a high surface tension. As a result, this molecule at the surface tends to be pulled into the bulk of the liquid and thus minimizes the surface area of a liquid
16. Describe an amphiphilic molecule: A chemical compound possessing both hydrophilic (water-lov- ing,
polar) and lipophilic (fat-loving) properties
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29. Explain "oxidation", "reduction", "catabolic", and "anabolic" reactions.: Oxidation is the
loss of electrons by a molecule (increase in oxidation state). Reduction is the gain of electrons (decrease in oxidation state). Catabolic ’oxidative ’release energy Anabolic ’reductive ’use energy
30. What is a redox reaction? Why are redox reactions common in biological systems?:
Chemical reaction that involves a transfer of electrons between two species. An oxidation-reduction reaction is any chemical reaction in which the oxidation number of a molecule, atom, or ion changes by gaining or losing an electron Common because they allow the molecules and changes to be conserved within the system.
31. Provide an example of a redox reaction: breakdown of glucose in the human body to get ATP for
energy involves the oxidation of glucose to carbon dioxide and the reduction of oxygen to water: Glucose (C6H12O6) loses electrons (oxidized) to form carbon dioxide (CO2) and oxygen (O2) is reduced to form water (H2O).
32. In the combustion of wood, oxygen from the air transfers electrons to the carbon in
the wood. Is the oxygen being oxidized or reduced?: In the combustion of wood, the oxygen is being reduced because it is losing electrons to the carbon in the wood.
33. Is the utilization of glucose to produce ATP catabolic or anabolic? Is synthesis of nucleic
acids catabolic or anabolic?: The utilization of glucose to produce ATP is catabolic, and the synthesis of nucleic acids is anabolic.
34. What is the role of enzymes in energy coupling?: The role of enzymes in energy coupling is to
provide energy for the reaction by binding ATP and the other molecules involved in the reaction. Using the ATP for energy and hydrolyzing the ATP to ADP + Pi the enzyme can catalyze the reaction.
35. Describe the two laws of thermodynamics.: 1. Energy can be exchanged between physical
systems as heat and work.
- Entropy (disorder) increases in an isolated system
36. Define enthalpy (H): the heat content of a system
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37. Define entropy (Delta S): Entropy is a measurement of the molecular disorder in a system
38. Define Gibbs Free Energy and calculate the change in Gibbs Free Energy (ΔG).:
Gibb's Free Energy is a measurement of thermodynamic potential
7 / 30 membrane within mitochondria to form a gradient of protons that drives the creation of adenosine triphosphate (ATP)
47. Describe the sequence of components of the electron transport chain.:
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48. Explain why NADH and FADH2 yield different amounts of ATP.: NADH produces 3 ATP
during the ETC (Electron Transport Chain) with oxidative phosphorylation because NADH gives up its electron to Complex I, which is at a higher energy level than the other Complexes. When Complex I transfers the electron to Complex III, energy is given ott to pump protons across the membrane, creating a gradient. The electron moves again to Complex IV and again pumps more electrons across the membrane. Because NADH started with Complex I, it had more chances to pumps more protons across the gradient, which powers the ATP synthase and gives us 3 ATP per molecule of NADH. FADH2 produces 2 ATP during the ETC because it gives up its electron to Complex II, bypassing Complex I. By bypassing Complex I, we missed a chance to pump protons across the membrane, so less protons have been pumped by the time we get to Complex IV. Protons still have been pumped, enough to fuel 2 ATP created by ATP synthase.
49. Define oxidative phosphorylation: The production of ATP using energy derived from the redox
reactions of an electron transport chain; the third major stage of cellular respiration.
50. Use the "chemiosmotic hypothesis" to explain how the energy from electron
transport is "coupled" to ATP synthesis.: the action of ATP synthase is coupled with that of a proton gradient. It is the action of the proton gradient that causes a proton motive force that allows ATP synthase to phosphorylate ADP and inorganic phosphate to ATP
51. Explain why aerobic ATP production is much more efficient than anaerobic
production.: This is because oxygen is an excellent electron acceptor for the chemical reactions involved in generating ATP
52. Identify one advantage of anaerobic glycolysis over aerobic metabolism.: -
Speed (Produces ATP very quickly, but runs out)
53. What is the basis for ATP generation through substrate-level phosphoryla- tion?: ATP
is synthesized directly through ADP and a reactive intermediate (a high-energy phosphate-containing molecule)
54. How does the generation of a proton gradient contribute to synthesis of ATP in
electron transport?: provides the energy for ATP synthase to make ATP.
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63. What is a futile cycle? What do they produce? Give an example of an animal process that
relies on a futile cycle.: two metabolic pathways run simultaneously in opposite directions producing no net ettect except heat & ATP loss. thermal homeostasis in brown tissues of young mammals, insect flight muscles for heat,
64. How are muscles able to have stores of energy readily available for use?
Explain the mechanism.: store creatine phosphate & ADP Becomes creatine and ATP.
65. Explain Creatine phosphate shuttle:
66. UNIT 3 Identify the 20 common amino acids.:
67. Amino Acid Structure: a carboxyl group, amine group, and R group
68. What is the R group in an amino acid basic structure?: unique side chain
69. Compare the arrangement of hydrophobic and hydrophilic amino acids in a protein
in an aqueous environment to that of a membrane.: Aqueous environment - hydrophilic side chains face outside of the protein to interact with water hydrophobic on interior of the protein.
11 / 30 Membrane - hydrophobic face the outside where they interact with hydrophobic fatty acids hydrophilic side on inside or any place they can interact with water.
70. Protein Structure:
71. As you will see in the final lesson of this unit, a protein depends on its tertiary
structure to perform its functions. A mutation in the interior of a given protein inactivated the protein. This mutation is ala ’val. A second mutation, ile ’gly, restored the activity of the protein. Explain these results.: First mutation substituted larger amino acid for smaller one, thus distorting the tightly packed protein interior. The second mutation reversed this change by substituting a smaller amino acid for a larger one.
72. Explain why proline is not common in α-helices, but can be found frequently in
collagen.: Proline is the least flexible amino acid, too rigid and does not "bend" or fit with other amino acid side chain. Proline found in collagen because of the abundance of glycine which has the smallest side chain. allow for proline to fit into this type of helical structure.
73. Identify the six most abundant amino acids in proteins.: The six most abundant amino acids
in proteins are: leu - leucine ala - alanine gly - glycine ser - serine val - valine glu - glutamic acid
74. Why it is important to know the protein sequence in addition to the DNA sequence
of a particular gene?: it reveals information about the protein structure that is not possible with nucleic acid sequencing alone
75. Wool consists of α-keratin. Pure wool sweaters exposed to hot water shrink
13 / 30 phenomenon?: When wool is processed ("spun"), the fibres are teased to an elongated shape. Exposure to steam or hot water will cause the processed fibres to revert to their original, tightly H-bonded α-helices
76. Describe the hydrogen-bonding pattern of an α-helix.: The regular coding of an α-helix is
caused by H-bonding of the −−C==O group of the first amino acid residue to the −−N−−H group of the fifth amino acid residue.
77. List the two advantages of multiple subunits in proteins.: having subunits that are
assembled rather than one large polypeptide facilitates repair of a defective protein better manipulation and regulation of the protein. (can make enzyme bigger)
78. Explain how cooperativity between haemoglobin and oxygen is achieved.: - Hemoglobin
binds oxygen by the iron of the heme group in one of the subunits. The heme iron is attached to a histadine side chain. This changes the conformation and allows binding of oxygen
79. Describe the energy and entropy changes that occur during protein folding.-
: increase in conformational stability of the folded protein results in a decrease in free energy. Folded = low-energy, low-entropy
80. Antibodies are proteins that recognize and help to inactivate foreign proteins (called
antigens). Why do such antibodies rarely react to denatured proteins? A few antibodies do recognize denatured proteins. How can this occur?: Antibodies bind to the surface of an antigen. Therefore, part of the "recognition" is the specific arrangement of amino acids at a particular spot on the surface of an antigen. Denaturation destroys the spatial arrangement of amino acids which form the surface of a protein. antibody may have been raised toward a denatured antigen (lab setting), area of recognition on an antigen may be held together, at least partially, by disulphide bonds. Disulphide bonds are covalent bonds and will not break under the conditions of temperature, pH, solvent, and agitation which will dissociate H-bonds and hydrophobic interactions.
81. What information is provided by comparing the sequences of proteins from different
organisms?: possible functional ditterences or binding specificities, whether the protein is a membrane protein or secreted protein, evolutionary relationships between organisms, and conserved regions or sequences, which can be very useful for predictions of protein function.
hen the
carboxyl
water (H2O)
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82. How is a phylogenetic tree constructed?: classifying the organisms under study according to
similarities (e.g., are they mammals, insects, reptiles, etc.). noting the amino acid sequence of a protein common to all of the organisms. Grouping the organisms according to common alterations in an amino acid sequence.
83. Which side chains normally occur on a protein's interior? On its surface?: Typ- ically the
nonpolar residues Val, Leu, Ile, Met, and Phe occur most often in the interior. The charged polar residues Arg, His, Lys, Asp, and Glu are located on the protein surface. Uncharged polar side chains, Ser, Thr, Asn, Gln, and Tyr, are typically on the surface, but may be found in the interior of a protein H- bonded to other groups (this neutralizes their polarity).
84. Describe the forces that stabilize proteins.: Hydrophobic ettect - stabilizes proteins by causing nonpolar
groups to minimize their association with water. Electrostatic interactions, such as Van der Waals forces, hydrogen bonding, and ionic associations stabilize proteins by allowing side chains to bond or associate. Chemical cross-linking through the formation of disulphide bonds or by the cross-linking of metal ions to a protein add stability to the folding of the protein.
85. List and describe two functions of proteins.: Enzymes - catalyse reactions in the cell.
Growth factors - induce growth and ditterentiation of specialized cells.
86. What is an invariant region and what does in mean in terms of enzymes?: - section of
primary structure that is identical or conserved across all species. For enzymes, this is usually in the catalytic region.
87. What is a prion?: infectious protein. causes misfolding of the PrP protein which is found in the brain
88. Describe and draw a peptide bond.: bond formed between two molecules w
group of one molecule reacts with the amino group of the other molecule, releasing a molecule of
89. Define primary, secondary, tertiary, and quarternary protein structure.:
osin
e
d
uracil.:
16 / 30 tRNA - Transfer RNA: Brings amino acids to ribosomes during translation. rRNA - Ribosomal RNA: With ribosomal proteins, makes up the ribosomes, the organelles that translate the mRNA.
99. Describe the chemical differences between DNA and RNA, and explain why DNA is the
more stable molecule.: RNA contains A, U, G, C; DNA contains the nitrogenous bases A, T, G, C. RNA is usually single stranded; DNA is double stranded. Normally the nitrogenous bases in RNA are chemically modified, while those in DNA are not. RNA contains an hydroxyl group at the 2 position of ribose. DNA does not. The presence of a hydroxyl group destabilizes RNA, because the 2′-hydroxyl of ribose is close to a phosphate group in the phosphodiester backbone of RNA.
100. List the functions of DNA and RNA.: DNA is responsible for storing and transferring genetic
information, while RNA directly codes for amino acids and acts as a messenger between DNA and ribosomes to make proteins
101. What are the four nitrogenous bases: Adenine, Thymine, Guanine, Cyt
102. What difficulties can you see in producing proteins by inserting the mam- malian
genes into bacterial hosts?: The proteins produced by mammalian genes inserted into bacterial hosts will lack sugar groups. This is because bacteria cannot glycosylate proteins like mammalian cells do.
103. Draw the structures of adenine, cytosine, guanine, thymine, an
104. List and describe the major features of the Watson-Crick model of DNA
structure.: -two polynecleotide chains that form a double helix structure. -anti-parallel DNA strands -major and minor grooves as a result of the bases on the periphery.
17 / 30 -Each base is hydrogen bonded: complementary base pairing.
105. What are the structural differences between DNA and RNA?: DNA is double-strand- ed and RNA
is single-stranded. DNA contains deoxyribonucleotides as the pentose sugar is deoxyribose. RNA contains ribonucleotides as the pentose sugar is ribose. The nitrogenous bases in DNA are A-T and G-C, but in RNA they are A-U and G-C, whereby A pairs with uracil instead of thymine.
106. Would you expect DNA and RNA to be water-soluble? Explain.: With both an anion
(phosphate) and a sugar on every monomer unit, DNA and RNA are readily hydrated
107. Why would you expect RNA viruses to have double stranded RNA? While many RNA
viruses are double stranded, not all are. What comments can you make on this latter class of viruses in light of your first answer?: RNA viruses have just as great a need to preserve their genomes from generation to generation as other species do. Double stranding would protect the base composition from chemical attack (mutation, destruction, or both), just as duplex DNA is protected. Single strand RNA viruses may mutate faster than duplex RNA viruses; they many have protective protein coats surrounding the RNA; or the RNA may double back on itself to give internal double stranding
108. It was stated that (A + G) always equals (T + C) for duplex DNA. Is this restriction also
true for single strands of DNA? Justify your answer.: The restriction is true for double stranded DNA because every purine is H-bonded to a pyrimidine. Therefore, the sum of the purines (A
- G) must equal the sum of the pyrimidines (T + C). There is no such restriction for each individual strand of DNA.
109. What differences would you expect between a duplex DNA which has more A-T
base pairs and a duplex DNA which has more G-C pairs?: A and T are joined by two H-bonds, while G and C are joined by three H-bonds. Therefore, the duplex with more G-C pairs will have a higher melting temperature; and it may replicate more slowly.
110. What are the forces that stabilize nucleic acids? What can be used to de- nature
nucleic acids? Can nucleic acids renature?: The forces that stabilize nucleic acids are H-bonding. In addition a stabilizing force for DNA is stacking interactions between bases in a strand. Nucleic acids can be denatured by heat (to boiling) and urea. Yes, nucleic acids can renature.
111. Outline the role of the 2′ hydroxyl group in RNA. What is the reason this group is
lacking in DNA?: The role of the 2′ OH group in RNA is to render it sensitive to degradation so that RNA can send messages and be involved in protein synthesis, but be broken down shortly after. The lack of this group in DNA makes the DNA more stable and resistant to degradation in order to protect the genetic information of the cell.
112. Outline the flow of genetic information in a cell.: DNA to RNA to protein.
DNA is transcribed to mRNA (transcription)
19 / 30 Glycogen is the primary energy reserve for animals.
121. Structure of cellulose, chitin, starch, and glycogen.:
122. What common biochemical structure is found in cartilage and hyaluronic acid?
Where are cartilage and hyaluronic acid found in the body? Why do they have such different physical properties?: Both are glycoproteins Joint lubricating fluid (hyaluronic acid) consists of a gel-like matrix of modified, highly charged polysaccharides. This matrix is more highly hydrated and more flexible than any of the other glycoproteins. Cartilage is the least hydrated and thus the least flexible of the structures.
123. If lysozyme is so effective in cleaving the heteropolysaccharide of the bacte- rial cell
wall, why isn't it used clinically to fight bacterial infection?: It kills everything, including host polysaccharides
124. Outline the structure of peptidoglycan.:
125. What is the mechanism of penicillin's action on the bacterial cell wall?: Penicillin
specifically binds to and inactivates enzymes that cross-link the peptidoglycan strands of the bacterial cell wall, thus preventing growing cells from synthesizing the cell wall needed for protection from the hypotonic environment. As a result, the bacterial cells lyse
126. What are the major roles of lipids: -main components of membranes
-fuel molecules -precursors of hormones and prostaglandins -protective coatings on fur, feathers, fruits, etc.
127. What are the 5 major groups of lipids: -fatty acids (building blocks of 2 and 3 below)
-triacylglycerols (primary form of energy storage for metabolic activity)
20 / 30 -glycerophospholipids (major lipid component of membranes)
