BIOCHEM 2nd Edition Miesfel and McEvoy Chapter 1

Biochemistry, 2nd edition, Roger L Miesfeld and Megan M. McEvoy

1. LECTURE SLIDES Chapter 1 Principles of Biochemistry Copyright © 2021 W. W. Norton & Company, Inc.

2. Chapter Outline 1.1 What Is Biochemistry? 1.2 The Chemical Basis of Life: A Hierarchical Perspective 1.3 Storage and Processing of Genetic Information 1.4 Determinants of Biomolecular Structure and Function

3. 1.1 What Is Biochemistry? Biochemistry aims to explain biological processes at the molecular and cellular levels. It is a core discipline in life sciences. It is at the interface of biology and chemistry. It relies heavily on the quantitative analysis of data. It often studies in vitro (outside a living cell) systems.

4. It All Started with Fermentation… Fermentation is the conversion of rotting fruit or grain into alcohol solutions through the action of yeast. Yeast was determined to be the catalyst. Used to produce wine and beer from yeast

5. Alcoholic Fermentation This reaction has been around since 2000 B.C . Buchner demonstrated that CO 2 and CH 3 CH 2 OH were produced in vitro from sugar using brewer’s yeast in 1897. Buchner is credited with proposing that “enzymes” helped speed up this reaction.

6. Catalysts Biomolecules that increase the rate (catalyze) of biochemical reactions dramatically Found in all living cells Responsible for the following reactions: Aerobic respiration Fermentation Nitrogen metabolism Energy conversion Programmed cell death Examples: Proteins or ribonucleic acid (RNA)

7. Biochemistry: An Applied Science Biochemistry uses advanced experimental methods to develop in vitro conditions for exploiting cellular processes and enzymatic reactions.

8. 1.2 The Chemical Basis of Life: A Hierarchical Perspective The foundation of this hierarchy includes chemical elements and functional groups. Chemical elements: Element Symbol Percent dry weight (percent) Additional trace elements (less than 0.1 percent), element Additional trace elements (less than 0.1 percent), Symbol Carbon Upper C 62 Manganese Upper M, n Nitrogen Upper N 11 Iron Upper F, e Oxygen Upper O 9 Cobalt Upper C, o Hydrogen Upper H 6 Copper Upper C, u Calcium Upper C, a 5 Zinc Upper Z, n Phosphorous Upper P 3 Selenium Upper S, e Potassium Upper K 1 Molybdenum Upper M, o Sulfur Upper S 1 Iodine I Chlorine Upper C, l Less than 1 Fluorine Upper F Sodium Upper N a Less than 1 Chromium Upper C, r Magnesium Upper M, g Less than 1 Tin Upper S, n

9. Organizational Hierarchy of Biochemistry

10. Chemical Bonding Observed in Biochemistry The most common carbon bonds are C—C, C C, C—H, C O, C—N, C—S, and C—O.   Atom Number of unpaired electrons Upper H, one unpaired atom 1 Upper O, four paired and two unpaired atom. 2 Upper N, two paired and three unpaired atom. 3 Upper C four unpaired atom. 4

11. Molecular Geometry Revisited A carbon atom can bind up to four single bonds to form a tetrahedron. The rotation around a single bond is very easy due to its sigma bond, whereas a carbon–carbon double bond includes a pi bond and rotation is not possible without breaking this pi bond.

12. Trace Elements In addition to the elements observed in Table 1.1, trace elements are used as cofactors in proteins and are required for life. These elements are required in smaller (“trace”) amounts. These elements include: Zinc Iron Manganese Copper Cobalt

13. Essential Ions Play a key role in cell signaling and neurophysiology Include: Calcium Chloride Magnesium Potassium Sodium

14. Functional Groups Play an important role in structure and function of biomolecules

15. Biomolecules, Part 1 Four major types: Amino acids Nucleotides Simple sugars Fatty acids

16. Biomolecules, Part 2 Primary cellular function Amino acid Protein function Neurotransmission Nitrogen metabolism Energy conversion Nucleotides Nucleic acid function Energy conversion Signal transduction Enzyme catalysis Simple sugar Energy conversion Cell wall structure Cell recognition Nucleotide structure Fatty acid Cell membranes Energy conversion Cell signaling

17. Amino Acids Nitrogen-containing molecules that function primarily as the building blocks of protein Covalently linked into a linear chain to form polypeptides Differ from each other by the side chain attached at the central carbon

18. Nucleotides Include the nucleic acids, DNA and RNA Consist of the following: Nitrogenous base Five-membered sugar 1–3 phosphate groups Examples include: Cytosine ATP cAMP NAD +

19. Simple Sugars Carbohydrates Contain C, H, and O atoms only Have a 2:1 ratio of hydrogen atoms to oxygen atoms Include: Monosaccharides Disaccharides

20. Fatty Acids Amphipathic molecules Act as components of plasma membrane lipids Act as a storage form of energy (i.e., fats) Consist of: Carboxyl group attached to a hydrocarbon chain

21. Saturated vs. Polyunsaturated Fatty Acids Saturated fatty acids contain no C C double bonds in the hydrocarbon chain. Polyunsaturated fatty acids contain multiple C C double bonds in the hydrocarbon chain.  

22. Macromolecules Higher-end structural form of biomolecules Include: Chemical polymers such as: Proteins—amino acid polymers Nucleic acids—nucleotide polymers Polysaccharides—polymers of glucose molecules

23. Polymers in Macromolecules: Nucleic Acids Covalently linked nucleotides Include DNA and RNA Nucleotides are linked together by phosphodiester bonds.

24. Polymers in Macromolecules: Proteins Covalently linked amino acids Also known as polypeptides R = different amino acid side chains

25. Polymers in Macromolecules: Polysaccharides Consist of mixtures of simple sugars of repeating units of glucose Covalent linkage between glucose units (i.e., glycosidic bond) is key to the identification and chemical properties of the polysaccharide.

26. Various Examples of Polysaccharides

27. Metabolic Pathways Enable cells to coordinate and control complex biochemical processes in response to available energy Function within membrane-bound cells Examples include: Glycolysis and gluconeogenesis (glucose metabolism) Citrate cycle (energy conversion) Fatty acid oxidation and biosynthesis (fatty acid metabolism)

28. Metabolic Pathway Terminology Metabolites Small biomolecules that serve as both reactants and products in biochemical reactions within cells Frequently observed in reactions that are essential in life-sustaining processes Metabolic flux The rate at which reactants and products are interconverted in a metabolic pathway

29. Metabolic Pathway Example: The Urea Cycle

30. Metabolic Pathway Formats

31. Cellular Structures

32. Key Cellular Structure Functions, Part 1 Genome All encoded genes and other DNA elements specifying genetic composition of prokaryotic and eukaryotic cells Nucleolus Site of ribosome assembly Ribosomes Location of protein synthesis

33. Key Cellular Structure Functions, Part 2 Mitochondria Responsible for ATP production Peroxisomes and lysosomes Involved in macromolecule degradation and detoxification Endoplasmic reticulum Sequester ribosomes for protein synthesis Golgi apparatus Involved in protein translocation and protein secretion in the plasma membrane

34. Cell Specialization A higher level of organizational complexity Allows multicellular organisms to exploit their environment through signal transduction

35. Signal Transduction

36. Organisms A complex organization level that consists of specialized cells Allow multicellular organisms to respond to environmental changes Can adapt to change through signal transduction mechanisms that facilitate cell–cell communication

37. The Circulatory System

38. Ecosystems Highest level of hierarchical organization Include cohabitation of different organisms in the same environmental niche Involve a shared use of resources and waste management

39. Ecosystem Examples This is the top rung of the hierarchal ladder of life. This is how organisms interact with their environment and each other.

40. 1.3 Storage and Processing of Genetic Information 1952 – DNA was determined to be sufficient to promote viral replication. Rosalind Franklin collected X-ray diffraction data to determine the structure of DNA.

41. Watson and Crick’s Discovery 1953 – Watson and Crick determined that DNA is a double helix. This discovery explained how DNA was used to pass on genetic material. 1962 – The duo were awarded the Nobel Prize in Physiology or Medicine.

42. Deoxyribonucleotides vs. Ribonucleotides Deoxyribonucleotides are monomeric units of DNA that lack an OH group on the C-2' of the ribose sugar. Ribonucleotides are structurally similar to deoxyribonucleotides, except they contain an OH at the C-2' position in the ribose sugar.

43. Nucleotide Base Pairs The complimentary base pairs are as follows: in DNA: G-C and A-T in RNA: G-C and A-U

44. Nucleotide Base Pairs in the Helix

45. Central Dogma Describes how information is transferred between DNA, RNA, and protein

46. Relationship between DNA and Protein

47. “-ome” Biochemistry Genome Collection of genes Transcriptome Collection of DNA transcripts (RNA products) generated by DNA transcription Proteome Collection of proteins produced by mRNA translation either in the entire organism or under special conditions

48. 1.4 Determinants of Biomolecular Structure and Function Structure determines function for DNA.

49. Mutant Genes Proteins acquire a bounty of molecular structures through random mutations.

50. Mutations Can be germ-line cell Passed from parents to offspring Result in inherited genetic diseases Can be in somatic cells Not inherited by the offspring Limited to the individual organism

51. Random Mutation and Natural Selection

52. Gene Duplications

53. Clicker Question 1 The second half of alcoholic fermentation is an example of a(n) __________ reaction. oxidation reduction redox hydration dehydration

54. Clicker Question 1 (Answer) The second half of alcoholic fermentation is an example of a(n) __________ reaction. oxidation reduction redox [Correct Answer] hydration dehydration

55. Clicker Question 2 Based on the structure of palmitate, this can be classified as a __________ fatty acid. saturated monounsaturated polyunsaturated all of the above a and b only

56. Clicker Question 2 (Answer) Based on the structure of palmitate, this can be classified as a __________ fatty acid. saturated [Correct Answer] monounsaturated polyunsaturated all of the above a and b only

57. Clicker Question 3 Based on the structure below, a peptide bond (highlighted in the boxed area) is an example of what type of functional group? amine amide carbonyl ketone aldehyde

58. Clicker Question 3 (Answer) Based on the structure below, a peptide bond (highlighted in the boxed area) is an example of what type of functional group? amine amide [Correct Answer] carbonyl ketone aldehyde

59. Clicker Question 4 A coding strand of DNA is shown below: 5’-AAATTTGGCTCAGGCCTGACG-3’ What is the correct template strand? 5'-UUUAA5'-TTTAAACCGAGTCCGGACTGC-3' ACCGAGUCCGGACUGC-3' 3'-TTTAAACCGAGTCCGGACTGC-5' 3'-UUUAAACCGAGUCCGGACUGC-5' 3'-AAATTTGGCTCAGGCCTGACG-5'

60. Clicker Question 4 (Answer) A coding strand of DNA is shown below: 5’-AAATTTGGCTCAGGCCTGACG-3’ What is the correct template strand? 5'-UUUAA5'-TTTAAACCGAGTCCGGACTGC-3' ACCGAGUCCGGACUGC-3' 3'-TTTAAACCGAGTCCGGACTGC-5' [Correct Answer] 3'-UUUAAACCGAGUCCGGACUGC-5' 3'-AAATTTGGCTCAGGCCTGACG-5'

61. Clicker Question 5 Fatal familial insomnia is a rare inherited disorder in which persons have progressively worsening insomnia. It is caused by a mutation on codon 178 of the prion protein. The cells affected in this mutation are _______ cells. egg sperm somatic a and b b and c

62. Clicker Question 5 (Answer) Fatal familial insomnia is a rare inherited disorder in which persons have progressively worsening insomnia. It is caused by a mutation on codon 178 of the prion protein. The cells affected in this mutation are _______ cells. egg sperm somatic a and b [Correct Answer] b and c

63. This concludes the Lecture Slide Set for Chapter 1 BIOCHEMISTRY , SECOND EDITION Find more learning resources for Biochemistry , 2e here. Copyright © 2021 W. W. Norton & Company, Inc.