Elementary Biochemistry Lecture Slides 2025 PDF

Elementary Biochemistry CHE-303-01-2025 Chapter 01 Introduction to Biochemistry Dr.Shukare 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 an...

Elementary Biochemistry CHE-303-01-2025 Chapter 01 Introduction to Biochemistry Dr.Shukare 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? ▪ The science concerned with the chemical basis of life (Gk bios “life”) ▪ 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.  5 The Science of Biochemistry  The Origin of Biochemistry 6 Friedrich Wöhler (1800-1882) is credited with challenging the doctrine of “Vital Force Theory” in 1828 when he carried out a simple experiment showing that the organic molecule, urea, could be synthesized from an inorganic salt, ammonium cyanate According to Vital Force Theory, ” all organic compounds are created in living beings by some mysterious natural force and since such mysterious force which was termed “Vital Force” could not be created artificially, there is no possibilities of preparing organic compounds manually or in laboratory from inorganic sources.” German chemist Friedrich Wöhler urinary excretion product Copyright © 2019, 2016 Pearson Education, Inc. All Rights Reserved.  Catalysts and Alcoholic Fermentation The Origin of Biochemistry … 7 ✦ Additional evidence was provided by the brothers, Eduard and Hans Buchner. ✦ They studied yeasts ability to ferment sugar into CO2 and ethanol. ✦ Eduard (1860-1917) and Hans (1850- 1902) Buchner were able to show that living yeast cells were not required for alcohol fermentation. Extracts from dead yeast cells could also carry out fermentation of sugars. Buchner is credited with proposing that “enzymes” helped speed up this reaction. Copyright © 2019, 2016 Pearson Education, Inc. All Rights Reserved. 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)  The Origin of Biochemistry … 9 Structure of DNA ▪ In 1953, the American biologist James Watson and the English physicist Francis Crick described the double-helical structure of DNA Copyright © 2019, 2016 Pearson Education, Inc. All Rights Reserved.  A Brief History of Biochemistry Early 19th Century World made of either "living matter" (organic) or "non-living matter" (inorganic).(Vitalism) 1828 Friedrich Wohler accomplished the synthesis of Urea from inorganic matter. 1897 Edvard and Hans Buchner showed dead cell extracts can perform reactions of living cells……enzymes Late 1800's Emil Fischer suggested Substrate º Key, Enzyme º Lock Early 1900's Field of biochemistry emerges Structure and function of enzymes Elucidating enzymatic pathways 1944 Genes composed of DNA 1953 Watson and Crick determine the structure of DNA Copyright © 2019, 2016 Pearson Education, Inc. All Rights Reserved. 10 Biochemistry for ? Biochemistry: An Applied Science ▪ Biochemistry uses advanced experimental methods to develop in vitro conditions for exploiting cellular processes and enzymatic reactions. 12 We are what we eat Water 13 1.2 The Chemical Basis of Life: A Hierarchical Perspective ▪ The foundation of this Element Symbol Percent dry Additional trace Additional trace hierarchy includes weight (percent) elements (less than 0.1 percent), elements (less than 0.1 percent), chemical elements and element Symbol Carbon Upper C 62 Manganese Upper M, n functional groups. Nitrogen Upper N 11 Iron Upper F, e Oxygen Upper O 9 Cobalt Upper C, o ▪ Chemical elements: 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 Organizational Hierarchy of Biochemistry 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 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. Figure 1.6 Covalent bonds containing carbon can vary in their characteristics. a. Methane: Carbon has four unpaired valence electrons in its outer shell and can form four covalent bonds in a tetrahedral arrangement at angles of 109.5‹. b. Ethane: Carbon–carbon single bonds (C-C) can rotate freely relative to each carbon atom. c. Ethylene: Rotation around a carbon–carbon double bond (C=C) is restricted so the atoms are held in place with respect to each other. The bond angles are approximately 120‹. Carbon atoms are shown as gold spheres and hydrogen atoms as white spheres. 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 Essential Ions ▪ Play a key role in cell signaling and neurophysiology ▪ Include: Calcium Chloride Magnesium Potassium Sodium  Functional Groups ▪ Play an important role in structure and function of biomolecules Figure 1.7 Six chemical groups are very commonly found in biomolecules. The methyl group has a single protonation state. However, the amino, hydroxyl, sulfhydryl, phosphoryl, and carboxyl groups may have different protonation states from what is shown, depending on the nature of other atoms in the vicinity. R represents the rest of the molecule to which the functional group is attached. Biological Macromolecules Biomolecules, Part 1 ▪ Four major types: ❑Amino acids ❑Nucleotides ❑Simple sugars ❑Fatty acids 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 a. 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 b. 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+ c. Simple Sugars ▪ Carbohydrates Contain C, H, and O atoms only ▪ Have a 2:1 ratio of hydrogen atoms to oxygen atoms ▪ Include: Monosaccharides Disaccharides d. 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 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. 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  Polymers in Macromolecules: Nucleic Acids ▪ Covalently linked nucleotides ▪ Include DNA and RNA ▪ Nucleotides are linked together by phosphodiester bonds. Figure 1.10 DNA is a polymeric macromolecule consisting of nucleotides that are covalently linked through a phosphodiester bond (shown in red), which connects the 3′- carbon of one nucleotide to the 5′-carbon of a second nucleotide. DNA polymers have chemical polarity, meaning that the 5′-phosphoryl and the 3′-hydroxyl termini are distinct. Polymers in Macromolecules: Proteins ▪ Covalently linked amino acids ▪ Also known as polypeptides R = different amino acid side chains 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. Various Examples of Polysaccharides Amylose (starch) Figure 1.12 The polysaccharides amylose and cellulose contain the same repeating unit of glucose, but differ in the structure of the glycosidic bond linking adjacent units (shown in red). Cellulose a. Amylose (starch) is a polymer of glucose containing α(1→4) glycosidic bonds between glucose units. b. Cellulose, contained in plant cell walls, is identical in composition to amylose; however, the glycosidic bonds between glucose units are in the β(1→4) configuration, and adjacent glucose residues are rotated 180‹. Chitin c. Chitin is the primary carbohydrate component in the exoskeletons of insects and crustaceans. Chitin contains a β(1→4) glycosidic bond linking adjacent N-acetylglucosamine units.  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) 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 Metabolic Pathway Formats Metabolic Pathway Example: The Urea Cycle Figure 1.13 Metabolic pathways consist of linked biochemical reactions in which the product of one reaction is the reactant for the next reaction. In this example, the two urea cycle enzymes, argininosuccinate synthetase and argininosuccinase, function in a mini-pathway that converts citrulline and aspartate into arginine and fumarate through formation of argininosuccinate.  Cellular Structures Bacteria are prokaryotic cells Animal cells -eukaryotic cell Plant cells -eukaryotic cells Figure 1.15 The diameter of eukaryotic cells is as large as ∼10–100 um, whereas the diameter of prokaryotic cells is only ∼1 um. a. Bacteria are prokaryotic cells with a cytosolic compartment surrounded by a plasma membrane that forms a barrier separating the cell from the environment. Most bacteria contain a single circular chromosome and move using flagellar structures or pili located on the outside of the cell. b. Animal cells are a type of eukaryotic cell and contain numerous intracellular membrane- bound compartments, which create microenvironments for biochemical reactions. Membrane-bound organelles in all types of eukaryotic cells include mitochondria, lysosomes, and peroxisomes, which are subcellular sites for specific metabolic reactions. c. Plant cells are eukaryotic cells that contain chloroplasts, which convert light energy into chemical energy by the process of photosynthesis. Plant cells also contain large vacuoles, which are responsible for maintaining metabolite pools. The plasma membrane of plant cells is surrounded by a cell wall consisting of cellulose, which provides structural integrity to the plant. Key Cellular Structure (organelles) 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 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 Cell Specialization ▪ A higher level of organizational complexity ▪ Allows multicellular organisms to exploit their environment through signal transduction  Signal Transduction Cell functions in multicellular organisms are coordinated by signal transduction mechanisms involving ligand activation of cellular receptor proteins. In this example, an extracellular ligand is shown binding to a membrane- bound receptor protein, resulting in conformational changes that activate the receptor. The activated receptor can influence processes inside the cell in response to the ligand, examples of which include ion transport, enzyme activation, and protein synthesis. When ligand concentrations decrease, the ligand is released from the receptor protein, allowing it to return to the inactive (nonsignaling) conformation. ligand and the receptor 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 The Circulatory System 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. 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.  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. Nucleotides are the building blocks of nucleic acids Nucleotide Base Pairs ▪ The complimentary base pairs are as follows: in DNA: G-C and A-T G-C base pairs contain three hydrogen in RNA: G-C and A-U bonds. c. A-T base pairs in DNA–DNA hybrids contain two hydrogen bonds.  Nucleotide Base Pairs in the Helix The two antiparallel DNA strands are held in The DNA double helix is a right-handed helix that register by hydrogen bonds between the G-C and can be copied through complementary base pairing A-T base pairs. to produce two exact DNA replicas.  Central Dogma ▪ Describes how information is transferred between DNA, RNA, and protein The central dogma of molecular biology describes the transfer of information between nucleic acids and proteins. The genome is copied during cell division by the process of DNA replication. A variety of RNA products are generated by DNA transcription, one of which is mRNA, which is used to synthesize proteins by mRNA translation. The majority of RNA produced by DNA transcription is required for protein synthesis (rRNA and tRNA), RNA processing (snRNA), and regulation of gene expression or protein synthesis (miRNA). Under some conditions, RNA molecules can also be converted back into DNA by reverse transcription.  Relationship between DNA and Protein The relationship between the DNA sequence of a gene and the amino acid sequence of the protein product is shown. Using the genetic code, the primary amino acid sequence of a protein can be determined from the DNA sequence of the coding strand, with thymine (T) in place of uracil (U). The DNA coding strand has the same 5′ to 3′ polarity of the corresponding mRNA transcript. “-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 1.4 Determinants of Biomolecular Structure and Function ▪ Structure determines function for DNA. Mutant Genes ▪ Proteins acquire a bounty of molecular structures through random mutations. 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 Clicker Question 1 The second half of alcoholic fermentation is an example of a(n) __________ reaction. a. oxidation b. reduction c. redox d. hydration e. dehydration Clicker Question 2 Based on the structure of palmitate, this can be classified as a __________ fatty acid. a. saturated b. monounsaturated c. polyunsaturated d. all of the above e. a and b only 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? a. amine b. amide c. carbonyl d. ketone e. aldehyde Clicker Question 4 A coding strand of DNA is shown below: 5’-AAATTTGGCTCAGGCCTGACG-3’ What is the correct template strand? a. 5'-UUUAA5'-TTTAAACCGAGTCCGGACTGC-3' b. ACCGAGUCCGGACUGC-3' c. 3'-TTTAAACCGAGTCCGGACTGC-5' d. 3'-UUUAAACCGAGUCCGGACUGC-5' e. 3'-AAATTTGGCTCAGGCCTGACG-5' 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. a. egg b. sperm c. somatic d. a and b e. b and c This concludes the Lecture Slide Set for Chapter 1 BIOCHEMISTRY, SECOND EDITION Find more learning resources for Biochemistry, 2e here.