Introduction to Biochemistry Quiz

Biochemistry: An Evolving Science

• Biochemistry is the study of the chemistry of life processes
• The first synthesis of urea from ammonium cyanate was a landmark moment in 1828
• AgNCO + NH4Cl → Urea + AgCl was the reaction
• Friedrich Wöhler performed the synthesis
• Treating silver isocyanate with ammonium chloride yielded urea
• This event marked the beginning of biochemistry for many historians
• Biochemistry is applied to various fields, notably medicine, dentistry, agriculture, forensics, and environmental sciences

Diverse Biochemical World

• Various life forms exhibit biochemical diversity
• Organisms range from the animal kingdom, encompassing nearly microscopic insects and large mammals like elephants and whales, to the plant kingdom, varying from small algae to giant sequoias
• The microscopic world includes single-celled organisms such as bacteria and yeast, showing immense diversity in different habitats like water, soil, and within larger organisms
• Some organisms even thrive in extreme environments like hot springs and glaciers

Common Features in All Organisms

• Large organisms are composed of numerous cells resembling single-celled microorganisms
• Life processes utilize two main classes of molecules: macromolecules (e.g., proteins, nucleic acids) and metabolites (e.g., glucose, glycerol)
• Deoxyribonucleic acid (DNA) is the genetic material in all cells
• Proteins play crucial roles in biological processes, constructed from 20 building blocks with similar roles and 3D structures
• The TATA-box-binding protein, a key molecule in gene regulation, has a similar shape across diverse organisms, showcasing the underlying evolutionary unity

Common Metabolic Processes

• Fundamental biochemical processes like converting glucose and oxygen into carbon dioxide and water are universal in simple organisms like Escherichia coli and complex organisms like humans
• Photosynthesis in plants and carbohydrate breakdown in animals are analogous metabolic processes with a common evolutionary heritage
• All living things originated from a common ancestor, which explains these similarities

A Possible Timeline for Biological Evolution

• Life on earth emerged approximately 3.5 billion years ago
• Key events like the formation of cells with nuclei and the emergence of an oxygen atmosphere are highlighted on the timeline
• Human beings emerged more recently in the evolution timeline

The Three of Life

• Organisms are broadly categorized into three groups (eukaryotes, bacteria, archaea) based on their biochemical characteristics
• The tree of life depicts a possible evolutionary path from a common ancestor that existed approximately 3.5 billion years ago

History of DNA Research

• Friedrich Miescher isolated nuclein in 1869 from surgical bandages, finding it within cell nuclei
• Albrecht Kossel isolated the non-protein component of nuclein, nucleic acid, and five primary nucleobases, in 1878
• Phoebus Levene identified the base, sugar, and phosphate nucleotide unit in 1919, proposing DNA's structure as a chain of nucleotides linked by phosphate groups
• Frederick Griffith's experiments in 1928 demonstrated that traits could be transferred between bacteria, suggesting DNA's role in heredity
• Avery, MacLeod, and McCarty in 1943 identified DNA as the transforming principle
• William Astbury produced the first X-ray diffraction patterns of DNA in 1937, revealing its regular structure
• Hershey and Chase in 1952 confirmed DNA as the genetic material in the T2 phage
• James D. Watson and Francis Crick proposed the double helix model of DNA structure in 1953
• Franklin and Gosling produced the X-ray diffraction image of DNA which influenced Watson and Crick
• Watson, Crick, and Wilkins jointly received the Nobel Prize in 1962

Four Building Blocks of DNA

• DNA is a linear polymer composed of four different monomer types
• The backbone of DNA is composed of repeating sugar-phosphate units
• Each sugar is attached to two phosphate groups through distinct linkages, giving each DNA strand directionality
• The four bases attached to the sugar are adenine, cytosine, guanine, and thymine

Double-Helix Formation

• DNA molecules typically consist of two strands
• The sugar-phosphate backbone is located on the exterior, while the bases are positioned inside
• Specific base pairs (A-T and G-C) are held together by hydrogen bonds
• This arrangement comprises the well-known double helix structure

Importance of DNA Structure

• DNA structure, with its base pairs having uniformly consistent shape, accommodates any base-pair sequence
• DNA sequence dictates the sequences of RNA and protein molecules
• The sequence of bases along one DNA strand entirely determines the complementary sequence along the other strand, acting as a template for replication

Chemical Concepts

• Concepts from chemistry are critical for understanding biological molecules
• The types of chemical bonds, water structure, thermodynamics, and acid-base chemistry are significant concepts

Covalent and Noncovalent Bonds

• Covalent and noncovalent bonds form the structural basis and contribute to the stability of biological molecules
• Covalent bonds arise from shared electron pairs between adjacent atoms
• Covalent bonds are strong bonds
• C-C bond has a length of 1.54 Å and bond energy of 355 kJ/mol (85 kcal/mol)
• C=C bond has a length of 1.34 Å and bond energy of 614 kJ/mol
• Resonance structures are important structures

Noncovalent Interactions

• Noncovalent interactions are weaker than covalent bonds but essential for biochemical processes
• Electrostatic interactions are crucial for interactions between charged molecules and are described by Coulomb's law; the dielectric constant has a significant impact on these interactions
• Hydrogen bonds facilitate specific base-pair formation in DNA double helix
• Hydrogen bonds are significantly weaker than covalent bonds (ranging from 4 to 20 kJ/mol)
• Hydrogen bonds are significantly longer than covalent bonds (ranging from 1.5 to 2.6 Å)
• van der Waals interactions are transient, weak attractions emerging from temporary dipoles induced between atoms or molecules; these are particularly important for large molecules

Properties of Water

• Water is the crucial solvent for most biochemical reactions
• Its properties (e.g., polarity, cohesiveness) are crucial for forming macromolecular structures and facilitating chemical reactions
• Water's high cohesiveness results from hydrogen bonds, creating strong interactions
• Water's density is higher in liquid form than in ice form
• Liquid water has a specific density of 1 gram/mL at 0°C, and ice has a lower density of 0.917 gram/mL
• The hydrophobic effect describes the tendency of nonpolar substances to aggregate in aqueous solutions, displacing water molecules

Interactions in the Double Helix

• Electrostatic interactions between negatively charged phosphate groups play a role in DNA structure
• Electrostatic repulsions between phosphate groups are reduced by their spatial separation
• Water and ions further reduce repulsions
• Hydrogen bonds are vital for forming specific base pairs in the DNA double helix
• Stacking interactions between base pairs further stabilize the double helix structure in terms of the usual 3.4 Å separation distance

The Laws of Thermodynamics

• The first law of thermodynamics asserts that energy can neither be created nor destroyed, only transformed
• The second law of thermodynamics states that the entropy of the universe increases during spontaneous processes

Entropy Changes in Surroundings

• Heat transfer affects entropy changes in surroundings during isothermal process
• At constant pressure, qsys equals ∆H° for the process

Gibbs Free Energy

• Gibbs free energy (G) is a thermodynamic potential that describes the maximum reversible work that may be performed by a thermodynamic system at a constant temperature and pressure
• Spontaneous reactions have negative Gibbs free energy values
• Reactions at equilibrium have zero Gibbs free energy values
• Non-spontaneous reactions require an input of energy to occur

The Formation of the Double Helix

• The formation of a double helix reduces the entropy of the system
• Heat is released during the process; Gibbs free energy change is also crucial for double-helix formation
• The change in Gibbs free energy accounts for any unfavorable change in entropy

Acid-Base Reactions

• The addition or removal of hydrogen atoms is crucial for many biochemical processes
• Water undergoes autoionization, essentially dissociation, into hydrogen and hydroxide ions
• The ion-product constant of water (Kw) is important for understanding the pH
• Kw= 1.0 × 10⁻¹⁴ at 25°C

The pH Scale

• pH relates to the concentration of hydrogen ions in solution
• pH = -log₁₀[H+]
• Neutral solutions have a pH of 7

How Important is [H+] in Biology?

• Hydrogen ion concentration greatly impacts biological processes, influencing effects like reaction rates of biological reactions
• Changes in [H+] can influence reaction rates

DNA Denaturation at Low or High pH

• DNA base pairing can be disrupted by low or high pH; high pH values often denature the DNA structure
• The denaturation generally follows an S shaped curve

Buffered Solutions

• Buffers are solutions of a weak conjugate acid&base pair that resist pH changes
• Human blood pH is 7.4, whereas seawater's pH is 8.2

The HH Equation

• The Henderson-Hasselbalch equation (HH equation) describes the pH of a buffer solution
• pH depends on pKa of the acid and the ratio of conjugate base to acid

The Genomic Revolution

• The discovery of DNA structure initiated the genomic revolution
• Hereditary information is stored as a sequence of bases in DNA strands
• This insight has revolutionized biology, offering new views about biochemistry related to DNA-to-protein flow of genetic information
• This revolution has enabled full genomic sequencing in many organisms, including humans
• This has also aided our understanding of genetic basis of some human diseases that results from single base changes

Sequencing of the Human Genome

• The human genome comprises approximately 3 billion base pairs
• Sequencing the human genome represents a significant milestone in scientific history
• Genome sequencing leads to identification of genetic variations linked to human diseases; sickle cell is a good example
• Comparing sequences between individuals and other organisms offers insights into human biology and evolution

What Are the Roles of Genome Sequences?

• DNA's primary function is to encode protein sequences
• Proteins are linear polymers of amino acids
• The human genome has about 23,000 protein-encoding genes
• The number of proteins in humans is expanded by translational complexity and modification
• Only a small fraction of the human genome is responsible for encoding proteins, a larger portion consists of regulatory information for various cellular functions, and diverse protein contents like hemoglobin and hormones

Factors Affecting Individuality

• Genetic variations, epigenetic factors (like DNA methylation and histone modification), and environmental factors (like diet and exercise) shape individual differences
• The intricate interplay of genetic variations, epigenetic factors, and environmental influences drives the diversity of human traits, and influence biological mechanisms, and cellular phenotypes