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Introduction to Biochemistry

• Welcome to Biochemistry for BMS 1021

• Instructor: Jerome Lenos, Structural Biologist at Monash University

• Feel free to reach out via the Moodle portal with queries.

Overview of Cell Composition

• Composition of the human body compared to E. Coli:

  • 60% water

  • 15% fat (energy storage)

  • 15% proteins (cell architecture)

  • 1% carbohydrates

• Importance of water in the context of life on Earth:

  • 75% of Earth's surface covered by water

  • Represents 0.02% of Earth's mass

Chemical Characteristics of Water

• Focus on:

  • Structure of water

  • Interactions: Intramolecular and intermolecular bonding

  • Properties of water:

    • Cohesion

    • High heat capacity

    • Boiling point

    • Density

    • Solvent properties

    • Ionizations and pH relevance

Learning Objectives

• Describe water's structure, geometry, polarity, and dynamics

• Explain hydrogen bond formation and water's properties

• Understand water ionization and its pH effect on biological molecules

Representations of Water

• Molecular formula: H2O

• Structural formula; Electron representations; Space-fill models

• Water's geometry: Oxygen partially negatively charged, hydrogen partially positively charged

• Distance between atoms: 0.1 nm (O-H); 0.3 nm (H-H)

• Approx. 40 million water molecules fit in one centimeter

Polar Nature of Water

• Water is a polar molecule with dipole properties due to partial charges resulting from the unequal sharing of electrons between oxygen and hydrogen atoms, which leads to a partial negative charge on the oxygen atom and partial positive charges on the hydrogen atoms, leading to intramolecular forces.

• Hydrogen bonds:

  • Formed via interactions between partially charged atoms from different molecules

  • Water can form 4 hydrogen bonds with neighbouring molecules

  • Up to four hydrogen bonds per water molecule

• Strength comparison:

  • Hydrogen bonds: 1/20 strength of covalent bonds

Properties of Water Derived from Hydrogen Bonds

Cohesion

• Water molecules attract each other - due to hydrogen bonds ,which leads to high cohesion and surface tension, allowing small objects to rest on the water's surface without sinking. This property is crucial for various biological processes, including the transport of nutrients in plants and the formation of water droplets.

• Examples:

  • Water droplets on glass

  • Capillary action in narrow tubes

  • Surface tension allows insects to walk on water

High Heat Capacity

• Requires more energy to raise water temperature due to strong hydrogen bonds, so needs more energy to break the hydrogen bond network between molecules

• Heat capacity defined as the energy required to change the temperature of one gram of water by one degree Celsius

• The specific heat capacity is given by the rate of the the increase in temperature of water from a solid (ice) to a gas (steam).

Boiling Point and Heat of Vaporisation (latent heat)

• High boiling point due to hydrogen bonding

• Heat of vaporisation is the energy needed to convert liquid water to vapor (over 2000 kJ/kg)

Density of Water and Ice

• Water density changes with temperature; unique property of ice floating

• As temperature decreases, the density of water increases until it reaches 4°C, where it is at its maximum density; below this temperature, the density begins to decrease, causing ice to float on water.

• Ice has stable hydrogen bond networks, making it less dense than liquid water which has changing hydrogen bonds that are breaking and forming constantly

Water as a Solvent

• Water dissolves ionic compounds (salts) due to its polarity. Salts are formed when metal cations bond with nonmetal anions through ionic bonds, resulting in the formation of neutral compounds, such as sodium chloride (NaCl).

• Example of sodium chloride (NaCl) dissociation in water

• Water can interact with hydrophillic (water loving molecules) and facilitate their solvation, leading to a homogeneous mixture. This property makes water an excellent solvent for ionic and polar substances, while it effectively excludes nonpolar substances, resulting in separation.

• Cannot dissolve non-polar molecules (hydrophobic) like oil (long alkane chain) due to lack of interaction so no dipole interaction will be possible

• Example: Water forms a cage around hydrophobic molecules preventing the alkane to interact with the water to be dissolved

Ionization of Water and pH

• Water can ionise into H+ (proton) and OH− (hydroxide ion) -both in equal concentrations - equilibrium that happens all the time in pure water at 25ºc

• The proton can then recombine with water to form a hydronium ion (H3O+)

• This allows water to act as both a proton donor and acceptor

• Ionisation impacts biological molecules and their charge states

• pH scale indicators:

  • Low pH (acidic): High proton concentration

  • High pH (basic): Low proton concentration

• Examples of compounds with varying pH levels

Effects of pH on Biological Molecules

• pH affects amino acid charge states and biological molecules

• Example: Changes in alanine’s structure at various pH levels

• Isoelectric point (pl) is the pH at which the molecule as NO net charge

• pKa value is also the pH where each form is present at 50%

• pKa values measures acidity of solution, representing the pH where particular acid donates half of its protons, resulting in 50% [ ] of protonated and deprotonated forms of the acid. Species A and B are present at 50% same as B and D.

pH affect on structure and activity of enzymes

• Enzymes have optimal pH for activity based on composition

• Protein structure also dependent on charges and interactions of amino acids, which can be influenced by pH levels, ultimately affecting enzyme functionality.

• Additionally, deviations from this optimal pH can lead to denaturation of enzymes or reduced activity, as the ionisation states of key residues change, breaking hydrogen bonds

• This affects the active sights of the enzyme , inhibiting substrate binding and consequently reducing the overall rate of the enzymatic reaction.

• Maintaining pH inside cells is achieved by buffering systems

Buffer Systems

• Buffers resist pH changes via weak acid/base equilibrium

• Good buffering system will have equal amount of each products in solution

• Examples and mechanisms of buffers in biological systems

Summary of Water Properties

• Water is a polar molecule that forms hydrogen bonds and ionizes

• Properties of water have profound implications for biological systems

• Membrane functionalities and stabilization of biological activity

Transition to Lipids and Nucleic Acids

• Upcoming focus on structures/functions of lipids and nucleic acids

• Understanding the role of lipids in cellular membranes and energy storage, as well as the significance of nucleic acids in heredity and protein synthesis.

  DNA in genetics:

  • Contains vast information; fundamental building blocks shared across life

• Overview of nucleotides in DNA/RNA:

  • Building blocks of DNA and RNA, including nucleotide sequences

  • DNA; deoxyribonucleic acid - Made up of deoxyribonucleotides - Contained in our chromosomes - A molecule composed of two strands forming a double helix, containing the genetic instructions for the development and function of living organisms. Made from nucleotides

  • RNA; ribonucleic acid A single-stranded molecule that plays a crucial role in coding, decoding, regulation, and expression of genes - composed of ribose sugar, phosphate group, and nitrogenous bases (adenine, guanine, cytosine, and uracil)

  • Nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base. DNA is structured as a double helix formed by two complementary strands of nucleotides held together by hydrogen bonds between the base pairs (adenine-thymine and guanine-cytosine).

  • 4 deoxyribonucleotides: A, G, T, C: Deoxyadenosine, Deoxyguanosine, Deoxycytidine, Deoxycytidine

• Structure of DNA:

  • Double-stranded, complementary strands held by hydrogen bonds

  • One strand: sense strand (5 prime to 3 prime) and antisense strand (3 prime to 5 prime)

  • The sense strand serves as the template for mRNA synthesis during transcription, while the antisense strand complements the sense strand. The sequence of nucleotides in the sense strand determines the amino acid sequence during protein synthesis, highlighting the importance of accurate transcription and translation processes.

  • Base pairing rules (A-T, G-C): The specific pairing of adenine with thymine and guanine with cytosine ensures that the genetic information is accurately replicated and transmitted during cell division.

Lipids Overview

• Diverse but hydrophobic group: fats (triglycerides), phospholipids, steroids

• Have hydrophobic tails (4-36 carbons in length) and a COOH head

• Fatty acids explained:

  • Saturated (fully hydronated, no c-c double bonds) vs. unsaturated fatty acids (one or more c-c double bond )

  • Saturated fatty acids can pack more efficiently

  • Unsaturated acids cause kinks and bends in the carbon chain which prevent tight packing, resulting in lower melting points and making them typically liquid at room temperature.

  • Degree of saturation gives unique properties to lipid

• Triacylglycerol (trygliceride) formation:

  • Glycerol is linked by an ester bond to three fatty acids - condensation reaction

  • Triacylglycerols are formed when three fatty acids esterify with a glycerol molecule, resulting in a highly efficient form of energy storage that is hydrophobic and does not mix with water.

  • Energy storage molecules, saturated/unsaturated properties impact functionality

• Phospholipids and membrane structure:

  • Phospholipids made of glycerol linked to two fatty acids and one phosphate group

  • Provides amphipathic properties: hydrophilic phosphate head and hydrophobic fatty acid tail

  • Key components of cell membranes, forming bilayers with amphipathic properties

• Membrane fluidity impacted by lipid composition - not static

  • Self organised and in constant motion

Conclusion of Lecture One

• Recap on nucleic acids and lipids as essential biomolecules

• Highlight invitation for Lecture Two focusing on carbohydrates and proteins.