Tema 2

Functional Groups and Their Importance in Biochemistry

Introduction to Functional Groups

• The discussion begins with an overview of functional groups, focusing on nomenclature and the relationship between biomolecules' structure and function.

• Different types of chemical bonds are introduced, including ionic bonds, which involve electrostatic forces holding ions together.

Types of Chemical Bonds

• Ions are defined as atoms with a net positive or negative charge.

• Covalent bonds are strong connections where two atoms share electrons; they can be classified into coordinated, polar, or non-polar types.

• Metallic bonds connect atomic nuclei and valence electrons in metals; weak interactions include Van der Waals forces and hydrogen bonds.

Characteristics of Electrons and Bonding

• Van der Waals forces depend on atomic radii for attraction strength; hydrogen bonds occur between hydrogen atoms and acceptor groups like carbonyl or NH3.

• A comparison is made between covalent (shared electrons) and ionic (electrostatic attraction without sharing) bonds.

Electron Configuration and Reactivity

• The number of unpaired electrons determines how many bonds an atom can form; for example, hydrogen forms H2 while carbon can bond with up to four hydrogens to create methane.

• The ability of atoms to donate or accept electrons leads to diverse chemical compounds influenced by their electronegativity.

Functional Groups in Biochemistry

• Various functional groups containing carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus provide specific physical and chemical characteristics to molecules.

Aliphatic Compounds

• Aliphatic compounds include alkanes, alkenes, and alkynes characterized by chains of carbon-hydrogen associations that are generally non-polar due to saturated hydrocarbon links.

Aromatic Compounds

• Aromatic compounds like phenol have cyclic structures common in organic solvents; they may contain substituents such as hydroxyl groups.

Alcohols and Carbonyl Groups

• Alcohol (hydroxyl group ROH), unlike aliphatic compounds, is polar. Carbonyl groups can be aldehydes or ketones found in carbohydrates.

Carboxylic Acids and Esters

• Carboxylic acids (COOH group), known for their acidic nature. Esters (COO group), often associated with two radical chains.

Amino Groups

• Amino groups (NH2R), which can vary structurally based on the number of radicals attached. Amides show characteristics from both amino and carbonyl groups.

Sulfur-containing Compounds

• Thiols (or sulfhydryl groups), featuring sulfur linked to hydrogen. Sulfur-containing compounds contribute unique properties due to their acidic nature.

Phosphorus Compounds

• Phosphoryl groups play significant roles in various biological structures including nucleic acids.

Conclusion: Biomolecules Overview

The session concludes by highlighting carbohydrates as a major class of biomolecules essential for energy cycles on Earth.

Carbohydrates and Lipids: Structure and Function

Overview of Carbohydrates

• The primary energy generation process in cells is due to carbohydrate metabolism, which also plays structural roles, such as forming cell walls.

• Carbohydrates can be classified based on the position of the carbonyl group, the number of carbon atoms, and the quantity of saccharide units.

Classification by Carbonyl Position

• Carbohydrates are categorized into aldoses (with an aldehyde group) and ketoses (with a ketone group), exemplified by compounds like glyceraldehyde and dihydroxyacetone. These differ structurally in hydrogen positioning and double bonds.

Monosaccharides

• Monosaccharides are simple carbohydrates that cannot be broken down further; they include trioses, tetroses, pentoses, and hexoses based on their carbon count. Common examples are glucose and fructose.

• Aldoses contain an aldehyde functional group while ketoses have a ketone functional group; for instance, glyceraldehyde is an aldotriose while dihydroxyacetone is a ketotriose.

Oligosaccharides

• Oligosaccharides consist of 2 to 10 monosaccharide units linked by glycosidic bonds formed between hydroxyl groups; examples include sucrose (disaccharide), lactose, and trehalose.

Polysaccharides

• Polysaccharides are large molecules formed from more than 10 monosaccharide units via glycosidic linkages; starch (in plants) and glycogen (in animals) serve as energy storage forms. Cellulose contributes to plant cell wall structure while chitin forms insect exoskeletons.

• They can be classified into homopolysaccharides (single type of monomer) or heteropolysaccharides (multiple types). Understanding their structure aids in studying their biological functions.

Role of Lipids

• Lipids serve multiple cellular functions including energy storage in adipose tissue, thermal insulation in subcutaneous tissues, membrane structure for selective permeability, hormone formation, and interaction with proteins to form lipoproteins for organic molecule transport.

Importance in Medicine

• The biochemical study of lipids is crucial for understanding diseases such as atherosclerosis, diabetes mellitus, obesity among others due to their significant physiological roles.

Structural Characteristics

• Lipids typically exhibit a head-tail structure where the hydrophilic head interacts with water while the hydrophobic tail does not; they can associate through non-covalent interactions contributing to various biological processes including signaling pathways within cells.

Lipid Structures and Functions

Interaction of Lipids with Water

• Lipids interact through their hydrophobic hydrocarbon tails and hydrophilic heads, forming structures like micelles, bilayers, and vesicles.

Types of Lipids

Fatty Acids

• Fatty acids consist of a hydrophilic carboxyl group attached to a hydrocarbon chain, which can be saturated or unsaturated based on hydrogenation levels.

Triacylglycerols

• Triacylglycerols are formed from three fatty acid esters linked to glycerol. They vary in fatty acid composition (R1, R2, R3), affecting solubility and storage as lipid droplets in cells.

Membrane Lipids

• Membrane lipids include phosphoglycerides, sphingolipids, and sterols. They play crucial roles in cell membrane structure and function.

Phosphoglycerides Structure

• Composed of two esterified fatty acids with glycerol, phosphate group, and amino alcohol; they influence membrane shape based on saturation and chain length.

Sphingolipids and Glycolipids

• Sphingolipids have long chains that affect membrane thickness; glycolipids are derived from ceramide with added sugars for cellular signaling.

Cholesterol's Role in Membranes

• Cholesterol interacts with phospholipid heads via its hydroxyl group while stabilizing membranes by modulating fluidity through its presence among the lipid bilayer.

Nucleotides and Nucleic Acids

Overview of Nucleic Acids

• DNA contains genetic information within chromosomes; RNA transcribes this information into proteins primarily through messenger RNA (mRNA).

Structure of Nucleotides

• A nucleotide consists of a phosphate group, a sugar (ribose for RNA or deoxyribose for DNA), and nitrogenous bases (adenine/guanine as purines; cytosine/thymine/uracil as pyrimidines).

Differences Between DNA and RNA

• The key difference lies in the sugar: ribose has an -OH group at carbon 2 while deoxyribose lacks it. Additionally, thymine is exclusive to DNA while uracil is found only in RNA.

Covalent Bonding in Nucleotides

• Nucleotides link covalently via phosphate groups connecting the hydroxyl groups on sugars to form nucleic acid chains essential for genetic functions.

DNA Structure and Function

Nucleotide Bonding and DNA Orientation

• The 3' end of one nucleotide bonds to the 5' phosphate group of another via a phosphodiester bond, establishing the directionality of DNA and RNA chains as 5' to 3'.

• Adenine pairs with thymine through two hydrogen bonds, while guanine pairs with cytosine through three hydrogen bonds, contributing to the stability of the double helix structure.

• DNA strands are antiparallel and complementary; for every cytosine in one strand, there is a guanine in the opposite strand.

• Hydrogen bonds are weak, allowing DNA to hybridize and dehybridize within cells.

Genes and RNA Functions

• DNA constitutes genes, segments that encode information necessary for protein or RNA synthesis. It stores and transmits biological information through transcription.

• Transcription produces messenger RNA (mRNA), which carries genetic information from DNA to ribosomes for translation into proteins.

Types of RNA

• Various types of RNA play distinct roles:

• Ribosomal RNA (rRNA) forms part of ribosomes essential for protein synthesis.

• Messenger RNA (mRNA) transports genetic information from DNA to ribosomes.

• Transfer RNA (tRNA) translates mRNA into amino acids during protein synthesis.

Amino Acids, Peptides, and Proteins

Amino Acid Structure and Classification

• Amino acids have a central carbon atom bonded to an amino group, carboxyl group, hydrogen atom, and variable R group. They are crucial for protein formation.

• Two types exist: L-amino acids (found in proteins) and D-amino acids (found in bacterial cell walls). Their spatial arrangement affects biological function.

Functions of Amino Acids

• Amino acids serve multiple functions including:

• Building blocks for enzymes involved in metabolic regulation.

• Precursors for neurotransmitters and hormones.

• Components in immune response by forming antibodies.

Peptide Formation

• Amino acids link via peptide bonds—joining the carboxyl group of one amino acid with the amino group of another—releasing water. This process leads to peptide formation followed by protein assembly based on specific sequences.

Protein Structure and Function

Primary Structure of Proteins

• The primary structure is defined by the sequence of amino acids in a protein.

• An example provided is the Gnrh (gonadotropin-releasing hormone), which consists of 10 amino acids arranged in an aminocarboxyl direction.

Secondary Structure of Proteins

• The secondary structure refers to local folding patterns within the protein, established by Linus Pauling in 1930.

• Two main configurations are identified: alpha helices and beta sheets, determined by chemical interactions between amino acids.

Tertiary Structure of Proteins

• The tertiary structure describes the overall three-dimensional folding of a protein, which can be either globular or fibrous.

• Examples include insulin and albumin as globular proteins, while collagen is noted for its fibrous configuration.

Quaternary Structure of Proteins

• The quaternary structure involves the assembly of multiple polypeptide chains into a regular arrangement, classified as homotypic (identical chains) or heterotypic (different chains).

• Hemoglobin serves as an example with four subunits forming a central pore for water molecule transport; aquaporin also has a similar structural feature.

Functions of Proteins

• Proteins play crucial roles in cellular shape and function due to their complexity and diverse functions. They are involved in mobility (e.g., actin and myosin), hormonal signaling (e.g., insulin), protection (e.g., antibodies), transport (e.g., hemoglobin), enzymatic activity, storage (e.g., ferritin), structural support, and receptor functions (e.g., rhodopsin).