Biochemistry: Cells, Biomolecules, and Composition

Biochemistry Overview

• Biochemistry studies the chemical and physicochemical processes in living organisms

Outline of Topics

• Introduction to the cell
• Biomolecules: carbohydrates, lipids, proteins, amino acids, peptide bonds, enzymes, nucleic acids
• Energy generation and storage

Introduction: The Cell

• The cell is the basic functional and structural unit of life

Types of Cells

• Prokaryotes - bacteria and archaea
• Eukaryotes - algae, protozoa, fungi, plants, and animals

Cell Composition by Weight

• Oxygen - 65%
• Carbon - 18.6%
• Hydrogen - 9.7%
• Nitrogen - 3.2%
• Calcium - 1.8%
• Phosphorus - 1.0%
• Potassium - 0.4%
• Sodium - 0.2%
• Chlorine - 0.2%
• Magnesium - 0.06%
• Sulfur - 0.04%
• Iron - 0.007%

Cell Organelles

• Nucleus
• Golgi apparatus
• Lysosomes
• Mitochondria
• Cytoskeleton
• Cilia
• Flagella
• Proteasome
• Chloroplasts

Nucleus Details

• Contains chromatin and nucleoli
• Chromatin is 30% DNA
• Nucleosomes make up fundamental units
• Human somatic cells have 46 chromosomes
• Nucleoli are sites of RNA synthesis and rRNA assembly, not membrane-bound

Other Cell Structures

• Nuclear membrane - a double lipid bilayer
• Cytoplasm includes cytosol and organelles
• Ribosomes facilitate protein synthesis
• Endoplasmic reticulum (ER) has rough and smooth variations
• Golgi apparatus modifies and packages proteins
• Lysosomes have digestive enzymes for breaking down materials

Mitochondria Structure

• Cristae are a series of folds in the inner mitochondrial membrane
• Matrix is the central fluid-filled cavity

Plasma Membrane

• The plasma membrane is a fluid-mosaic lipid bilayer composed of phospholipids, cholesterol and glycolipids, studded with proteins around the cytoplasm
• Protects cellular contents and mediates entry and exit of substances
• Cell walls in plants are made of cellulose
• Cell walls in bacteria are made of peptidoglycan
• Cell walls in fungi are made of chitin

Transport Mechanisms

• Diffusion is movement down the concentration gradient
• Facilitated diffusion is carrier and channel mediated
• Osmosis is movement of solvent
• Tonicity measures a solution's ability to change cell volume by altering water content

Cell Division

• Cell division is a process by which cells reproduce themselves

Somatic Cell Division

• It is cell multiplication, cytokinesis = 2 genetically identical cells
• Occurs for somatic/body cells
• Involved with the replacement of dead/injured cells and adds new cells for tissue growth
• Are diploid (2n), containing two sets of 23 chromosomes
• Humans have 46 chromosomes in 23 pairs
• Gametes make up 1 pair and somatic pairs make up 22

Variations in Chromosome Number

• Aneuploidy results from having more or less chromosomes than the usual number whereas euploidy results from duplication of entire sets of chromosomes
• Chromosomal alterations include trisomies, monosomies, and syndromes like Down syndrome

Biomolecules: Reactions in Living Cells

• Oxidation-reduction
• Cleavage and formation of C-C bonds
• Internal rearrangements
• Group Transfers
• Condensations
• Reactions are catalyzed by enzymes
• Involve anabolism (synthesis) or catabolism (breakdown that releases energy)

Carbohydrates: Basic Info

• Carbohydrates are hydrates of carbon, described by the formula $C_n(H_2O)n$ or $[C_n H{2n} O_n]$
• They consist of polyhydroxyaldehydes and polyhydroxyketones
• Monosaccharides are linked via glycosidic bonds
• Carbohydrates are the most abundant group of organic molecules, composing >75% of dry weight in plants and <1% of weight in animals, and are the first products of photosynthesis

Carbohydrates: Classification

• By functional group:
  • Aldose (aldehyde)
  • Ketose (ketone)
• By number of carbons:
  • Triose (3 carbons)
  • Pentose (5 carbons)
  • Hexose (6 carbons)

Carbohydrates: Functions

• Energy source (blood glucose)
• Energy storage (glycogen, starch)
• Industrial use (sweeteners)
• Structural function (cellulose, chitin)
• Pharmaceutic use (lactose, starch, sorbitol)
• Pharmacologic effects (mannitol, heparin, aminoglycosides, cardiac glycosides)

Carbohydrates: Structure

• Linear (Fischer projection)
• Cyclic (Haworth projection)
• Isomerism: functional, anomers, epimers, enantiomers, diastereomers

Carbohydrates: Reactions

• Oxidation (gluconic, glucuronic, glucaric acids)
• Reduction (sugar alcohols) Glycosidic bond formation:
  • $R-OH + HO-R' → R-O-R' + H_2O$
• Phosphate formation (organophosphates in DNA, RNA)
• Amine formation (amino sugars)

Glycoproteins: Definition

• Carbohydrates attached to proteins, either N-linked (to asparagine) or O-linked (to serine/threonine)

Glycoproteins: Function

• Structure
• Protection
• Reproduction
• Hormones
• Immunological Response - determined by carbohydrate structure

ABO System

• Determines specificity of antibodies
• Two antigens, Type A and Type B, occur on the surfaces of RBCs
• The O allele is recessive to both A and B

Glucose

• Reacts with HgB to form Glycated HgB (HbA1C), indicating average blood glucose for 2-3 months prior

Proteins

• Amino acids form proteins like enzymes, hormones, collagen, and immunoglobulins

Amino Acids: Basic Info

• Contain an amino group, a carboxyl group, a hydrogen, and a distinctive R-group, all attached to a central alpha carbon

Amino Acids: Properties

• Amphoteric with dual acid/base nature
• Can act as acid at alkaline medium when protonated
• Can act as a base at acidic medium with negative charge
• Exhibit stereoisomerism (chirality)
• ALL AA chiral except Glycine
• Absolute configuration specified by D & L system
• L- = $NH_2$ on left of chiral carbon

Amino Acids: Reactivity

• UV absorption, limited to aromatic AAs (F, Y, W), with max absorption at 280 nm

Amino Acids: Separation Techniques

• Gel electrophoresis based on pI or MW
• Paper and TLC
• Ion-exchange chromatography
• Size exclusion chromatography

Amino Acids: Classifications Based on Polarity

• Non-Polar / Hydrophobic
  • Aliphatic (glycine, alanine, valine, leucine, isoleucine, proline, methionine)
  • Aromatic
• Polar / Hydrophilic
  • Uncharged (serine, tyrosine, threonine, cysteine, asparagine, glutamine)
  • Charged
    • Acidic: aspartic acid, glutamic acid
    • Basic: lysine, histidine, arginine

Non-Polar Amino Acids: Basic Infos

• Glycine is the simplest amino acid and classified as a polar/hydrophilic molecule
• Alanine is a major gluconeogenic AA and converted to pyruvate by transamination via ALT/SGPT
• Valine, leucine, isoleucine serve as an alternative source of energy during fasting
• Proline is has and is an imino acid with a 2° amine
• Methionine can be converted to S-adenosyl methionine (SAM), a cofactor in methylation reaction

Polar AA: Basic Infos

• Tyrosine is precursor to catecholamines, thyroid hormones, and melanin
• Cysteine can capable of forming disulfide bonds
• Asparagine is a metabolic precursor of aspartic acid/aspartate and has anti cancer properties

Peptide Bonds

• Amide linkages formed by dehydration
• Exhibit partial double bonds
• Polarized and involved in H-bonding

Protein Structure and Properties

• Primary structure - amino acid sequence
• Secondary structure - alpha-helix, beta-pleated sheet, stabilized by hydrogen bonds

Secondary Structure Details

• Alpha-helix: stabilized by intrachain H-bonds, with 3-4 AA residues per turn, often disrupted by proline and glycine
• Beta-pleated sheet: stabilized by H-bonds between adjacent polypeptide strands, can be parallel or antiparallel
• Beta-turns: connect adjacent secondary structures

Tertiary and Quaternary Protein Structure

• Tertiary Structure: folding, stabilized by interactions, determines function
• Quaternary Structure: association of multiple polypeptide chain

Protein Folding and Denaturation

• The native state is the default shape, proteins require chaperone proteins to fold correctly
• Denaturing agents: heat, pH, solvents
• Renaturation = return to native structure

Protein Classification by Biological Role/Function

• Storage and Transport: Heme, Myoglobin/Hgb, Transferrin, Ferritin
• Contractile and Motile

Structural Proteins

• Collagen (skin and cartilage)
• Elastin (vessels)
• Keratin (hair)
• Provides support

Protein Classification by Physio-Chemical Properties

• Simple proteins contain only amino acids
• Conjugated proteins contain amino acids plus prosthetic groups
• Derived proteins result from breaking down in the middle of processing

Protein Misfolding

• Amyloid disease: accumulation of misfolded proteins
• Prion: transmissible spongiform encephalopathies

Globular Protein-Related Disease

• Hemoglobinopathies (sickle cell anemia)

Fibrous Protein Related Disease

• Scurvy (collagen defect due to lack of vitamin C)

Enzymes: Overview

• Biological catalysts which expedite chemical reactions but remain unchanged throughout
• Composed of proteins or Ribozymes (RNA molecules)
• May function independently or alongside a non-protein moiety (cofactor)

Structure of an Enzyme

• Active Site: The zone of an enzyme where a reaction occurs
• Zymogen/Proenzyme: An inert precursor
• Apoenzyme: The protein segment of an enzyme, non functional when isolated
• Holoenzyme: The full, functional enzyme, incorporating both the apoenzyme and cofactor

Cofactors Types and Details

• Organic coenzymes from Vitamins
• Organic groups not from Vitamins
• Inorganic metal enzymes

Enzyme Properties

• Catalytic Activity: Increase in biochemical reaction rate.
• Specificity: the reaction is selective due to the 3D structure
• Can be segmented through protection from inhibitors
• Can be modulated or suppressed

Mechanism of Catalysis

• Acid base catalysis
• Substrate strain
• Covalent catalysis
• Transition state stabilization

Enzymes in Diagnosis

• Enzymes released in higher amounts when tissue damage
• Creatine Kinase (CK)
• Lactate Dehydrogenase (LDH)
• Alkaline Phosphatase (ALP)
• Acid Phosphatase (ACP)
• Aspartate Aminotransferase (AST)
• Alanine Aminotransferase (ALT)

Enzyme Kinetics

• Factors affecting reaction velocity:*
• Substrate concentration
• Michaelis-Menten equation describing these factors
• Temperature
• pH
• Enzyme Inhibition and Regulation:
  • Inhibitors: substances which diminishes of an enzyme-catalyzed reaction.

Major Classes of Enzymes

• Oxidoreductases: Redox reactions
• Transferases: Reactions involving transfer of a group of molecules.
• Hydrolases: Hydrolytic breakdown, requires adding water.
• Lyases: Non-hydrolytic cleavage or addition to double bonds.
• Isomerases: Bond rotation or stereo-arrangement alterations.
• Ligases: Binding molecules by use of ATP.

Lipids

• Lipids are a chemically diverse group that are related more by physical than chemical properties

Lipid Functions

• Structural components of cell membranes
• Energy storage
• Regulatory functions
• Phosphatidyl inositol is involved in cell signaling

Lipid Groups

• Saturated and unsaturated fatty acids
• Hydrolyzable lipids: triglycerides, phospholipids, sphingolipids
• Non-hydrolyzable lipids: sterols, fat-soluble vitamins, terpenoids, eicosanoids

Fatty Acids (FA)

• Saturated fatty acids have single bonds
• Unsaturated fatty acids have double bonds and cause them to become compact
• Monounsaturated fatty acids have one double bond
• Polyunsaturated fatty acids (PUFA) have multiple double bonds

FattyAcid Reactions

• Hydrogenation/Saturation makes the compound a more stable
• Oxidation leads to rancidity
• Saponification results in soap formation
• Sulfonation used for surfactants

Hydrolyzable Lipids: Types

• Triglycerides (TAGs)
• Phospholipids: (Glycerophospholipids)
• Sphingolipids
• Glycolipids
• Waxes
• Leukodystrophies: progressive disorders caused by enzymatic deficiencies during normal life

Triglycerides (TAG)

• Neutral lipids used for stroage
• Upon reaction you recive glycerol and Fatty acids

Phospholipids

• Polar with hydrophilic and hydrophobic regions
• Glycerophospholipids include phosphatidylserine, phosphatidylcholine, phosphatidylethanolamine
• Cardiolipin is major component of mitochondrial membranes

Non-Hydrolyzable Lipids

• Sterols have a cyclopentanoperhydrophenanthrene nucleus (CPPP)

Sterols

• Function as steroid hormones
• Terpenoids / Isoprenoids are composed of isoprene units
• Fat soluble vitamins
• Eicosanoids are derived from C20 PUFAs

Eicosanoids

• Act as chemical messengers
• Produced from COX or LOX
  • i. PROSTAGLANDINS
  • ii. THROMBOXANES
  • iii. LIPOXINS
  • iv. LEUKOTRIENES

Nucleic Acids

• Store genetic information
• Polymers of nucleotides

Nucleotides

• Building blocks of nucleic acids
• Linked by phosphodiester bonds
• They are comprised of a pentose sugar, a nitrogenous base, and a phosphate group
• Nucleobases like, guanine, adenine, cytosine, uracil, and thymine

RNA

• Ribonucleic Acid
• "Working copies" of the DNA

DNA

• Deoxyribonucleic Acid
• Genetic master plan

Properties of DNA

• Complementary base pairing (A with T, G with C)
• Anti-parallel strands
• Can be denatured and renatured
• Double helix structure with major and minor grooves

Mutation Types: Spontaneous and Induced

• Point Mutation / Small Scale Mutation includes base substitution AA/codon
  • includes Substitution that encodes same AA
  • Missense
  • Nonsense
• FRAMESHIFT MUTATION / Large Scale
  • Includes Insertion, Deletion, Transition and Transversion
• Chromosome Mutation is either deletion, duplication, translocation, inversion, or nondisjunction

Central Dogma

• Replication transfers molecules from DNA
• Transcription from DNA to RNA
• Translation from to RNA to Protein

3 Main Steps of DNA Replication

• Initiation: recognition of a origin and DNA-A protein
• Elongation: primase, replication etc by polymerase
• Termination: completion of process

Protein and Vitamin Metabolism

• Protein Metabolism is the transformation of proteins
• Nitrogen Disposal + Urea Cycle
• Vitamin B Metabolism is how energy os obtained by enzymes to maintain the normal metabolic functions