Cell Structure and Function - Cell Biology PDF

LU | Faculty of Sciences Cell Structure and Function - Cell Biology - Reem Dakhil M1 Biochemistry (Lebanese University) M2 Physiology, Epigenetics, Differentiation, and Cancer (Université Grenoble Alpes) Chapter 1 Cell Biolog...

LU | Faculty of Sciences Cell Structure and Function - Cell Biology - Reem Dakhil M1 Biochemistry (Lebanese University) M2 Physiology, Epigenetics, Differentiation, and Cancer (Université Grenoble Alpes) Chapter 1 Cell Biology Birth Definitions – Cell doctrine  Cell Biology vs Cytology Cell Biology Cytology The study of cells and their The study of cells and their components structurally and components structurally functionally  The Cell Doctrine Unit Division Organism Fundamental unit of Cells divide Cells + their products structure & function = organism Life Double-life Basis of life continuity One for its own, (mitosis – meiosis – one for the organism fertilization)  Chapter 2 Molecular Components of cells Inorganic and Organic Compounds What atoms and molecules are found in our cells?  Atomic level 96% 4% Very low C, H, N, O Na, K, Cl, S, P Trace elements Most abundant atoms B, F, Mn, Fe, Co, Cu, Zn, Se, I…  Molecular Level Organic molecules “Biomolecules” Inorganic molecules Proteins Water Carbohydrates Mineral salts Lipids Nucleic acids 1. Water ✓ Basis of cell life ✓ Most abundant ✓ Electrically neutral ✓ Extremely polar: partially (-) O & partially (+) H → Forms Hydrogen bonds (with H2O or with other molecules) & ionic bonds (solubilizes salts) → H2O is found free or interacting with molecules  2. Mineral Salts ✓ Found dissolved & ionized by water (due to water polarity) ✓ [ ] inside cell ≠ [ ] interstitial fluid → Balance in [ ] is essential for: membrane permeability, nerve impulse, muscle contraction, cell division … ✓ Metal ions are essential for the activity of certain proteins (muscle contraction, O2 transfer, intercellular signaling…)  3. Organic Compounds Molecules Macromolecules +Vitamins amino acids proteins needed at low [ ] monosaccharaides polysaccharides can be carbs (vit. C) fatty acids lipids or lipids (vit. A, E, D) nucleotides DNA, RNA  I. Proteins 1. Introduction ✓ Most abundant organic molecules ✓ Most diverse (encoded by genes) → diversity in functions ✓ Unbranched polymers of aminoacids  I. Proteins 2. Function ~ All functions for cell & organism life Morphology – cell’s molecular identity (HLA, blood groups) – gene expression & DNA replication – storage & transportation – intercellular & organ communication – immunity – senses – cell cycle – muscle contraction * but they are not energetic molecules  I. Proteins 3. Diverse Chemical Composition Although diverse, but chemically: proteins are a homogeneous class (1 unbranched chain of aa) They differ by number & sequence of aa, which are identical for a protein type Diverse sequences → diverse 3D structures → diverse functions  I. Proteins 4. The Amino Acids ✓ Made of: C, H, N, O, S ✓ Cα linked to: NH3, COOH, H, and side chain R ✓ They differ by R only → 4 groups: - Non-polar (Alkyl, benzyl) - Polar uncharged (NH2, CO, OH) - Polar positive / basic (NH3+) - Polar negative / acidic (COO-) ✓ 20 types, 9 of them are essential aa (can’t be synthesized by cells, must be supplied by diet) ✓ Only L-stereoisomers form polypeptides  I. Proteins 4. The Amino Acids ✓ All aa are soluble in water (due to amino & carboxyl groups) BUT not all proteins/peptides are soluble in water ✓ aa ionization depends on: pH & R ✓ Zwitterions: aa with uncharged R and ionized groups (NH2 & COOH) at pH=7  I. Proteins 5. Polypeptide  I. Proteins 5. Polypeptide ✓ Linear unbranched chain of aa joined by covalent bonds “peptide bonds” ✓ Formed by ribosome; digested by proteases ✓ Reaction: nucleophile attack between NH2 of aa (n) & COOH of aa (n-1) → “amide bond” CO – NH → H2O is eliminated ✓ Backbone: repeating N – Cα – C → polarized: N-terminus (Amino terminus NH2) & C-terminus (Carboxy terminus COOH)  I. Proteins 6. Polypeptide Flexibility Extended groups (R, H, =O) are not in the same plane, they rotate in different directions → confers flexibility → helps folding to adopt 3D conformations  I. Proteins 7. Structures of Proteins a. Primary Structure b. Secondary Structure c. Tertiary Structure d. Quaternary Structure  I. Proteins a. Primary Structure ✓ Linear aa sequence ✓ Determined by: nucleotide sequence in DNA ✓ Stabilized by: covalent bonds between aa ✓ Determines all of the other structures → its alteration impairs protein functions ✓ All copies of the same protein have identical primary structures  I. Proteins b. Secondary Structure ✓ Folding of aa portions into: helices & β-pleated sheets (+ turns & irregular random coiling) ✓ Stabilized by hydrogen bonds (except for supercoiling: covalent bonds) ✓ A specific aa sequence will acquire the same folding wherever it is found  I. Proteins c. Tertiary Structure ✓ Helical & non-helical regions are folded back in precise positions ✓ Determined by secondary structures ✓ Hides hydrophobic aa in core & exposes charged aa ✓ Brings distant segments together → active domains ✓ Stabilized by: - hydrogen bonds - ionic bonds - hydrophobic interactions - salt bridges - disulfide bridges  I. Proteins c. Tertiary Structure ▪ Protein Denaturation ✓ Unfolding + segment separation of proteins ✓ By: physical agents (low pH, high temp) & chemical agents (detergents, urea) ✓ Protein loses its activity ✓ Irreversible unless mild  I. Proteins d. Quaternary Structure ✓ Some proteins need it ✓ Assembly of ≥2 subunits (identical or different) → forms active domains ✓ Stabilized by: weak bonds (+ sometimes covalent) ✓ Protein activation / deactivation: by changing its 3D conformation: by: - Phosphorylation / dephosphorylating - Allosteric transition (ligand binding / dissociation)  I. Proteins 8. Classification of Proteins ✓ By composition - Holoproteins / apoproteins: only aa - Heteroproteins: aa + other molecules ex: lipoproteins, glycoproteins, nucleoproteins, hemoproteins (ion) ✓ By structure - Fibrous: insoluble in water (keratin, collagen) - Globular: soluble in water (globulin, albumin, histones) ✓ By function Structural – defense – regulatory – transporter – catalytic – contraction…  FS.I Partial 2020 7)c 8)b 18)b 21)d  II. Carbohydrates Functions ✓ Energetic ✓ Structural ✓ Cell identity glycogen in animals cellulose in plant cell wall blood groups  II. Carbohydrates 1. Monosaccharides Definition ✓ aka “simple oses” ✓ Most are D-stereoisomers ✓ CnH2nOn (3≤n≤6) ✓ Less diverse than proteins since: - Only a few monosaccharaides can form polymers - Different types do not combine much (max 2) D-glucose C6H12O6  II. Carbohydrates 1. Classification of Monosaccharides ✓ By functional group - Aldoses (aldehyde group) - Ketoses (ketone group) ✓ By n 3: trioses – 4: tetroses – 5: pentoses – 6: hexoses Aldose pentose: ribose Aldose hexoses: glucose, galactose, mannose Ketose hexose: fructose ribose glucose galactose mannose fructose  II. Carbohydrates 2. Cyclic Oses ✓ n>4 → straight chain or cycle → cycle is more stable → or → Pyranoses (6C) & furanoses (5C) α β ✓ From intramolecular reaction between OH & aldehyde/ketone group ✓ α & β isomers: differ by orientation of OH that replaced the aldehyde/ketone - α: downward - β: upward ✓ Usually cyclic oses are switchable between α & β until polymerized.  II. Carbohydrates 4. Modification ✓ Osamines addition of amine group (---NH2) eg: glucose→glucosamine. galactose→galactosamine ✓ N-acetyl osamines addition of acetyl group (---COCH3) to the amine group eg: NAG: N-acetyl galactosamine ✓ Uronic acids acidification of CH2OH into COOH eg: NANA: N-Acetyl Neuraminic Acid (from mannose)  II. Carbohydrates 5. Dimers and Polymers ✓ Disaccharide: 2 oses joined by covalent bond “glycosidic bond” Its formation releases H2O - Saccharose = glucose + fructose - Lactose = glucose + galactose - Maltose = 2 glucose ✓ Oligosaccharide: short polymer of monosaccharaides can be branched / unbranched can be linked to proteins / lipids for maturation  II. Carbohydrates 5. Dimers and Polymers ✓ Polysaccharide (Glycan): long chain of monosaccharides branched / unbranched simple or modified oses Functions: Structural - cellulose in plant cell wall – peptidoglycans in bacterial cell wall Energetic - glycogen in muscles – starch in plants  II. Carbohydrates 5. Dimers and Polymers ✓ Homopolysaccharide: polymer of the same molecule - Starch & glycogen = branched polymers of α-D-glucose - Cellulose = unbranched polymer of β-D-glucose - Chitin = polymer of N-acetyl glucosamine, in insects shell ✓ Heteropolysaccharide: polymer of 2 diferent simple/modified oses - GAG = glucosamine + galactosamine - Hyaluronic acid = glucoronic acid + N-acetyl glucosamine - Chondroitin Sulfate = glucuronic acid + N-acetyl galactosamine - Keratan Sulfate = N-acetyl glucosamine + D-galactose  FS.I Partial 2020 13)b, 14)d, 15)a, 12)c, 13)b FS.I Partial 2019  II. Carbohydrates Functions ✓ Energetic ✓ Structural ✓ Cell identity glycogen in animals cellulose in plant cell wall blood groups  II. Carbohydrates 1. Monosaccharides Definition ✓ aka “simple oses” ✓ Most are D-stereoisomers ✓ CnH2nOn (3≤n≤6) ✓ Less diverse than proteins since: - Only a few monosaccharaides can form polymers - Different types do not combine much (max 2) D-glucose C6H12O6  II. Carbohydrates 1. Classification of Monosaccharides ✓ By functional group - Aldoses (aldehyde group) - Ketoses (ketone group) ✓ By n 3: trioses – 4: tetroses – 5: pentoses – 6: hexoses Aldose pentose: ribose Aldose hexoses: glucose, galactose, mannose Ketose hexose: fructose ribose glucose galactose mannose fructose  II. Carbohydrates 2. Cyclic Oses ✓ n>4 → straight chain or cycle → cycle is more stable → or → Pyranoses (6C) & furanoses (5C) α β ✓ From intramolecular reaction between OH & aldehyde/ketone group ✓ α & β isomers: differ by orientation of OH that replaced the aldehyde/ketone - α: downward - β: upward ✓ Usually cyclic oses are switchable between α & β until polymerized.  II. Carbohydrates 4. Modification ✓ Osamines addition of amine group (---NH2) eg: glucose→glucosamine. galactose→galactosamine ✓ N-acetyl osamines addition of acetyl group (---COCH3) to the amine group eg: NAG: N-acetyl galactosamine ✓ Uronic acids acidification of CH2OH into COOH eg: NANA: N-Acetyl Neuraminic Acid (from mannose)  II. Carbohydrates 5. Dimers and Polymers ✓ Disaccharide: 2 oses joined by covalent bond “glycosidic bond” Its formation releases H2O - Saccharose = glucose + fructose - Lactose = glucose + galactose - Maltose = 2 glucose ✓ Oligosaccharide: short polymer of monosaccharaides can be branched / unbranched can be linked to proteins / lipids for maturation  II. Carbohydrates 5. Dimers and Polymers ✓ Polysaccharide (Glycan): long chain of monosaccharides branched / unbranched simple or modified oses Functions: Structural - cellulose in plant cell wall – peptidoglycans in bacterial cell wall Energetic - glycogen in muscles – starch in plants  II. Carbohydrates 5. Dimers and Polymers ✓ Homopolysaccharide: polymer of the same molecule - Starch & glycogen = branched polymers of α-D-glucose - Cellulose = unbranched polymer of β-D-glucose - Chitin = polymer of N-acetyl glucosamine, in insects shell ✓ Heteropolysaccharide: polymer of 2 diferent simple/modified oses - GAG = glucosamine + galactosamine - Hyaluronic acid = glucoronic acid + N-acetyl glucosamine - Chondroitin Sulfate = glucuronic acid + N-acetyl galactosamine - Keratan Sulfate = N-acetyl glucosamine + D-galactose  FS.I Partial 2020 13)b, 14)d, 15)a, 12)c, 13)b FS.I Partial 2019  III. Lipids All are non-polar → insoluble in water, soluble in non-polar solvents Functions Structural: phospholipids: component of cell membrane Energetic: triglycerides: stored in plants seeds & animal adipose tissue Communication: steroid hormones, eicosanoids, phosphatidylinositol 2 Types Saponifiable: have f.a, can undergo saponification reaction Non-saponifiable: no f.a, can not undergo saponification Saponification or NaOH  III. Lipids 1. Saponifiable Lipids a. Fatty Acids ✓ Amphipathic: 1 polar hydrophilic head (COOH) & nonpolar hydrophobic tail (hydrocarbon chain) ✓ Formula: CH3-(CH2)n-COOH (2≤n≤20) n is even ✓ Rarely occur free ✓ More energetic than carbs ✓ Differ by: length of chain & unsaturation degree (nb of C=C) → both affect membrane fluidity ✓ Saturated f.a.: no double bond, solid at room t◦ (Butyric acid, Myristic acid, Palmitic acid) ✓ Unsaturated f.a.: ≥1 double bond, fluid at room t◦ (Arachidonic acid, Linoleic acid, Oleic acid)  III. Lipids 1. Saponifiable Lipids b. Triglycerides / Triacylglycerols / neutral fats ✓ Neutral fats → no polar groups ✓ Glycerol + 3 f.a joined by ester bonds ✓ Diverse since many f.a types can form it ✓ Function: stored energy reserve ✓ Hydrolysis: by lipases or: by alkaline medium + heating  III. Lipids 1. Saponifiable Lipids c. Phospholipids ✓ Function: Structural (found in cell membranes) ✓ Amphipathic: 1 large polar head (phosphate) + 2 hydrophobic tails ✓ Glycerol-derived: Glycerophosphatides: Phosphate + glycerol + 2 f.a ✓ Sphingosine-derived: Sphingophospholipids: Phosphate + sphingosine + 1 f.a Found in myelin sheath (sphingomyelin) * Ceramide = sphingosine + f.a ✓ Choline, Serine, Ethanolamine, or Inositol can be added to increase head polarity  III. Lipids 1. Saponifiable Lipids d. Glycolipids ✓ Function: cell identity (blood group – immunity – cell-cell recognition) → found on outer cell membrane ✓ - Glycerol-derived: in plants & bacteria (Sugar + glycerol + 2 f.a ) - Sphingosine-derived: in animals (Sugar + sphingosine + 1 f.a) ✓ - Cerebrosides: Sugar is a simple ose (eg: galactocerebroside in brain’s myelin sheath) - Gangliosides: Sugar is an oligosaccharide  III. Lipids 1. Saponifiable Lipids e. Cerides ✓ Esters of f.a + “fatty alcohol” (long hydrocarbon chain ending with OH) ✓ In bee wax, leaf cuticle, cork  III. Lipids 2. Non-saponifiable Lipids a. Terpenes ✓ Polymers of propene with cyclization at one end & (maybe) polar OH at the other → moderately amphipathic ✓ Vit. A, E, K & carotenoids (lycopene, carotene)  III. Lipids 2. Non-saponifiable Lipids b. Steroids cholesterol ✓ Cyclic molecules carrying different functional groups ✓ Functions: Communication: Steroid hormones (estrogen, progesterone, testosterone, corticosterone, adrenal hormones…) Vitamins: Vit. D for growth & bone development (synth in skin) Structural: Cholesterol in plasma membrane controls its fluidity (bidirectionally) *It’ a precursor for steroid hormones, vit. D, bile salts… (Found in animal products)  III. Lipids 3. Hydrophobic Interactions Lipids are amphipathic→ water insoluble→ mixing forms heterogeneous mixtures ✓ Monolayers ✓ Bilayers: polar hydrophilic surfaces, hydrophobic center that prevents diffusion of large hydrophilic molecules ✓ Micelles: sphere of hydrophilic surface & hydrophobic core ✓ Liposomes: long bilayer folded back → hydrophilic surfaces & lumen FS.I Partial 2020 FS.I Partial 2019 10. a 11. b 12. a 14. a 15. a 23. b 30. energetic  IV. Nucleic Acids 1. Composition ✓ Nucleic Acid = Unbranched chain of nucleotides (DNA/RNA) ✓ Nucleotide = Nucleoside + phosphate (nucleoside monophosphate) ✓ Nucleoside = Nitrogenous base + Pentose Nitrogenous bases: Purines (A, G) – Pyrimidines (C, U, T) Nucleosides: Adenosine, Guanosine, Thymidine, Uridine, Cytidine Nucleotides: AMP, ADP, ATP, GMP, GDP, GTP, CMP, CDP, CTP, TMP, TDP, TTP, UMP, UDP, UTP * Precede by d (deoxy) for DNA * NTP is used when building nucleotides → 2 P used for energy  Purines Pyrimidines phosphodiester bond Phosphoester bond N-glycosidic bond  IV. Nucleic Acids 1. Composition Bonds: Nitrogenous Base & pentose: N-glycosidic bond (1’) Pentose & phosphate: phosphoester bond (5’) Adjacent nucleotides: phosphodiester bond (5’ & 3’) Facing nitrogenous bases: hydrogen bond  IV. Nucleic Acids 1. Composition DNA RNA Pentose Deoxyribose Ribose Nitrogenous Thymine Uracil base 2◦ structure Double-stranded Single-stranded Nucleus, mitochondria, Nucleus, mitochondria, Location chloroplast chroloplast + cytoplasm Stability More stable Less stable  IV. Nucleic Acids 2. DNA Structure ✓ 2 polynucleotide chains (strands) forming a double helix ✓ - Backbone: phosphate & sugar - Nitrogenous bases: in the middle of the double helix ✓ Nitrogenous bases pairing: - hydrogen bonds - complementary purine-pyrimidine (A&T, C&G) - antiparallel (one strand rotated 180◦ wrt the other) ✓ Grooves (major & minor) → their functional groups bind to proteins for condensation, replication, & transcription ✓ Dimensions: diameter=20 A, distance 2 bp=3.4 A, turn=34 A or 10 bp ✓ Helix forms: A-helix (in a water-poor medium) ; B-helix (usual form) ; Z-helix (in vitro) ✓ DNA denaturation: heating (100◦C) or alkaline medium → double strand unwinds & hydrogen bond is broken BUT it’s reversible DNA 5’ 3’ 3.4 A 34 A 5’ 3’ 20 A  IV. Nucleic Acids 3. DNA replication ✓ During S phase of interphase ✓ Aim: transmission & preservation of genetic information ✓ Replication complex = set of enzymes: - helicase - primase - topoisomerase (gyrase) - DNA polymerase - ligase ✓ Requires a lot of energy (from precursors: dNTPs) ✓ Semi-conservative: each new DNA molecule contains 1 old template strand and 1 newly synthesized strand  IV. Nucleic Acids 3. DNA replication Nuclease activity Some polymerases have the ability to degrade DNA Exonuclease activity: ability to degrade DNA from extremities. Some polymerases degrade 3’-5’ direction, others 5’-3’, others both  IV. Nucleic Acids 3. DNA replication 1. Helix unwinding: helicase separates the 2 strands at specific points (origin) * eukaryotes have many replication origins per chromosome * replicon: long segment of replicated DNA starting from origin 2. Primase (RNA polymerase) adds a primer (RNA sequence) to provide 3’OH end for DNA polymerase to start 3. DNA polymerase binds and starts synthesizing new strand using dNTPs and adding them in a complementary manner (A՞T, C՞G) template is read 3’-5’, new strand is synthesized 5’-3’ 4. Topoisomerase (gyrase): releases the tension → relaxes supercoiled DNA 5. DNA polymerase I removes primers (5’-3’ exonuclease) 6. Ligases join Okazaki fragments  IV. Nucleic Acids 3. DNA replication = region where old strands are unwound and polymerization occurs  Topoisomerase Relaxes the tension of DNA supercoiling Messenger RNA Transfer RNA Secondary Structure Tertiary Structure Ribosomal RNA Large subunit Small subunit Small Nuclear RNA (many types)  IV. Nucleic Acids 4. RNA Structure ✓ Single polynucleotide chain ✓ Some intramolecular pairing snRNA mRNA tRNA rRNA Abundance - Least abundant intermediate Most abundant Diversity - Most diverse (encoded intermediate Least diverse by many genes) (2 genes) Structure Bound to proteins → Single-stranded with 2◦: trefoil (3 loops) Highly structured form snRNP some pairing * middle loop has (many pairs & folds) anticodon Binds to proteins → * ends in 5’CCA3’ forms ribosome which carries aa 3◦: L-shaped Function mRNA maturation by Translated into Translation of mRNA Translation of mRNA splicing proteins Transcription: from DNA to RNA  IV. Nucleic Acids Replication vs. Transcription Replication Transcription Both DNA segments are templates Only 1 strand is a template The whole strand is replicated Only genes are transcribed Uses helicase, ligase.. + DNA Uses helicase, ligase.. + RNA Polymerase polymerase