Cell Biology Part 2: Macromolecules (BES 107, Winter 2025) PDF

BES 107 Introduction to Cell Biology Part 2 – STRUCTURE AND FUNCTION OF MACROMOLECULES Campbell’s Biology Chapters 4 & 5 Winter 2025 Sophon Bailey All figures are from Ca...

BES 107 Introduction to Cell Biology Part 2 – STRUCTURE AND FUNCTION OF MACROMOLECULES Campbell’s Biology Chapters 4 & 5 Winter 2025 Sophon Bailey All figures are from Campbell’s Biology, © 2021 Pearson Press, unless otherwise attributed. Course content, digital or otherwise, created and/or used within the context of the course is to be used solely for personal study, and is not to be used or distributed for any other purpose without prior written consent from the content author(s). LEARNING OBJECTIVES Describe the role of carbon as a key element of biomolecules › Identify the valence of carbon and how it dictates the formation of bonds in organic molecules › Identify some common functional groups found in biomolecules Understand the difference between biomolecules as monomers and polymers and how properties change between thetwo › Discuss the common chemistry of polymers – condensation and hydrolysis Describe the monomeric and polymeric structure of common biopolymers › Carbohydrates/polysaccharides, amino acids/polypeptides, nucleotides/nucleicacids Apply organic chemistry principles to understand the behaviour of biopolymers in life Discuss the chemical structure of lipids and the assembly of lipids into larger structures 2 ORGANIC CHEMISTRY Organic chemicals are those thatcontain carbon (and usually hydrogen) Inorganic compounds do not All known life uses carbon-based chemicals › Proteins Adenosine triphosphate (ATP) › Nucleic acids (DNA, RNA) › Carbohydrates (sugars, starch) › Lipids 3 Principles of Biochemistry 5e, Moran et al, © 2012 Pearson CARBON CAN FORM 4BONDS Carbon-carbon bonds have alot of stored energy Carbon can bond easily with many other elements using the chemistry of the cell Campbell’s Biology © 2021 PearsonPress 4 R OH hydroxyl (polar, H-bondsdonor) O carbonyl (polar, H-bond acceptor) FUNCTIONAL GROUPS R1 R2 O Seven functional groups that are most carboxyl (acidic, charged) important in the chemistry of life: – R O › Hydroxyl R NH + amino (basic, charged) › Carbonyl 3 › Carboxyl R SH sulfhydryl (polar, crosslinks) › Amino O › Sulfhydryl – R O P O phosphate (highly charged) › Phosphate – › Methyl O R CH3 methyl (non-polar, bulky) 5 *R is any other organic group (usually CH/CH2/CH3)  M A C R OM OL E C U L E S ‘big’ ‘molecules’ Biological macromolecules are polymersformed from some repeating unit Polymers have emergent properties that cannot be easily predicted from the individual monomers 6  Monomer Polymer BIOLOGICAL POLYMERS Each biopolymer sugar (glucose) polysaccharide (starch) has a repeating O – chemistry but can have a variety of R HO O O O – + O + NH N N NH H3N H 3N NH O N N NH2 functional groups O O O amino acids polypeptide O NH2 Repeats of identical – (protein/peptide) O P O OH N monomers are O N O NH2 O homopolymers N N OP – O O OH N NH2 while different monomers are O O O N – N O P O P O P O N O N N – – – O O O O O nucleic acids (DNA/RNA) heteropolymers O – O P O OH OH OH nucleotides O 7 Principles of Biochemistry 5e, Moran et al, © 2012 Pearson  R1 R2 O – – O POLYMERIZATION + H3N + H3N + REACTIONS O O The same reaction chemistry is used for all macromolecules Condensation Hydrolysis (removes water) (adds water) Polymerization reactions remove water (condensation, dehydration) + H2O › Requires energy input and anenzyme R1 O catalyst for speed NH – H3N + O Hydrolysis reactions add water across a bond to break polymers into monomers O R2 8 HYDROLYSIS Cheese is produced by the hydrolysis of milk proteins to produce insoluble ‘curds’ Aging or ripening cheeses allows further bacterial hydrolysis to develop flavours and textures 11 https://foto.wuestenigel.com/sliced-brie-cheese-with-greens-on-black-background/ KEY POINTS All biomolecules arecarbon-based › 4 valence electrons = can form 4 bonds › Bonds easily with N, O, H › High energy storage in C-C, C-H bonds Macromolecules are polymers that form from repeating units of monomers › Have properties very different from the monomers (emergence) › Homopolymers have identical repeat units, heteropolymers are varied › Carbohydrates: monosaccharides  polysaccharides › Proteins: amino acids  polypeptides › Nucleotides  nucleic acids (DNA, RNA) All biopolymers are formed by condensation, degraded by hydrolysis 10  aldehyde MONOSACCHARIDES SIMPLE SUGARS Most are 5- or 6- carbon polyalcohols Monosaccharides can equilibrate between a linear glucose Fisher projection [α-D-glucopyranose] and ring form OH Carbohydrates are O H energy dense but OH H H O H also partially OH H HO HO H H oxidized (makes H HO OH OH reactions easier) H OH H OH Common formula CnH2nOn Chair presentation Haworth projection 11 Campbell’s Biology © 2021 PearsonPress  Hexose (6C) sugars[C6H12O6] ketone aldehyde COMMON H O OH C OH H C H H C OH HO O MONOSACCHARIDES OH C O H O HO C H H HO C H OH H H H C OH H C OH H HO OH H C OH Glucose – 6C aldose sugar usedfor H C OH H OH H C OH H C OH energy storage H glucose H fructose Fructose – 6C ketose sugar used for energy by plants Pentose (5C) sugars[C5H10O5] Ribose – 5C aldose sugar usedin aldehyde ketone H O H nucleotides (DNA/RNA) C HO H H C OH H OH H C OH O C O O Ribulose – 5C ketose sugar used for H H C C OH OH H H H OH H C OH H H H OH metabolism and photosynthesis H C OH H C OH OH OH H C OH OH OH H H ribose ribulose 12 Campbell’s Biology © 2021 PearsonPress Campbell’s Biology © 2021 PearsonPress Monosaccharides combine to form disaccharides glycosidic bond › Maltose (glucose-glucose), sucrose (glucose-fructose) Longer polymers are polysaccharides All are synthesized by adehydration/condensation reaction 13 POLYSACCHARIDES Storage polysaccharides – used for energy › Starch (plants), glycogen (mammals) › Glucose homopolymers with α 14 linkage Structural polysaccharides – used to build rigid, flexible materials › Cellulose (plants) – glucose homopolymer with β 1 4 linkage 14 Principles of Biochemistry 5e, Moran et al, © 2012 Pearson  Glycosidic bonds in storage polysaccharides are easily broken to release glucose for metabolism Glycosidic bonds in structural polysaccharides are highly resistant to breakdown 15 Campbell’s Biology © 2021 PearsonPress  CARBOHYDRATE DERIVATIVES Many additional biomolecules have different chemical substitutions N-acetyl modified polysaccharides are found in insect exoskeletons, bacterial cell walls, and the matrix of the human brain Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. Campbell’s Biology © 2021 PearsonPress 16 KEY POINTS Carbohydrates include sugars and their polymers › Monosaccharides – simple sugar monomers (usually 5-6C polyalcohols) › Disaccharides – 2 sugar residues › Polysaccharides – >2 sugar residues Monosaccharides have either aldehyde (aldose) or ketone (ketose) functionality Polymerize by condensation of the aldehyde/ketone to form a glycosidic link Storage polymers – for energy (starch,glycogen) Structural polymers – provide mechanical strength (cellulose, chitin) 17 PROTEINS Amino acid polymers are polypeptides › Peptides (few to ~20 amino acids) › Proteins (20 to 1000s of amino acids) Proteins are the major functional component of biology › Protein sequence is defined in the genome › Proteins form enzymes, transporters, and structural components of cells and tissues 18 Campbell’s Biology © 2021 PearsonPress Proteins are heteropolymers made of up to 20 different common amino acids Can make a nearly unlimited variety of different proteins 19  Campbell’s Biology © 2021 PearsonPress PEPTIDE BONDS Polypeptides are formed by condensation of one amino group and one carboxy group to form a peptide bond (amide) Polypeptides have the same peptide backbone with a wide variety of side groups/chains 20  Campbell’s Biology © 2021 PearsonPress LEVELS OFPROTEIN Primary structure is the linear sequence of amino acids (NC) Secondary and tertiary structure are local folds that contribute STRUCTURE to the final, functional, quaternary structure 21  PROTEIN FOLDING Quaternary structures include assembling multiple polypeptides (identical or different subunits) into one final protein Can also include non-protein co- factors/co-enzymes required for Hemoglobin – heterotetramer (2α, 2β) protein function Each subunit binds one heme molecule 22 Campbell’s Biology © 2021 PearsonPress  MISFOLDING Changes in primary sequence or other changes can cause proteins to misfold Sickle-cell anemia, Alzheimer’s, Huntington’s, prion disease, muscular dystrophy, etc are diseases of protein folding 23 Campbell’s Biology © 2021 PearsonPress KEY POINTS Amino acids all have the same corestructure › Amino and carboxy functional groups, variable sidegroups Polypeptides form by condensation of the amino and carboxy groups to form a peptide bond Polypeptides are linear polymers having a common peptide backbone with variable side groups Primary sequence carries all necessary information for correct protein folding Complete, correct protein folding (quaternary structure) can includemultiple polypeptides and co-factors/metals 24 NUCLEIC ACIDS Polymers of nucleotides are used for information storage and processing, aswell as active functional roles DNA, RNA carry and transfer information in the cell Many RNAs are functional and can have enzymatic activity 25 Campbell’s Biology © 2021 PearsonPress  Ribose/deoxyribose Nitrogenous base NUCLEOTIDES Phosphoanhydride bonds The monomers of nucleic acids are nucleotides In the cell these are usually found as a triphosphate >> diphosphate > monophosphate Phosphoester bond Phosphoanhydride bonds have high Adenosine triphosphate (ATP) energy and are used in the cell as an energy currency (usually ATP) 26 Principles of Biochemistry 5e, Moran et al, © 2012 Pearson  DNA RNA Protein CENTRAL DOGMA Nucleic acids are involvedin information flow but are much more than informationcarriers that which is not 27 to be questioned POLYMER STRUCTURE Nucleic acids are polynucleotides Polynucleotides have a repetitivesugar- phosphate backbone with varying nitrogenous nucleoside bases The backbone linkages arecovalent bonds DNA and RNA vary in the sugar incorporated into nucleotides 28 Campbell’s Biology © 2021 PearsonPress  DNA forms an anti- parallel double helix structure with a sugar phosphate backbone and complimentary nucleotide base pairs at the centre RNA is generallysingle stranded The two nucleic acids differ in the sugar component of the nucleotides (ribose vs deoxyribose) 29 https://commons.wikimedia.org/w/index.php?curid=11133531  COMPLEMENTARY BASE PAIRS H-bonds between two DNA strands hold the helix together Base pairing is specific (always A-T or G-C) Two strands have complementarity 30 Campbell’s Biology © 2021 PearsonPress Principles of Biochemistry 5e, Moran et al, © 2012 Pearson COMPLEMENTARITY The two strands are complementary – each can serve as a template for the reciprocal strand, but they are not identical Complementarity is defined by the specific pairing of A-T and C-G RNA can also be complementary to DNA – we can generate RNA from a DNAtemplate (& vice versa) › RNA uses U in place of T so we instead see A-U pairing 31 RNA STRUCTURE RNA has a less defined structure and can form many different shapes Many RNA molecules fold to form complementary stretches within one structure › mRNA – messenger template for protein synthesis › tRNA – transfers amino acids during protein synthesis › rRNA – ribosomal structure and function 32 Campbell’s Biology © 2021 PearsonPress  INFORMATION FLOW IN THECELL Transcription Translation Structure & DNA (RNA synthesis) RNA (Protein synthesis) Protein Function Coding mRNA DNA replication Non-coding RNA: Functionalroles rRNA tRNA microRNA other known & unknownncRNA 75% of the human genome is transcribed, but only 1.5% is protein coding 33 KEY POINTS Nucleotides have a ribose/deoxyribose sugar, a variable nucleoside base, and 1-3 phosphate residues › Nucleotides are common in the cell as an energy currency due to the high energy of phosphoanhydride bonds Nucleotides polymerize by condensation of the 5’ phosphate and a 3’ –OH to form a repetitive sugar-phosphate backbone with variable nitrogenous bases Nucleoside bases can H-bond specifically with other strands › Always G-C and A-T or A-U › DNA (double stranded) base pairs with a second complementary strand › RNA (single stranded) can fold and base pair with itself to form diverse structure RNA is produced from a DNA template and can hybridize (base pairs between RNA-DNA) 34 LIPIDS Polar (Hydrophilic) Lipids are a diverse class ofbiomolecules with similar properties, but variable structure All are amphipathic withhydrophobic structures that dislike water Non-polar (Hydrophobic) Lipids form large assemblies ratherthan polymers Includes fatty acids, phospholipids,sterols 35 Principles of Biochemistry 5e, Moran et al, © 2012 Pearson  FATTY ACIDS Hydrocarbon chains C16:0, palmitic acid with carboxyl functionality at one end Can be conjugated to many molecules by condensation (termed acyl group) Conjugated to glycerol to form triacylglycerols 36 Campbell’s Biology © 2021 PearsonPress PHOSPHOLIPIDS Two fatty acids conjugated to a phosphate containing structure (e.g. glycerol phosphate) are phospholipids Major lipid found in cellmembranes In mammals typically have one saturated and one unsaturated fatty acylgroup 37 Campbell’s Biology © 2021 PearsonPress ASSEMBLIES Lipids spontaneously form assemblies driven by hydrophobic forces › Water interacts favourably with headgroups, repels fattytails Have emergent properties like biopolymers but not covalently linked, does not require energy to assemble Assemblies are impermeable to other polar molecules 38 https://commons.wikimedia.org/w/index.php?curid=3032610 STEROLS hydrophilic hydrophobic H3C Cholesterol is the parent compound of CH3 sterols and steroids CH3 › All share a rigid fused ringstructure CH3 H3C › Highly hydrophobic with minimal hydrophilic –OH headgroup HO Essential in cell membranes and common Cholesterol as signalling molecules (steroid hormones) and essential vitamins (D vitaminfamily) 39 KEY POINTS Lipids are amphipathic molecules that form largeassemblies › Hydrophilic head groups, hydrophobic tails › Similar emergent properties to biopolymers but are not covalently linked Fatty acids are hydrocarbons with one carboxylgroup › Saturated – straight hydrocarbon chains, pack tightly › Unsaturated – have one or more double bonds, kinked, packloosely Spontaneously assemble bilayers that can be impermeable to polar molecules 40