Macromolecules(1)

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  • This image shows the primary structure of glycophorin A , a glycoprotein that spans the plasma membrane ("Lipid bilayer") of human red blood cells. Each RBC has some 500,000 copies of the molecule embedded in its plasma membrane. Fifteen carbohydrate chains are "O-linked" to serine (Ser) and threonine (Thr) residues. One carbohydrate chain is "N-linked" to the asparagine (Asn) at position 26. Two polymorphic versions of glycophorin A, which differ only at residues 1 and 5, occur in humans. These give rise to the MN blood groups The M allele encodes Ser at position 1 (Ser-1) and Gly at position 5 (Gly-5) The N allele encodes Leu-1 and Glu-5 Genotype to Phenotype Individuals who inherit two N alleles have blood group N. Individuals who are homozygous for the M allele have blood group M. Heterozygous individuals produce both proteins and have blood group MN . Glycophorin A is the most important attachment site by which the parasite Plasmodium falciparum invades human red blood cells.
  • Black alpha carbon. Grey carbon, red oxygen, blue nitrogen
  • Macromolecules(1)

    1. 1. Biological Macromolecules Structure and Function of Carbohydrates, Nucleic Acids, Proteins, Lipids
    2. 2. Cells as chemical reactors  Living organisms obey the laws of chemistry and physics  Can think of cells as complex chemical reactors in which many different chemical reactions are proceeding at the same time  All cells more similar then different if looked at on the inside!  Strip away the exterior and we see that all cells need to accomplish similar tasks and in a broad sense they use the same mechanisms (chemical reactions)  Reflects a singular origin of all extant living things!
    3. 3. Similarities among all types of cells  All cells use nucleic acids (DNA) to store information  RNA viruses, but not true cells (incapable of autonomous replication)  All cells use proteins as catalysts (enzymes) for chemical reactions  A few examples of RNA based enzymes, which may reflect primordial use of RNA  All cells use lipids for membrane components  Different types of lipids in different types of cells  All cells use carbohydrates for cell walls (if present), recognition, and energy generation  All cells use nucleic acids (RNA) to access stored information
    4. 4. Macromolecules  Large Molecules  Macromolecules are formed when monomers are linked together to form longer chains called polymers.  The same process of making and breaking polymers is found in all living organisms.
    5. 5.  Consider some generic monomers with OH groups on their ends.  These monomers can be linked together by a process called dehydration synthesis (also called a condensation reaction) in which a covalent bond is formed between the two monomers while a water molecule is also formed from the OH groups.  This reaction is catalyzed by a polymerase enzyme.  This same type of condensation reaction can occur to form many kinds of polymers, from proteins to carbohydrates, nucleic acids to triglycerides. Condensation Reaction
    6. 6. Hydrolysis Reactions  Polymers of all sorts can be broken apart by hydrolysis reactions. In hydrolysis the addition of a water molecule (with the help of a hydrolase enzyme) breaks the covalent bond holding the monomers together.
    7. 7. Macromolecules  Biotechnology often concerned with the manipulation of cells through the manipulation of the macromolecules contained within those cells  DNA  Proteins  Lipids & Carbohydrates (indirectly)
    8. 8.  Biologically important macromolecules are “polymers” of smaller subunits  Created through condensation reactions Carbohydrates : simple sugars Lipids : CH2 units Proteins : amino acids Nucleic acids : nucleotides Macromolecule Subunit
    9. 9. Where do the subunits come from?  All cells need a source of the atomic components of the subunits  (C, O, H, N, P, and a few other trace elements )  Some cells can synthesize all of the subunits given these atomic components and an energy source  Some cells can obtain these subunits from external sources  Some cells can convert other compounds into these subunits  We will discuss further in section on metabolism and cell growth
    10. 10. Carbohydrates  All have general formula CnH2nOn (hydrates (H2O) of carbon)  A variety of functions in the cell  Large cross-linked carbohydrates make up the rigid cell wall of plants, bacteria, and insects  In animal cells carbohydrates on the exterior surface of the cell serve a recognition and identification function  A central function is energy storage and energy production !
    11. 11. Carbohydrates  Carbohydrates are always composed of carbon, hydrogen and oxygen molecules  Monosaccharides typically have five or six carbon atoms.  Monosaccharides can, such as the ribose and deoxyribose of RNA and DNA, can serve very important functions in cells.
    12. 12. Carbohydrates  Condensation reactions form covalent bonds between monosaccharides, called glycosidic linkages.  Monosaccharides are the monomers for the larger polysaccharides.  Polysaccharides play various roles, from energy storage (starch, glycogen) to structure (cellulose).
    13. 13. Carbohydrates  Cell structure:  Cellulose, LPS, chitin Cellulose in plant cell walls Lipopolysaccharides (LPS) in bacterial cell wall Chitin in exoskeleton
    14. 14. Carbohydrate Structure Monosaccharides may also form part of other biologically important molecules
    15. 15. Carbohydrate Structure  Complex carbohydrates built from simple sugars  Most often five (pentose) or six (hexose) carbon sugars  Numerous –OH (hydroxy) groups can form many types of “cross links”  Can result in very complex and highl;y cross linked structures ( cellulose, chitin, starch, etc.)
    16. 16. Carbohydrate Structure A Few Examples  Triose (3 carbon)  Glyceraldehyde  Pentose (5 carbon)  Ribose
    17. 17. Carbohydrate Structure Example of two hexoses  Glucose Galactose  What’s the difference? Both are C6H12O6  They are isomers of one another!  Same formula, but different structure (3D-shape).
    18. 18. Carbohydrate Structure  Monosacharides can be joined to one another to form disaccharides, trisaccharides, ……..polysaccharides  Saccharide is a term derived from the Latin for sugar (origin = "sweet sand")  Carbohydrates classified according to the number of saccharide units they contain.  A monosaccharide contains a single carbohydrate, over 200 different monosaccharides are known.  A disaccharide gives two carbohydrate units on hydrolysis.  An oligosaccharide gives a "few" carbohydrate units on hydrolysis, usually 3 to 10.  A polysaccharide gives many carbohydrates on hydrolysis, examples are starch and cellulose.
    19. 19. Carbohydrate Structure Ring (cyclic) form Pentoses and hexoses are capable of forming ring (cyclic) structures. An equilibrium exists between the ring and open form. Linear form
    20. 20. Carbohydrate Structure  Monosaccharides can link to form disaccharides Glucose Fructose Sucrose +
    21. 21. Complex Carbohydrates  Cellulose Most abundant carbohydrate on the planet!  Component of plant cell walls  Indigestible by animals  β 1-4 bonds  Starch  Energy storage molecule in plants  Can be digested by animals  α 1-6 bonds
    22. 22. Cellulose  Cellulose is a linear polysaccharide in which some 1500 glucose rings link together. It is the chief constituent of cell walls in plants.  Human digestion cannot break down cellulose for use as a food, animals such as cattle and termites rely on the energy content of cellulose. They have protozoa and bacteria with the necessary enzymes in their digestive systems. Only animals capable of breaking down cellulose are tunicates.
    23. 23. Starches  Starches are carbohydrates in which 300 to 1000 glucose units join together. It is a polysaccharide used to store energy for later use. Starch forms in grains with an insoluble outer layer which remain in the cell where it is formed until the energy is needed. Then it can be broken down into soluble glucose units. Starches are smaller than cellulose units, and can be more readily used for energy. In animals, the equivalent of starch is glycogen, which can be stored in the muscles or in the liver for later use.  α-1,6 bonds
    24. 24. Complex Carbohydrates  Glycogen  Branched chain polymer of glucose  Animal energy reserve  Found primarily in liver and muscle  α 1-4 & α 1-6 bonds
    25. 25.  Glycogen
    26. 26. polysaccharides can be linked to other molecules to form glyco-proteins and glyco-lipids
    27. 27. Glycoproteins Some examples  Polysaccharide component of antibodies has major effect on antibody function  Polysaccharides attached to proteins on surface of red blood cells (RBC) determine blood type (A,B,O)  Polysaccharides are attached to proteins in the Golgi apparatus through a process of post-translational modification  Different types of cells do different post-tranlational modifications  More about this later
    28. 28. Glycolipids  Polysaccharides can also be attached to lipid molecules •An outer-membrane constituent of gram negative bacteria, LPS, which includes O-antigen, a core polysaccharide and a Lipid A, coats the cell surface and works to exclude large hydrophobic compounds such as bile salts and antibiotics from invading the cell. O-antigen are long hydrophilic carbohydrate chains (up to 50 sugars long) that extend out from the outer membrane while Lipid A (and fatty acids) anchors the LPS to the outer membrane.
    29. 29. Glycolipids  Polysaccharides (blue) are also used in animal cells to link surface proteins and lipid anchors to the membrane.
    30. 30. Lipids  Lipids  Fatty acids (Polymers of CH2 units)  Glycerol  Triglycerides  Other subunits (phosphate, choline, etc) may be attached to yield “phospholipids”  Charged phosphate groups will create a polar molecule with a hydrophobic (nonpolar) end and a hydrophillic (polar) end
    31. 31. Lipids  Lipids constitute a very diverse group of molecules that all share the property of being hydrophobic.  Fats and oils are lipids generally associated with energy storage.  Fatty acids, which make up fats and oils, can be saturated or unsaturated, depending on the absence or presence of double bonded carbon atoms.  Other types of lipids are used for a other purposes, including pigmentation (chlorophyll, carotenoids), repelling water (cutin, suberin, waxes) and signaling (cholesterol and its derivatives).
    32. 32. Lipids  Lipids are joined together by ester linkages.  Triglyceride is composed of 3 fatty acid and 1 glycerol molecule  Fatty acids attach to Glycerol by covalent ester bond  Long hydrocarbon chain of each fatty acid makes the triglyceride molecule nonpolar and hydrophobic
    33. 33. Lipids
    34. 34. Lipids
    35. 35. Phospholipids
    36. 36. Lipids Function  Energy Storage  Triglycerides  Cell membranes and cell compartments  Bi-layer structure  Outer or plasma membrane  Nuclear membrane  Internal structures  Er, Golgi, Vesicles, etc.
    37. 37. Phospholipid bilayer Hydrophillic heads Hydrophobic tails
    38. 38. Steroids
    39. 39. Proteins  Proteins serve many essential roles in the cell  Polymers of amino acids  20 naturally occurring amino acids  A few modified amino acids are used  The large number of amino acids allows huge diversity in amino acid sequence N = # of amino acids in a protein N20 = # of possible combinations
    40. 40. Proteins  Proteins consist of one or more polymers called polypeptides, which are made by linking amino acids together with peptide linkages.  Peptide linkages are formed through condensation reactions.  All proteins are made from the same 20 amino acids.  Different amino acids have different chemical properties.
    41. 41. Proteins  Protein’s primary structure largely determines its secondary, tertiary (and quaternary) structure.  Proteins subjected to extreme conditions (large changes in pH, high temperatures, etc.) often denature.  Proteins act as enzymes, and catalyze very specific chemical reactions.
    42. 42. Protein Function Some examples  Structure- form structural components of the cell including:  Cytoskeleton / nuclear matrix / tissue matrix  Lamins, collagen, keratin…….  Movement - Coordinate internal and external movement of cells, organells, tissues, and molecules.  Muscle contraction, chromosome separation, flagella………  Micro-tubueles, actin, myosin  Transport-regulate transport of molecules into and out of the cell / nucleus / organelles.  Channels, receptors, dynin, kinesin  Communication-serve as communication molecules between different organelles, cells, tissues, organs, organisms.  Hormones
    43. 43. Protein Function Some examples  Chemical Catalyst – serves to make possible all of the chemical reactions that occur within the cell.  Enzymes (thousands of different enzymes)  Defense-recognize self and non-self, able to destroy foreign entities (bacteria, viruses, tissues).  Antibodies, cellular immune factors  Regulatory-regulates cell proliferation, cell growth, gene expression, and many other aspects of cell and organism life cycle.  Checkpoint proteins, cyclins, transcription factors
    44. 44. Protein Structure  Polymers of 20 amino acids  All amino acids have a Common “core”  Amino end (N end)  Acid end (C end, carboxy end)  Linked by peptide bond  20 different side chains
    45. 45. Properties of amino acids  amino acids: acidic basic hydrophobic  Amino acids all have The same basic structure  Chemical properties of the amino acids yield properties of the protein!
    46. 46. Properties of amino acids
    47. 47. Protein Structure  The 3-D shape and properties of the protein determine its function.  Shape and properties of protein determined by interactions between individual amino acid components.  Four “levels” of protein structure  Primary (Io ), secondary (IIo ), tertiary (IIIo ), and quaternary (IVo ) (sometimes).
    48. 48. Levels of Protein Structure  I0 (primary) structure  Linear order of amino acids in a protein:  1 A A S X D X S L V E V H X X V F I V P P X I L Q A V V S I A  31 T T R X D D X D S A A A S I P M V P G W V L K Q V X G S Q A  61 G S F L A I V M G G G D L E V I L I X L A G Y Q E S S I X A  91 S R S L A A S M X T T A I P S D L W G N X A X S N A A F S S  121 X E F S S X A G S V P L G F T F X E A G A K E X V I K G Q I  151 T X Q A X A F S L A X L X K L I S A M X N A X F P A G D X X  181 X X V A D I X D S H G I L X X V N Y T D A X I K M G I I F G  211 S G V N A A Y W C D S T X I A D A A D A G X X G G A G X M X  241 V C C X Q D S F R K A F P S L P Q I X Y X X T L N X X S P X  271 A X K T F E K N S X A K N X G Q S L R D V L M X Y K X X G Q  301 X H X X X A X D F X A A N V E N S S Y P A K I Q K L P H F D  331 L R X X X D L F X G D Q G I A X K T X M K X V V R R X L F L  361 I A A Y A F R L V V C X I X A I C Q K K G Y S S G H I A A X  391 G S X R D Y S G F S X N S A T X N X N I Y G W P Q S A X X S  421 K P I X I T P A I D G E G A A X X V I X S I A S S Q X X X A  451 X X S A X X A Single letter code for amino acids, also a three letter code. Refer to your genetic code handout.
    49. 49. Levels of Protein Structure Primary Structure  Amino acids combine to form a chain  Each acid is linked by a peptide bond  Io structure by itself does not provide a lot of information.
    50. 50. Protein Structure  II0 (secondary) structure  Based on local interactions between amino acids  Common repeating structures found in proteins. Two types: alpha-helix and beta-pleated sheet.  In an alpha-helix the polypeptide main chain makes up the central structure, and the side chains extend out and away from the helix.  The CO group of one amino acid (n) is hydrogen bonded to the NH group of the amino acid four residues away (n +4).  Can predict regions of secondary structure
    51. 51. Ribbon Diagram α-helical regions
    52. 52. Beta sheet  Two types parallel and anti-parallel
    53. 53. Beta Sheet ribbon diagram antiparallel parallel
    54. 54. Protein Structure  III0 (tertiary structure)  Complete 3-D structure of protein (single polypeptide) Chymotrypsin with inhibitor hexokinase
    55. 55. Protein Structure  IV0 (quaternary) structure  Not all proteins have IV0 structure  Only if they are made of multiple polypeptide chains
    56. 56. Nucleic Acid  DNA is transmitted from generation to generation with high fidelity, and therefore represents a partial picture of the history of life.
    57. 57. Nucleic Acid  Two types of nucleic acids:  DNA  RNA  DNA stores the genetic information of organisms; RNA is used to transfer that information into the amino acid sequences of proteins.  DNA and RNA are polymers composed of subunits called nucleotides.  Nucleotides consist of a five-carbon sugar, a phosphate group and a nitrogenous base.  Five nitrogenous bases found in nucleotides:  the purines  adenine (A)  guanine (G)  the pyrimidines  cytosine (C)  thymine (T) (DNA only)  uracil (U) (RNA only)
    58. 58. Nucleic Acids  DNA –deoxyribonucleic acid  Polymer of deoxyribonucleotide triphosphate (dNTP)  4 types of dNTP (ATP, CTP, TTP, GTP)  All made of a base + sugar + triphosphate  RNA –ribonucleic acid  Polymer of ribonucleotide triphosphates (NTP)  4 types of NTP (ATP, CTP, UTP, GTP)  All made of a base + sugar + triphosphate  So what’s the difference?  The sugar (ribose vs. deoxyribose) and one base (UTP vs. TTP)
    59. 59. Function  Nucleic Acids  Information Storage  DNA / mRNA  Information transfer / Recognition  rRNA / tRNA / snRNA  Regulatory  microRNA ?
    60. 60. DNA Information for all proteins stored in DNA in the form of chromosomes or plasmids. Chromosomes (both circular and linear) consist of two strands of DNA wrapped together in a left handed helix. The strands of the helix are held together by hydrogen bonds between the individual bases. The “outside” of the helix consists of sugar and phosphate groups, giving the DNA molecule a negative charge.
    61. 61. Complimentary Base Pairs A-T Base pairing G-C Base Pairing
    62. 62. DNA Structure  The DNA helix is “anti-parallel”  Each strand of the helix has a 5’ (5 prime) end and a 3’ (3 prime) end.
    63. 63. DNA Structure Strand 1 (Watson strand) Strand 2 (Crick strand) 5 ‘ end 3 ‘ end 3’ end 5’end
    64. 64. DNA Structure  1 atgatgagtg gcacaggaaa cgtttcctcg atgctccaca gctatagcgc caacatacag  61 cacaacgatg gctctccgga cttggattta ctagaatcag aattactgga tattgctctg  121 ctcaactctg ggtcctctct gcaagaccct ggtttattga gtctgaacca agagaaaatg  181 ataacagcag gtactactac accaggtaag gaagatgaag gggagctcag ggatgacatc  241 gcatctttgc aaggattgct tgatcgacac gttcaatttg gcagaaagct acctctgagg  301 acgccatacg cgaatccact ggattttatc aacattaacc cgcagtccct tccattgtct  361 ctagaaatta ttgggttgcc gaaggtttct agggtggaaa ctcagatgaa gctgagtttt  421 cggattagaa acgcacatgc aagaaaaaac ttctttattc atctgccctc tgattgtata Because of the base pairing rules, if we know one strand we also know what the other strand is. Convention is to right from 5’ to 3’ with 5’ on the left.
    65. 65. Chromosomes and Plasmids  Chromosomes are composed of DNA and proteins.  Proteins (histone & histone like proteins) serve a structural role to compact the chromosome.  Chromosomes can be circular, or linear.  Both types contain an antiparallel double helix!  Genes are regions within a chromosome.  Like words within a sentence. For an animation of the organization of a human chromosome see: http://www.dnalc.org/ddnalc/resources/chr11a.html
    66. 66. RNA  Almost all single stranded (exception is RNAi).  In some RNA molecules (tRNA) many of the bases are modified (i.e. psudouridine).  Has capacity for enzymatic function.  One school of thought holds that early organisms were based on RNA instead of DNA (RNA world).
    67. 67. RNA  Several different “types” which reflect different functions  mRNA (messenger RNA)  tRNA (transfer RNA)  rRNA (ribosomal RNA)  snRNA (small nuclear RNA)  RNAi (RNA interference)
    68. 68. RNA function  mRNA – transfers information from DNA to ribosome (site where proteins are made)  tRNA – “decodes” genetic code in mRNA, inserts correct A.A. in response to genetic code.  rRNA-structural component of ribosome  snRNA-involved in processing of mRNA  RNAi-double stranded RNA, may be component of antiviral defense mechanism.
    69. 69. RNA A - hairpin loop B- internal loop C- bulge loop D- multibranched loop E- stem F- pseudoknot Complex secondary structures can form in linear molecule
    70. 70. mRNA  Produced by RNA polymerase as product of transcription  Provides a copy of gene sequence (ORF) for use in translation (protein synthesis).  Transcriptional regulation is major regulatory point  Processing of RNA transcripts occurs in eukaryotes  Splicing, capping, poly A addition  In prokaryotes coupled transcription and translation can occur

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