FSC111 Biomolecules Lecture slides.pdf

FSC111 - Introductory Biology S. Taiwo Fakorede Department of Cell Biology and Genetics [email protected] UNIVERSITY OF FIRST CHOICE AND THE NATION’S PRIDE Learning Objectives...

FSC111 - Introductory Biology S. Taiwo Fakorede Department of Cell Biology and Genetics [email protected] UNIVERSITY OF FIRST CHOICE AND THE NATION’S PRIDE Learning Objectives 2 At the end of this study session, you should be able to: list the four major classes of biomolecules/macromolecules describe the structure and function of lipids, proteins, carbohydrates and nucleic acids distinguish between monomers and polymers, and describe how monomers are linked to form polymers describe how glycosidic, phosphodiester, ester and peptide bonds form compare and contrast DNA and RNA understand the genetic code discuss the flow of genetic information (from DNA to RNA to protein) Biomolecules 3 Biomolecules are molecules that occur naturally in living organisms They also include small molecules like primary and secondary metabolites and natural products, that take part in maintenance and metabolic processes These are usually obtained from food Biomolecules 4 Classes of biomolecules Classes of Biomolecules 5 Carbohydrates Lipids Nucleic Acids Proteins Biomolecules 6 All Biomolecules contain CARBON (C) Carbon is the most versatile and prominent element of life Other elements include: HYDROGEN (H) OXYGEN (O) NITROGEN (N) SULPHUR (S) SODIUM (Na) CALCIUM (Ca) MAGNESIUM (Mg) Levels of Organization 7 Atoms → Molecules → Macromolecules… Macromolecules are large molecules composed of thousands of covalently connected atoms. Biomolecules and Functioning of the Human 8 Body ✓Carbohydrates are the body’s main source of energy. ✓Lipids provide stored energy reserves. This allows us to survive when carbohydrates are not being supplied to the body. ✓Protein helps us stay strong, by forming new bones and muscles, and helping us fight diseases. ✓Nucleic acids are responsible for making each person functional and unique; they are the blueprint for our genetic structure. Making/Breaking of Macromolecules 9 Macromolecules are polymers, built from monomers A polymer is a long molecule consisting of many similar building blocks known as monomers Three of the four classes of life’s organic molecules are polymers. These include: - Carbohydrates - Proteins, and - Nucleic acids A dehydration reaction occurs when two monomers bond together through the loss of a water molecule (also called Condensation) Conversely, polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction Making of Macromolecules 10 Dehydration: Two glucose...can bond molecules together to make (monomers)... maltose (dimer). Breaking of Macromolecules 11 Hydrolysis: A dimer such as...can be broken apart maltose, or any into its constituent other polymer... monomers. Bonds Involved in Biomolecules 12 Carbohydrates 13 Carbohydrates (polysaccharides) are long chains of sugars. General formula = (CH2O)n Monosaccharides are simple sugars that are composed of 3-7 carbon atoms. They have a free aldehyde (aldoses) or ketone (ketoses) group, which acts as reducing agents and are thus referred to as reducing sugars. Carbohydrates 14 Examples of Monosaccharides based on number of Carbon atoms ✓ 3C - TRIOSES (C3H6O3) e.g. Glyceraldehyde and Dihydroxy acetone ✓ 4C - TETROSE (C4H8O4) e.g. Erythrose and Threose ✓ 5C - PENTOSE (C5H10O5) e.g. Ribulose, D-arabinose, Ribose ✓ 6C - HEXOSES (C6H12O6) – e.g. Glucose, Fructose, Galactose, Mannose ✓ 7C - HEPTOSES (C7H14O7) – e.g. Glucoheptose, Sedoheptulose Carbohydrates 15 Oligosaccharide are formed by condensation of 2-9 monosaccharide units. These units are joined with the help of specialized glycosidic linkages. Examples of Oligosaccharides ✓Disaccharides e.g. lactose, maltose, sucrose ✓Trisaccharides e.g. raffinose ✓Tetrasaccharides e.g. stachyose, sesame Carbohydrates 16 Polysaccharides are polymers of monosaccharides. They are un-sweet and complex carbohydrates. They are insoluble in water and are not in crystalline form Examples of polysaccharides ✓Starch: energy storage in plants ✓Glycogen: energy storage in animals ✓Cellulose: provides structural support in plant (cell wall), gives us fibre ✓Chitin: found in: exoskeletons of arthropods (insects, spiders), cell wall of some fungi Lipids 17 Lipids function as stored energy, insulation for the body, and assist absorption of certain vitamins. Lipids are large molecules that can be categorized as fats or oils. Lipids are composed of triglycerides. These molecules are made up of carbon, hydrogen, and oxygen atoms. They are soluble in organic solvents Lipids 18 Lipids are hydrophobic (water fearing) and do not dissolve in water Lipids can be: Saturated: The bonds between all the carbons are single bonds. Solid at room temperature Mainly animal fats Clogs arteries (bad) E.g. stearic acid, palmitic acid, lauric acid, butyric acid Unsaturated: There is at least one double or triple bond between carbons present. Liquid at room temperature Mainly plant-based fats Lowers blood pressure (good) E.g. linolenic acid, linoleic acid, oleic acid, arachidonic acid Lipids 19 Saturated Fat Unsaturated Fat Lipids 20 Glycerol + 3 Fatty Acids → Triglyceride Chain of Triglycerides → Lipid Lipids 21 Phospholipids – major lipid-related molecule Major component of cell membrane One fatty acid is replaced by a polar phosphate group which creates: a hydrophilic “head” region a hydrophobic “tail” region Proteins 22 Proteins are very large molecules made of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur. Protein molecules are made of smaller molecules called amino acids. Proteins 23 Peptide bonds form between amino acids (polypeptide = many peptide bonds = protein) All proteins have a central Carbon atom with 1. carboxylic acid group 2. amino group 3. hydrogen 4. R Group AAs differ in their properties due to differing side chains, called R groups Classes of Amino Acids 24 R-groups determine the properties of individual amino acid. Nucleic Acids 25  Nucleic acids are molecules that store information for cellular growth and reproduction  There are two types of nucleic acids: - deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)  These are polymers consisting of long chains of monomers called nucleotides  Elements: C, H, N, O, P  A nucleotide consists of a nitrogenous base, a pentose sugar and a phosphate group: Chemical Structure of RNA vs DNA 26 RNA - Ribonucleotides have a 2’-OH DNA - Deoxyribonucleotides have a 2’-H Pentose Sugars 27 ❖ There are two related pentose sugars: - RNA contains ribose - DNA contains deoxyribose ❖ The sugars have their carbon atoms numbered with primes to distinguish them from the nitrogen bases Nitrogenous Bases 28 - Pyrimidines: single ring; cytosine (C), thymine (T) and Uracil (U) - Purines: double ring; adenine (A) and guanine (G) Note: Red arrows indicate where the bases link to ribose or deoxyribose sugars in the formation of nucleotides. Pairing of Nucleotides 29 Nucleotides bond between DNA strands Hydrogen bonds form between bases Purines pair with pyrimidines A :: T 2 H bonds G ::: C 3 H bonds Building the Polymer 30 Formation of Phosphodiester Bonds 31 DNA Structure 32 The nucleotide structure consists of: the nitrogenous base attached to the 1’ carbon of deoxyribose the phosphate group attached to the 5’ carbon of deoxyribose a free hydroxyl group (-OH) at the 3’ carbon of deoxyribose DNA Structure 33 Nucleotides are connected to each other to form a long chain Phosphodiester bond: bond between adjacent nucleotides formed between the phosphate group of one nucleotide and the 3’-OH of the next nucleotide The chain of nucleotides has a 5’ to 3’ orientation. DNA Structure 34 Erwin Chargaff (1905-2002) Investigated the composition of DNA determined that: amount of adenine = amount of thymine amount of cytosine = amount of guanine Chargaff’s rule: A = T & C = G Also, [A] + [T] + [C] + [G] = 100% ANSWER THIS!!! Based on Chargaff's rule for the base composition of double helical DNA, if a sample of DNA contains 18% T, what are the percentages of A, C, and G in the DNA? DNA Structure 35 Rosalind Franklin and Maurice Wilkins Franklin performed X-ray diffraction studies to identify the 3-D structure discovered that DNA is helical discovered that the molecule has a diameter of 2 nm (or 20 A°) and makes a complete turn of the helix every 3.4 nm (34 A°) (Note: 1 Nanometre, nm = 10 Angstrom, A°) X-ray diffraction pattern of DNA DNA Structure 36 James Watson and Francis Crick, 1953 deduced the structure of DNA using evidence from Chargaff, Franklin, and others proposed a double helix structure the model looks like a twisted ladder The double helix consists of: – 2 sugar-phosphate backbones – nitrogenous bases toward the interior of the molecule – bases form hydrogen bonds with complementary bases on the opposite sugar-phosphate backbone DNA Structure 37 The two strands of nucleotides are antiparallel to each other, one is oriented 5’ to 3’, the other 3’ to 5’ The two strands wrap around each other to create the helical shape of the molecule. Key structural features of the DNA double helix The A, B, and Z forms of DNA 38 The Watson-Crick structure of DNA is also referred to as B-form DNA, or B-DNA. B- DNA is the most stable structure for a random-sequence DNA molecule under physiological conditions and is therefore the standard structural reference in any study of the properties of DNA. Two structural variants that have been well characterized in crystal structures are the A- and Z-forms of DNA. In general, A-DNA is a dehydrated form of DNA that may not occur in cells. A similar type of structure does occur in double helical RNA. The DNA backbone of Z-DNA takes on a zig- zag conformation. Certain nucleotide sequences fold into left-handed Z helices much more readily than others. To form the left-handed helix in Z-DNA, the purine residues flip to the syn conformation, alternating with pyrimidines in the anti- conformation. The A, B, and Z forms of DNA 39 Comparison of different helical parameters for A-, B-, and Z-DNA Parameter A-DNA B-DNA Z-DNA Helix sense Right Right Left Shape Broadest Intermediate Narrowest Base pair per turn 11 10 12 Axial rise (nm) 0.26 0.34 0.45 Helix pitch (°) 28 34 45 Base pair tilt (°) 20 –6 7 Twist angle (°) 33 36 –30 Diameter of helix (nm) 2.3 2.0 1.8 anti for pyrimidines, Glycosidic bond formation anti anti syn for purines Activity I 40 Highlight the contributions of the following scientists to the elucidation of DNA structure and function. - Frederick Griffith - Oswald Avery - Erwin Chargaff - Rosalind Franklin & Maurice Wilkins - Alfred Hershey & Martha Chase - Linus Pauling - James Watson & Francis Crick - Friedrich Miescher The Central Dogma of Life 41 The Central Dogma holds that genetic information is expressed in a specific order. This order is as follows: From DNA to protein synthesis RNA vs DNA 42 RNA — Ribonucleic Acid RNA is a messenger that allows the instruction of DNA to be delivered to the rest of the cell RNA is different from DNA in that: 1. The sugar in RNA is ribose; the sugar in DNA is deoxyribose 2. RNA is a single strand of nucleotides; DNA is a double strand of nucleotides 3. RNA has Uracil (U) instead of Thymine (T) which is in DNA 4. RNA is found inside and outside of the nucleus; DNA is found only inside the nucleus RNA Structure 43 In RNA, A, C, G, and U are linked by 3’-5’ phosphodiester bonds between the ribose sugar and phosphate DNA Replication 44 Purpose: cells need to make a copy of DNA before dividing so each daughter cell has a complete copy of genetic information 3 proposed Models of Replication Models of DNA Replication 45 Alternative theories of replication are: Semiconservative: each daughter has 1 parental and 1 new strand Conservative: 2 parental strands stay together Dispersive: DNA is fragmented, both new and old DNA coexist in the same strand Meselson and Stahl Experiments 46 ✓Meselson and Stahl concluded that the mechanism of DNA replication is the semiconservative model. ✓Each strand of DNA acts as a template for the synthesis of a new strand. Meselson and Stahl Experiments 47 Activity II 48 Describe the Meselson and Stahl experiments in details. What would be the outcome if the experiment continued for: i. three generations? ii. four generations? iii. five generations ?  49 DNA Replication: Initiation Unwinding the double helix helicase unwinds part of DNA helix stabilized by single-stranded binding proteins (SSBs) - prevent DNA molecule from closing DNA gyrase (topoisomerases) prevents tangling upstream from the replication fork by relaxing excess twists known as “supercoils” Replication fork 50 As the double helix unwinds, the two complementary strands of DNA separate from each other and form a Y shape.  51 DNA Replication: Elongation DNA Polymerase III (enzyme that builds new DNA strand) can only add nucleotides to existing strands of DNA RNA Primase adds small section of RNA (RNA primer) to the 3’ end of template DNA  52 DNA Replication: Elongation DNA Polymerase III catalyzes the addition of a nucleotide to the 3′ end of a growing DNA strand, with the release of two phosphates. DNA Replication: Termination 53 Two DNA molecules are formed that are identical to the original DNA molecule Old DNA Replication is called semi-conservative because one half of the original strand is always saved or New DNA “conserved”  Okazaki Leading and Lagging Strands The synthesis of both DNA strands occurs in the 5' to 3' direction. One strand, known as the leading strand, is synthesized as a continuous process. The other strand, known as the lagging strand, is synthesized in pieces called Okazaki fragments, which are then joined together as a continuous strand by the enzyme DNA ligase Comparison: Leading strand Lagging strand Synthesized continuously Synthesized discontinuously DNA polymerase moves toward the DNA polymerase moves away from replication fork the replication fork No Okazaki fragments produced Produce Okazaki fragments DNA replication on the Lagging Strand 55 All known DNA polymerases catalyze chain formation in the 5’ → 3’ direction. DNA strands must be copied in both directions – BIDIRECTIONAL!!! Primase joins RNA nucleotides into a primer, serves as starter sequence for DNA polymerase III However, short segments called Okazaki fragments are made because it can only go in a 5’ → 3’ direction DNA pol III adds DNA nucleotides to the primer NEXT DNA polymerase I removes sections of RNA primer and replaces with DNA nucleotides The Okazaki fragments are then joined by DNA ligase A General Model for DNA Replication 56 1. The DNA molecule is unwound and prepared for synthesis by the action of DNA gyrase, DNA helicase and the single-stranded DNA binding proteins. 2. A free 3'OH group is required for replication, but when the two chains separate no group of that nature exists. RNA primers are synthesized, and the free 3'OH of the primer is used to begin replication. 3. The replication fork moves in one direction, but DNA replication only goes in the 5' to 3' direction. This paradox is resolved by the use of Okazaki fragments. These are short, discontinuous replication products that are produced off the lagging strand. This is in comparison to the continuous strand that is made off the leading strand. 4. The final product does not have RNA stretches in it. These are removed by the 5' to 3' exonuclease activity of Polymerase I. 5.The final product does not have any gaps in the DNA that result from the removal of the RNA primer. These are filled in by the 5’ to 3’ polymerase action of DNA Polymerase I. 6. DNA polymerase does not have the ability to form the final bond. This is done by the enzyme DNA ligase. The Fidelity of Replication 57 1000 bases/second = lots of typos! DNA polymerase I – proofreads & corrects typos – repairs mismatched bases – removes abnormal bases repairs damage throughout life – reduces error rate from 1 in 10,000 to 1 in 100 million bases DNA Replication Enzymes and Their Functions 58 /DNA Gyrase Transcription 59 Transcription is the process by which an RNA sequence is produced from a DNA template Three main types of RNA are predominantly synthesized: Messenger RNA (mRNA): A transcript copy of a gene used to encode a polypeptide Transfer RNA (tRNA): A clover leaf shaped sequence that carries an amino acid Ribosomal RNA (rRNA): A primary component of ribosomes Transcription Process 60 In the initiation process, the DNA is unwound in the front of the RNA polymerase to expose the template strand RNA polymerase II then begins RNA synthesis at the transcription start point which has the sequence TATAAA (TATA box) Only one of the two DNA strands is copied into an mRNA strand during transcription The RNA strand is made in the 5→3 direction using the 3→5 DNA strand as template. Transcription Process 61 The strand that gets transcribed is the template or antisense strand The strand that contains the gene is the coding or sense strand The RNA molecule produced during transcription is a copy of the coding strand with Uracil in place of Thymine The newly formed mRNA moves out of the nucleus to ribosomes in the cytoplasm and the DNA re-winds Translation: Protein Synthesis 62 Translation is the process of protein synthesis in which the genetic information encoded in mRNA is translated into a sequence of amino acids in a polypeptide chain A ribosome is composed of two halves, a large and a small subunit. During translation, ribosomal subunits assemble together like a sandwich on the strand of mRNA: Each subunit is composed of RNA molecules and proteins The small subunit binds to the mRNA The large subunit has binding sites for tRNAs and also catalyzes peptide bonds between amino acids Translation 63 The two main processes involved in protein synthesis are - the formation of mRNA from DNA (transcription) - the conversion by tRNA to protein at the ribosome (translation) Transcription takes place in the nucleus, while translation takes place in the cytoplasm Translation 64 The sequence of nucleotides in an mRNA strand determine the sequence of amino acids in a protein Process requires mRNA, tRNA & ribosomes Polypeptide chains are synthesized by linking amino acids together with peptide bonds Translation 65 First, an mRNA strand binds to the large & small subunits of a ribosome in the cytosol of the cell This occurs at the AUG (METHIONINE, initiation) codon of the strand The ribosome has 3 binding sites for codons --- E (exit site), P, and A (entry site for new tRNA) The ribosome moves along the mRNA strand Translation Process 66 An anticodon on tRNA binds to a complementary codon on mRNA The tRNA carrying an amino acid enters the A site on the ribosome The ribosome moves down the mRNA so the tRNA is now in the P site and another tRNA enters the A site A peptide bond is formed between the amino acids and the ribosome moves down again The first tRNA is released, and another tRNA binds next to the second, another peptide bond is formed This process continues until a stop codon (UGA, UAA, or UAG) is reached There is no tRNA with an anticodon for the “stop” codons. Therefore, protein synthesis ends (termination) Translation 67 Translation 68 Transfer RNA (tRNA) Anticodons on tRNA Amino acids are carried by transfer RNA (tRNA) The anti-codons on tRNA are complementary to the codons on mRNA Protein Synthesis & The Genetic Code 69 The genetic code is the set of rules by which information encoded in mRNA sequences is converted into proteins (amino acid sequences) by living cells It consists of sets of three nucleotides (triplets) in mRNA called codons that specify the amino acids and their sequence in the protein Codons are a triplet of bases which encodes a particular amino acid As there are four bases, there are 64 different codon combinations (4 x 4 x 4 = 64). Of these, 61 code for the 20 amino acids, 3 code for stop codons The codons can translate for 20 amino acids Codons of three bases on mRNA correspond to one amino acid in a polypeptide Genetic Code 70 Different codons can translate for the same amino acid (e.g. GAU and GAC both translate for Aspartate) therefore the genetic code is said to be degenerate The order of the codons determines the amino acid sequence for a protein The coding region always starts with a START codon (AUG) therefore the first amino acid in all polypeptides is Methionine The coding region of mRNA terminates with a STOP codon (UGA, UAA, or UAG). The STOP codons do not add an amino acid. Instead, it and causes the release of the polypeptide The Genetic Code 71 The Genetic Code (simplified) 72 Second base of codon U C A G U Phe Tyr Cys C U Ser Stop A Leu Stop Trp G First base of codon Third base of codon U His C C Leu Pro Arg A Gln G U Asn Ser Ile C A Thr A Lys Arg Met G U Asp C G Val Ala Gly A Glu G Features of the Genetic Code 73 The genetic code - is a triplet/three-letter code - is universal (exceptions exist) - is commaless - is degenerate/redundant - has start and stop signals - nonoverlapping Activity III 74 For the DNA template: 3′-TACCAAATTTGCTTAATT-5’ 1. what would be the sequence of its complimentary strand? 2. what would be the sequence of an mRNA transcribed from it? 3. what would be the anticodons of the complimentary tRNA strands for its mRNA? 4. how many amino acid would be formed from the DNA template? 5. what would be the amino acid sequence formed? Resources 75 YouTube: DNA Replication https://www.youtube.com/watch?v=3jslVQDGkLU Transcription and Translation https://www.youtube.com/watch?v=8wAwLwJAGHs Textbook: Russel, P. J., Hertz, P. E., & McMillan, B. (2017). Biology: The Dynamic Science. (4th ed.). Cengage Learning (Chapters 3, 14 & 15; pages 44-72, 300-353) NB: For the textbook, focus only on the areas that were taught or mentioned in class  76 That’s All