Bio101 - General Biology Lecture

# BIO101 - General Biology ## Biomolecules and the Central Dogma of Life **S. Taiwo Fakorede, Ph.D.** Department of Cell Biology and Genetics ## Learning Objectives At the end of this study session, you should be able to: - List the four major classes of biomolecules/macromolecules - Identify t...

# BIO101 - General Biology ## Biomolecules and the Central Dogma of Life **S. Taiwo Fakorede, Ph.D.** Department of Cell Biology and Genetics ## Learning Objectives At the end of this study session, you should be able to: - List the four major classes of biomolecules/macromolecules - Identify the chemical elements that constitute carbohydrates, fats, and proteins - Understand that large biological molecules are synthesized from smaller units - 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 - 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. ## Organic Compounds - [Diagram] A diagram of organic compounds with branches labeled: "Carbohydrates", "Lipids", "Proteins", "Nucleic Acids" and the top branch labeled "Macromolecules". ## Biomolecules - All Biomolecules contain CARBON (C). - Carbon is the msot 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 Atoms → Molecules → Macromolecules... - [Diagram] Diagram comparing levels of organization from atoms to macromolecules with the following: - **City:** "Cell" - **Building:** "Organelle" - **Brick:** "Macromoecule" Macromolecules are large molecules composed of thousands of covalently connected atoms. ## Functions of Biomolecules - 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 - 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 - 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/Polymers - **Dehydration:** [Diagram] 2 glucose molecules (monomers) bond together to make maltose (dimer). - ## Breaking of Macromolecules - **Hydrolysis:** [Diagram] A dimer such as maltose, or any other polymer, is broken apart into its constituent monomers ## Polymers - Macromolecules are made of polymers which are made of smaller, repeating parts called monomers. - **Carbohydrates** (polymer) - **Monosaccharides** are the monomers for carbohydrates, joined by glycosidic bond. - **Proteins** (polymer) - **Amino acids** are the monomers for protens (polypeptides), joined by peptide bond. - **Nucleic Acids** (polymer) - **Nucleotides** are the monomers for nucleic acids, joined by phosphodiester bond. - **Lipids** are not considered polymers. They have no monomers. ## Carbohydrates - Carbohydrates (polysaccharides) are long chains of sugars. - General formula = ($C_6H_{12}O_6$)_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 - [Diagram] Diagram showing structural difference between fructose, glucose and galactose. - **Building Blocks:** Composed of carbon (C), hydrogen (H), and oxygen (O) in a 1:2:1 ratio - **Components:** Monosaccharides are the monomer. - Examples: - Glucose - Galactose - Fructose - **Functions:** - Main source of energy for living things (Monosaccharides) - Energy Storage (polysaccharides) - glycogen in animals - starch in plants - **Structural:** - to build cell walls: cellulose (plants), chitin (fungi) ## Carbohydrates - **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 ## Lipids - 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 - **Building Blocks:** - Mostly made from carbon and hydrogen atoms, some oxygen. - **Components:** - A fat molecule consists of 3 fatty acids joined to a molecule of glycerol. - Phospholipids in cell membranes are made of a phosphate group and 2 fatty acid chains. - **Functions and Examples:** - **Long-term Energy storage molecules (fats)** - **Cell Membranes of organisms (phospholipids)** - **Steroid Hormone as chemical signals (testosterone/estrogen)** ## Lipids - **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 - 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 - [Diagram] - **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 - **Twenty Standard Amino Acids:** [Diagram] - **R-groups** determine the properties of individual amino acid. ## Protein Structure - **Primary structure:** The linear sequence of amino acids linked together by peptide bonds. - **Secondary structure:** Polypeptide folding into an alpha helix or a beta sheet arrangement. - **Tertiary structure:** 3-D folding of a single polypeptide chain. - **Quaternary structure:** Association of two or more folded polypeptides to form a multimeric protein. ## Nucleic Acids - Nucleic acids are molecules that store information for cellular growth and reproduction. - **Elements:** C, H, N, O, P - 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. - A nucleotide consists of a nitrogenous base, a pentose sugar and a phosphate group. ## Pentose Sugars - 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. - **Pentose sugars in RNA and DNA:** [Diagram] ## Structure of DNA/RNA - **Three Components:** Phosphate Group, Pentose Sugar and Nitrogenous base - [Diagram] ## Nitrogenous Bases - **Purines:** [Diagram] - **Pyrimidines:** [Diagram] - "I AGree to Purify a CUTe Pyramid" - A mnemonic for remembering the nitrogenous bases: **A**denine, **G**uanine, **C**ytosine, **T**hymine, **U**racil. ## Structure of DNA - **Watson and Crick (1953)** determined the three-dimensional structure of DNA by building models. - They realized that **DNA is a double helix that is made up of a sugar-phosphate backbone on the outside with bases on the inside.** ## Structure of DNA - Watson and Crick's discovery built on the work of **Rosalind Franklin** and **Erwin Chargaff**. - Franklin's x-ray images suggested that DNA was a double helix of even width. - Chargaff's rules stated that A=T and C=G. ## Structure of DNA - **Erwin Chargaff** gave the Chargaff's rule for the relative estimation of the different nucleotides in the DNA. - Chargaff's rule states the amount of adenine in the DNA of a living organism is equal to the amount of thymine in the DNA. - It also states that the amount of cytosine in the DNA of a living being is equal to the amount of guanine in the DNA. - **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 24% Thymine (T), what are the percentages of Adenine (A), Cytosine (C), and Guanine (G) in the DNA? ## Structure of DNA - Nucleotides always par in the same way. - The base-pairing rules show how nucleotides always pair up in DNA: - A pairs with T - C pairs with G - Because a **pyrimidine** (single ring) pairs with a **purine** (double ring), the helix has a uniform width. ## Structure of DNA - The backbone is connected by **covalent bonds**. - The bases are connected by **hydrogen bonds**. ## Formation of Phosphodiester Bonds - [Diagram] ## RNA vs DNA - **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 is found ***inside and outside of the nucleus***; DNA is found ***only inside the nucleus***. 4. Nitrogenous bases in DNA: GC**A**T 5. Nitrogenous bases in RNA: GC**U** ## Assignment I - Describe 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 - The Central Dogma holds that genetic information is expressed in a specific order, from DNA to protein synthesis. - [diagram] Diagram showing the central dogma of life, labeled: "Replication" (DNA to DNA); "Transcription" (DNA to RNA); "Translation" (RNA to protein) ## DNA Replication - DNA replication is the process of making copies of DNA. - A single strand of DNA serves as a template for a new strand. - The rules of base paring direct replication. - DNA is replicated during the S (synthesis) stage of the cell cycle. - Each body cell gets a complete set of identical DNA. ## Models of DNA Replication - There are three (3) Models of Replication: - 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. ## Semiconservative Replication - The Process fo DNA replication is called "semiconservative" replication. This means that in each new double helix of DNA, one stand was from the parent. ## Meselson and Stahl Experiments - [Diagram] Diagram showing predictions of the Meselson and Stahl experiment as it relates to the models of DNA replication. The semiconservative model is marked as correct, whereas the conservative and dispersive models are marked as incorrect. ## Assignment II - A. Describe the Meselson and Stahl experiments in details. - B. What would be the outcome if the experiment continued for: - i. three generation - ii. four generations - iii. five generations ## DNA Replication Enzymes and Their Functions - **Helicase:** unwinds parental double helix at replication forks - **Single-stranded binding protein:** binds to and stabilizes single-stranded DNA until it is used as a template. - **Topoisomerase/DNA Gyrase:** relieves overwinding strain ahead of replication forks by breaking, swiveling, and rejoining DNA strands. - **Primase:** synthesizes an RNA primer at 5' end of leading strand and at 5' end of each Okazaki fragment of lagging strand. - **DNA pol III:** using parental DNA as a template, synthesizes new DNA strand by adding nucleotides to an RNA primer or a pre-existing DNA strand. - **DNA pol I:** removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides added to 3' end of adjacent fragment. - **DNA ligase:** joins Okazaki fragments of lagging strand, on leading strand, joins 3' end of DNA that replaces primer to rest of leading strand DNA. ## Replication fork - As the double helix unwinds, the two complementary strands of DNA separate from each other and form a Y shape structure known as the **replication fork**: [Diagram] ## DNA Replication: Leading Strand - **RNA primase** enzymes begin the replication process by building a small complementary RNA segment called **RNA primers** (10-60 ribonucleotides long) - **DNA polymerase III** begins to add DNA nucleotides to the primer. - Since **DNA polymerase III** only builds in the 5'→3' direction, the two new strands begin to be assembled in opposite directions. - **DNA polymerase III** is able to continue continuously. - No need for the **RNA primase** to add additional primers. This is called the **leading strand**. ## DNA Replication: Lagging Strand - On the opposite strand, **DNA polymerase III** is moving away from the replication fork (**lagging strand**: [Diagram] - **RNA primase** attaches another primer allowing **DNA polymerase III** to begin from a new point. - The pattern created on the second strand is a series of RNA primers and short DNA fragments called **Okazaki fragments**. - **DNA polymerase I** removes the RNA nucleotides and replaces them with DNA nucleotides. - **DNA ligase** catalyzes the formation of phosphodiester bonds to seal the strand. ## A General Model for DNA Replication 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 th ep rimer 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**. ## Checking for Errors - DNA polymerases that care out replication also play another important role. - As they assemble new DNA strands, they proof-read and correct errors (base-pair mismatches). - **Proof-reading:** While creating the complementary strand, if a mismatch occurs, **DNA polymerase III** may back up, repair, and continue. - **Repairing:** DNA repair mechanisms of **DNA Polymerase I and II** may locate distortions in the strands between replication events and remove a piece of the strand, **DNA polymerase III** will fill the gap, and **DNA ligase** wll seal the strand. ## Proof-reading - **DNA polymerase III** continues adding nucleotides in the forward direction. - If the enzyme adds a mismatched nucleotide, the enzyme acts as a **exonuclease** (cleave nucleotides) to renmove the mismatched nucleotide. - The enzyme resumes activity as **DNA polymerase**. ## Repairing - **DNA polymerase II** repairs damage to DNA that occurs between replication events. - Repair complexes remove several to many bases, leaving a gap in the DNA. - Gap is filled in by a **DNA polymerase**, using the template as a guide. - Nick is sealed by **DNA ligase** to complete repair. ## Assignment III - Compare and contrast DNA replication on the leading and lagging strands. ## Transcription: DNA to mRNA - Transcription is the process by which an RNA sequence is produced from a DNA template. - [Diagram] - There are different types of RNA molecules. Each has a different function in making or synthesizing proteins. ## Types of RNA 1. **Messenger RNA (mRNA)** - carries DNA's message from the nucleus to the ribosome. - [Diagram] ## Types of RNA 2. **Transfer RNA (tRNA)** - carries the correct amino acids to the ribosome so they can be added to the growing protein chain. - [Diagram] ## Types of RNA 3. **Ribsomal RNA (rRNA)** - makes up part of the ribosome. - Helps read mRNAs message adn assemble proteins. - [Diagram] ## Transcription Process - In the initiation process, the DNA is unzipped by **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 strand that gets transcribed is the **template** or **antisense strand**. - The RNA strand is made in the 5'→3' direction using the 3'→5' DNA strand as template. ## Transcription Process - Nucleotides are added into a complementary strand of mRNA based on the DNA code. - **DNA:** 3'-ATTCGCACATCAGCT-5' - **mRNA:** 5'-UAAGCGUGUAGUCGA-3' - The newly formed mRNA moves out of the nucleus to ribosomes in the cytoplasm (for trasnlation) and the DNA re-winds. ## Translation: mRNA to proteins - **Translation** is the process of protein synthesis in which the genetic information encoded in mRNA is tranaslated into polypeptide chains of amino acids. - Once the DNA has been transcribed to mRNA, the codons must be translated to the amino acid sequence of the protein. - The first step in trasnlation is activation of the tRNA. - Each tRNA has a triplet called an **anticodon** that complements a codon on mRNA. ## Translation Process - Initiation of protein synthesis occurs when an mRNA attaches to a ribosome. - On the mRNA, the **start codon (AUG)** binds to a tRNA with methionine. - The second codon attaches to a tRNA with the nnext amino acid. - A peptide bond forms between the adjacent amino acids at the first and second codons. - The first tRNA detaches form the ribosome and the ribosome shifts to the adjacent codon on the mRNA (this process is called **translocation)**. - A third codon can now attach where the second one was before translocation. ## Translation Process - [Diagram] Diagram showing the steps of protein synthesis. ## Translation Process - After a polypetide with all the amino acids for a protein is synthesized, the ribosome reaches the **stop codon** - UGA, UAA, or UAG. - There is no tRNA with an anticodon for the "stop" codons. - Therefore, protein synthesis ends (**termination**). - Finally, the protein is shipped to the Golgi body where it is altered and shipped to wheer its destination. - At its final destination, the protein will perform its specific function. ## Genetic Code - 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. - The codons can translate for **20 amino acids**. - Codons of three bases on mRNA correspond to one amino acid in a polypeptide. - As there are four bases, there are 64 (4^3) different **codon combinations**. Of these, 61 code for the 20 ami acid, 3 code for stop codons. ## Genetic Code - Different codons can translate for the same amino acid (eg 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 - [Table] Table showing the genetic code with the following labels: "First base of codon", "Second base of codon", "Third base of codon" and a "Key" which lists the amino acid abbreviations and full names. ## Features of the Genetic Code - The genetic code: - is a triplet code - is universal (exceptions exist) - is commaless - is degenerate/redundant - has start and stop signals - nonoverlapping ## Protein Synthesis 1. First transcribe the DNA code into its mRNA. Do this by complimentary base-pairing (A-U, G-C) - **DNA:** TACGAATTAAGUCUG - **mRNA:** AUGCUUAAUUCAGAC 2. Next break the mRNA into codon or three letters. - **mRNA:** AUG CUU AAU UCA GAC ## Protein Synthesis 3. Plug the codons into the chart and find the amino acids. - **mRNA:** AUG CUU AAU UCU - **Amino Acid:** met-leu-asn-ser ## Protein Synthesis [Table] Table showing the DNA Triplet, mRNA Codon, tRNA Anticodon and the Amino Acid (and/or instruction) for each sequence.. ## Haemoglobin Mutations [Table] Table showing DNA, mRNA, Amino Acid, Properties of AA, Effect on protein, and Disease for different mutations in hemoglobin.