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Topic 2 Molecular Biology Biochemistry Introduction • Organic chemistry is the chemistry of carbon compounds. • Biochemistry is a branch of organic chemistry dealing with living organisms. • All living organisms are made of molecules that can be classified into one of four types. • Carbohydrates, lipids, proteins or nucleic acids Metabolism • Metabolism is all the enzyme catalyzed reactions that take place in an organism. • The four groups of molecules interact with each other to carry out the reactions of metabolism. • Example: Insulin (Protein) helps glucose (carbohydrate) travel through the cell membrane (lipid) and get into the cell. The insulin molecule itself is created by DNA (nucleic acid) Organic Chemistry • Not all molecules that contain carbon are considered organic, such as carbon dioxide. • Carbohydrates, lipids, proteins and nucleic acids are all organic and contain carbon. • Live is sometimes referred to as carbon based Carbon • • • • Atomic # 6, which means 6 protons. Also normally has 6 electrons. 2 electrons form the stable inner shell. 4 electrons are found in the second, unfilled shell. • Carbon likes to “fill” this second shell by sharing 4 electrons with other atoms. Each “sharing” forms a covalent bond, so each carbon atom can form 4 covalent bonds. Common Atoms other than Carbon • • • • Hydrogen Oxygen Nitrogen Phosphorus Building Blocks • • • • Carbohydrates – Monosaccharides Lipids – Glycerol and Fatty acids Proteins (polypeptides)– Amino acids Nucleic acids - Nucleotides Carbohydrates Monosaccharides Disaccharides Polysaccharides Glucose (2) Maltose Starch Galactose Lactose Glycogen Fructose Sucrose Cellulose Ribose Chitin PROTEINS • • • • • Polypeptide Chains made from amino acids Some types of proteins Enzymes Antibodies Hormones Lipids • Triglyceride – Fat stored in adipose tissue • Phospholipid – Form bilayer in cell membrane • Steroid – A type of hormone Nucleic Acids • DNA – deoxyribonucleic acid • RNA – ribonucleic acid • ATP – adenosine triphosphate Metabolism • In a multicellular organism, all of the reactions within all of the cells and fluids comprise the metabolism of the organism. • Reactions occur when certain molecules collide. • Cells use enzymes to increase reaction rates. • Enzymes are proteins with a very specific shape, that very specific molecules can fit into. • Area of enzyme that molecule fits into is called the active site. Enzyme at Work Example reaction: ADP + Pi = ATP Enzyme lowers the amount of energy needed for the reaction to begin – activation energy Metabolism = Catabolism + Anabolism • Catabolism is breaking down large, complex molecules (food) into smaller, simpler ones. • Anabolism is converting small, simple molecules into larger, more complex ones. • Catabolism involves hydrolysis reactions and hydrolytic enzymes • Anabolism involves condensation reactions Hydrolysis • Hydrolysis reactions break things apart and require a molecule of water to do so. • Example: Lactose + water = glucose + galactose Hydrolysis • Example: Triglyceride + 3 waters = Glycerol + 3 fatty acids. Condensation • Condensation reactions combine smaller molecules to create larger ones, and give off water as a byproduct. • Creating proteins from amino acids • Creating triglycerides from glycerol and fatty acids • Creating di and polysaccharides from monosaccharides. 2.2 Water • Water is a good solvent – “solvent of life” • Any solution where water is the solvent is called an aqueous solution. • To understand the properties of water, you have to understand the structure. Water molecular structure • Bonds between the oxygen and the two hydrogen atoms are polar covalent bonds. Due to unequal sharing, the Oxygen end is more negative and the hydrogen end is more positive. Hydrogen Bonding • Because of the polarity of a water molecule, the positive end of one water is attracted to the negative end of another water molecule. This attraction is called a hydrogen bond Cohesive property of water • Cohesion is when molecules of the same type are attracted to each other. So when one water molecule is attracted to another water molecule ( hydrogen bond) it’s called cohesion. • Explains water droplets, surface tension, how water is able to move in plants. Adhesive property of water • Adhesion is when a molecule is attracted to a different type of molecule. So if a water molecule is attracted to a different kind of polar molecule, it’s called adhesion. • Water moves upward in plants using both cohesion and adhesion. • When the water is being pulled up, it moves due to cohesion, when it isn’t being pulled, it remains in place due to adhesion with the tube it is traveling in. Thermal properties of water • Water has high specific heat – This means water can absorb or give off a great deal of heat with changing temperature very much. • Water helps to stabilize our temperature. • Water also has a high heat of vaporization, meaning it absorbs a lot of heat when it vaporizes. • As sweat evaporates from our skin, it cools our body. Solvent properties of water • Water is an excellent solvent of polar molecules. The vast majority of biological molecules are polar, including carbohydrates, proteins and nucleic acids. • Common aqueous solutions are cytoplasm, nucleoplasm, stroma and plasma. • Plants use water to transport material in xylem and phloem. Animals use water in blood to transport materials in arteries and veins Hydrophilic and Hydrophobic • Polar molecules, such as water, are “water loving” or hydrophilic. • Non-polar molecules are “water fearing” or hydrophobic. Hydrophobic molecules are usually made of large areas of only carbon and hydrogen. Fatty acids are hydrophobic. • Proteins can have areas that are hydrophobic and areas that are hydrophilic Solubility and Transport • Glucose: polar, very soluble in plasma • Amino acids: vary in polarity but all soluble in plasma • Cholesterol and fats: non-polar, low solubility, transported in plasma by blood proteins that have a polar area and a non-polar area. • Oxygen: non-polar, low solubility. Carried in plasma by hemoglobin of red blood cells. • Salt: polar, very soluble in plasma 2.3 Carbohydrates and Lipids • Most are very large molecules (polymers) made of smaller repeating units (monomers). • The monomers of carbohydrates are called monosaccharides. • These monosaccharides can be combined by anabolic condensation reactions to form larger molecules. Monosaccharides • • • • • Classified by how many carbons they contain. Most common are: Trioses (3) carbons – formula C3H6O3 Pentoses (5) carbons – formula C5H10O5 Hexoses (6) carbons – formula C6H12O6 • Notice the pattern for monosaccharides • CnH2nOn Monosaccharide Condensation Reaction • • • • • • Two monosaccharides become a disaccharide. Two glucose = maltose Glucose + fructose = sucrose Glucose + galactose = lactose A water molecule is produced by this reaction. An OH comes off of one of the sugars and an H comes off of the other one. • https://www.youtube.com/watch?list=PLvIduy9U GVRXMUBXEEwQ0QxfceFYJiZY6&v=RwYobhHi1lE Polysaccharides • Repeatedly bonding glucose together creates several polysaccharides. • Cellulose: plant cell walls, rigidity/support • Starch: Plants store glucose, product of photosynthesis, as starch, in roots and chlotoplasts. • Glycogen: Animals store excess glucose as glycogen, in liver and muscle tissue. Fatty Acids • All fatty acids have a carboxyl group (-COOH) at one end, and a methyl group (CH3-) at the other end. • In between, what makes them different is a chain of carbons and hydrogens that is usually 11-23 carbons long. Saturated Fatty Acids • Called saturated because all of the carbons have as many hydrogens as possible, saturated with hydrogens. • Means there are no double bonds in the chain • Mostly animal fat, solid at room temp, straight chains. Monounsaturated fatty acids • Contain one double bond • Double bond loses two hydrogen atoms, so no longer saturated, also causes the chain to bend at the bond. Polyunsaturated fatty acids • • • • Have at least two double bonds. Typically come from plants (olive oil example) Usually liquids at room temp. Very crooked, curves chains due to the double bonds. • Double bonds are usually cis, not trans Cis vs Trans Hydrogenation • Food processors add hydrogen to remove some or all of the double bonds. • This straightens out the molecules. • Naturally curved fatty acids are called cis fatty acids, the processed straightened out ones are called trans. • Usually not all the double bonds are broken so these fatty acids are called partially hydrogenated. Omega-3 fatty acids • The last carbon in a fatty acid chain, the one in the methyl group, is called the omega carbon • Counting from that carbon, you can show where a double bond is located in the chain. • Omega-3 means there is a double bond on the third carbon. • Fish are a good source Omega-3 Triglycerides • Triglycerides are basically fats in animal cells and oils in plant cells. • The are made of one (1) glycerol molecule with three fatty acid chains attached by condensation reactions. Energy storage • Humans and many other organisms store energy by using glucose to make glycogen, and making triglycerides to store energy as lipids. • Triglycerides can be broken down (hydrolysis) and used in the reactions of cellular respiration to make ATP, just as glucose is. • Triglycerides have twice the energy per gram as carbohydrates and proteins. • Triglycerides are also better for long term storage of energy because they are non-polar and not water soluble. They won’t cause osmosis issues in cells they are stored in as glucose will. Body Mass Index • Body mass index (BMI) is used as an indicator of healthy weight. • Uses both weight and height. • Three methods: • (1) Formula using weight and height • (2) Using a graph called a nomogram • (3) Using an on line calculator BMI • Use terms underweight, normal weight, overweight, or obese. • Should not be used with children or pregnant women. • Metric formula: weight (kg)/ height (m)2 • Imperial form: weight (lbs)/ height (in)2 x 703 BMI 2.4 Proteins • Cells use 20 amino acids to create polypeptide chains. • Controlled by DNA, with each different chain controlled by a specific piece of DNA called a gene. • Different types of cells use different genes to make the polypeptides that are specific to them. • Humans have between 20,000 and 25,000 genes in each cell. Amino Acids • Virtually all organisms use the same genetic code and the same 20 amino acids. • All 20 amino acids have the same structure except for one bonding location called the R or variable group. • In aqueous solutions (water) the OH of the acid group will lose a H+ to the amine group. • Polypeptide chains are made at the Ribosomes using condensation reactions. • The sequence of the amino acids is determined by the gene controlling the process. Levels of polypept/protein structure • Each polypeptide chain has its own 3D shape which determines it’s function. • Level 1 (primary) – order of the amino acids • Level 2 (secondary) – repeating pattern, either helix or pleated sheet. Example is spider silk • Caused by hydrogen bonding within the main chain, not the R groups. • Usually structural • Level 3 (tertiary) globular structure. Example: enzymes. Bonding involving the R groups • Level 4 (quaternary) 2 or more polypeptide chains bonded together. Example: hemoglobin. • A good example of why not all polypeptide chains are proteins. • Everyone has unique DNA (genome), unique proteins (proteome) Denaturing of proteins • The bonds that create secondary, tertiary and quaternary structure are susceptible to change due to heat and pH, which can change the structure, therefor the function of proteins. • If temp is too high, hydrogen bonds break, shape changes and protein wont function properly (DENATURED) • A change in pH causes the same thing 2.5 Enzymes • Enzymes are proteins, a type of protein that speeds up reactions. Anything that can speed up a reaction is called a catalyst, so some proteins (enzymes) are catalysts. • Each specific enzyme has a specific shape. • Within that shape is a certain area that matches a specific molecule. • The area is the active site of the enzyme, the molecule it matches is called the substrate. • A good analogy is lock and key. • The lock is the enzymes active site and the key is the substrate. • A certain minimum rate of motion is needed by the substrate when it enters the active site to supply the energy needed for the reaction. • This is called activation energy. • Enzymes lower the activation energy needed for a reaction to occur, they are not considered reactants and are not used up Factors affecting enzyme catalyzed reactions • Temp – cooler, slower – warmer, faster up to the point where the enzyme becomes denatured. • pH – proteins (amino acids)have charges, substrates have charges. • If there are too many H+ (low pH), or –OH (high pH) around the enzyme, they bond instead of the substrate. • Usually makes enzyme less efficient but can completely denature it if sufficient change in pH. Substrate Concentration • If there is constant amount of enzyme, increasing the substrate increases the rate of the reaction. (Increased collisions) • There is a limit, enzymes can only work so fast, there active sites can get full. • Rate increases then levels off. Immobilized enzymes • Industry uses enzymes to make products but enzymes are expensive. • How can you use enzymes to make product but keep the enzyme for future use and not sent it out with the produce. • Put the enzymes into calcium alginate beads so the beads can be easily separated from the product. Lactose free milk • Lactase is the enzyme that helps break lactose into glucose/galactose. • Some don’t have this enzyme. • Bacteria take over the job which causes problems • Milk products are treated with lactase before consumption. 2.6 Structure of DNA and RNA • Nucleotides are the building blocks of nucleic acids • There are three types of nucleic acids, adenosine triphosphate (ATP), deoxyribonucleic acid (DNA), and ribonucleic acid RNA) • We are going to focus on DNA and RNA, the genetic material of the cell. DNA is a polymer • DNA and RNA are polymers with the monomer being nucleotides • Each nucleotide consists of three parts: a pentose (5 carbon) sugar, a phosphate group and a single nitrogenous base. • Chemical bonds at specific locations create the appropriate structure. Nucleotide structure Nucleotide structure • The bond between the phosphate group and sugar, and the bond between sugar and base are covalent bonds. Nitrogenous bases • • • • • • The bases used in nucleotides are DNA RNA Adenine Adenine Cytosine Cytosine Guanine Guanine Thymine Uracil Pentose Sugar Making Polymers • DNA and RNA Monomers (nucleotides) bond together to form DNA and RNA polymers. • The reaction bonding the nucleotides together is a condensation reaction. Strands • RNA is composed of a single strand of nucleotides while DNA is two strands connected at the bases by hydrogen bonding • Complementary base pairing involves Adenine always attached to Thymine and Cytosine always attached to Guanine. • A=T C=G • 2 hydrogen bonds 3 hydrogen bonds Antiparallel and direction 2.7 DNA Replication, transcription and translation • Cells make a copy of their DNA during the S phase of their cell cycle. • Molecules needed for the process include enzymes and free nucleotides. • The first step of replication involves the separation of the double helix into two strands using the enzyme helicase. • Helicase separates the strands by breaking the hydrogen bonds between the bases. • Each strand is now used as a template to create two identical DNA strands. • The separation of the strands by helicase is sometimes referred to as unzipping. • Free nucleotides are added to the templates by DNA polymerase which bonds them together. • One strand replicates in the direction that the helicase is unzipping, while the other strand replicates in the opposite direction. • Called semi-conservative replication because each new DNA molecule is half original and half new. Protein Synthesis • DNA controls the proteins that are produced by the cell. • The sections of DNA that code for a certain protein are called genes. • Genes are specific codes for a specific protein • Transcription makes mRNA Transcription • Transcription begins with the DNA of one gene being unzipped by RNA Polymerase. • Only one of the strands will be used as a template – 3’ to 5’ in direction of unzipping • RNA Polymerase adds RNA nucleotides to the template. • The order of the bases in the mRNA will determine the order of the amino acids in the polypeptide chain created at the ribosome. • Every 3 bases is called a codon • These groups of three bases that code for a specific amino acid are called triplets. • Some codons don’t specify an amino acid so not all codons are triplets Translation • Summary of RNA: • mRNA – copied from DNA and codes for a polypeptide chain • rRNA – what ribosomes are made out of • tRNA – each type of tRNA transfers on of 20 amino acids to a ribosomes polypeptide chain. tRNA • mRNA will find a ribosome and align with it so that the first two codon triplets are inside the ribosome. • A specific tRNA with the anti codon that is complementary to the first mRNA codon attaches to the mRNA. • A second tRNA with the anticodon to the second codon attaches. • Now the two amino acids bond to each other forming a peptide bond • The first tRNA breaks loose from the amino acid chain which is being held by the second tRNA. • The ribosome moves down the mRNA chain to get to the next codon and the process repeats. • The last codon is a stop code telling the ribosome the polypeptide is finished. Polymerase Chain Reaction PCR • Developed in the 1970s • Allows DNA replication to be carried out in the lab. • Used in forensic investigations where there is only a small amount of DNA found. • Uses an enzyme from a heat loving bacteria called Taq polymerase. 2.8 Cellular Respiration C6H12O6 + 6O2 6CO2 + 6H2O + 36 ATP • Glucose, amino acids and fatty acids contain energy within their bonds. • Cells break down (metabolize) these molecules in a series of enzyme catalyzed reactions called cellular respiration. • Each time a covalent bond is broken, a small amount of energy is released. • The goal is to trap/store this released energy as ATP. Glucose is the molecule of choice but amino acids and fatty acids will also work. Glycolysis • Glycolysis is the first step. • Glucose enters the cells cytoplasm by diffusion. • A series of reactions breaks the 6 carbon glucose into two 3 carbon molecules called pyruvate. • This process uses 2 ATPs in the first step and creates 4 later for a net of 2 ATPs per glucose • • • • When ATP is used, it is changed into ADP When it is created, ADT converts to ATP Oxygen is not required for glycolysis Some organisms, called anaerobes, can survive on just these two ATPS per glucose so they don’t need oxygen to survive. • They do need to get rid of the pyruvate so they undergo fermentation. • Two types of fermentation, alcohol and lactic acid. • Alcohol fermentation (ex. Yeast) changes the 3 carbon pyruvates into a CO2 and a 2 carbon ethanol molecule. • Lactic acid fermentation changes the 3 carbon pyruvates into 3 carbon lactic acid molecules. • Reversible if oxygen shows up. Aerobic respiration • Begins with glycolysis and 2 ATPs being produced. • The pyruvates enter the mitochondria • Each 3 carbon pyruvate releases a CO2 and becomes a 2 carbon acetyl-CoA • Each 2 carbon acetyl-CoA enters into a series of reactions called the Kreb or citric acid cycle • Each Acetyl CoA releases two CO2 molecules • Each Acetyl CoA creates one ATP • Molecules are also created that go one to a final step where most of the ATP is formed. • Review: for each glucose entering anaerobic respiration, 2 ATPs are produced from glycolysis. • For each glucose entering aerobic respiration, 4 ATPs are produced, 2 from glycolysis and 2 from the Kreb cycle. Another 32 are produced in a final HL step 2.9 Photosynthesis 6CO2 + 6H2O C6H12O6 + 6O2 • Converts light energy into chemical energy. • The most common chemical produced by photosynthesis is glucose. • Plants use the pigment chlorophyll (green) to absorb light energy. • Chlorophyll is found in chloroplasts within leaves. • There are other pigments in leaves • Photosynthesis uses visible light from the electromagnetic spectrum. • Different pigments use different wavelengths. • Red and blue light are used the most, green is used the least. Green is reflected away • Photosynthesis occurs in two stages: • Light-dependent stage and light-independent Light-Dependent Reactions • Chlorophyll ( and other pigments) absorbs light energy and converts it to ATP. • Light energy is also used to cause a reaction called photolysis of water where water is split into hydrogen and oxygen. • The oxygen is released as a waste product. (Yea, we can breath) • The ATP and the hydrogen will be used later Light-Independent Reactions • ATP and Hydrogen are used as forms of chemical energy to combine CO2 and H2O into glucose. • Glucose is an organic molecule, where CO2 and H2O are inorganic. This is called fixation • So: Photosynthesis can be described as a series of reactions in which CO2 and H2O are fixed into glucose and O2 is produced as a waste product. Light-Dependent Reactions • The fixing of the CO2 and H2O require energy which is supplied by the ATP created during the light-dependent reactions. • Plants perform cellular respiration year round at a constant but low level. • Photosynthesis rates vary drastically, depending on intensity of light, air temp and CO2 levels. Rate of Photosynthesis • A direct way is to measure rate of CO2 usage or O2 production. • An indirect method involves measuring the biomass of the plant. • Light intensity: increasing light intensity will increase photosynthesis to a certain point where it will level off due to the enzymes being maxed out. • Increasing the CO2 levels increases the rate of photosynthesis to a certain point where it will level off due to the enzymes being maxed out. • Increasing temperature: As the temperature increases, the rate of photosynthesis increases to a point where it suddenly falls due to denaturing of the enzymes.