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Topic 2 Molecular Biology Biochemistry Introduction • Organic chemistry is the chemistry of _______ compounds. • Biochemistry is a branch of organic chemistry dealing with _________ ___________. • 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 __________ ___________ reactions that take place in an organism. • The four groups of molecules interact with each other to carry out the reactions of metabolism. • Example: _________ (Protein) helps glucose (carbohydrate) travel through the cell membrane (lipid) and get into the cell. The insulin molecule itself is created by ________ (nucleic acid) Organic Chemistry • Not all molecules that contain carbon are considered organic, such as ________ __________. • Carbohydrates, lipids, proteins and nucleic acids are all _______ and contain _________. • Life 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 _______ 4 electrons with other atoms. Each “sharing” forms a bond, so each carbon atom can form 4 covalent bonds. Common Atoms other than Carbon • • • • ____________ ____________ ____________ ____________ Building Blocks • • • • Carbohydrates – _________________ Lipids – ___________ and _____________ Proteins (polypeptides)– _____________ Nucleic acids - ______________ Carbohydrates Monosaccharides Disaccharides Polysaccharides Glucose (2) ________ Starch Galactose _________ Glycogen Fructose _________ Cellulose Ribose Chitin PROTEINS • • • • • Polypeptide Chains made from _____ ______ Some types of proteins ____________ ____________ ____________ Lipids • _____________ – Fat stored in adipose tissue • _______________ – Form bilayer in cell membrane • ___________ – 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 _________ 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 ____________ reactions and hydrolytic enzymes • Anabolism involves _____________ reactions Hydrolysis • Hydrolysis reactions break things apart and require a molecule of ________ to do so. • Example: Lactose + water = glucose + galactose Hydrolysis • Example: Triglyceride + 3 waters = Glycerol + 3 fatty acids. Condensation • Condensation reactions _________ smaller molecules to create larger ones, and give off __________ as a byproduct. • Creating __________ from amino acids • Creating triglycerides from _____________ and fatty acids • Creating di and polysaccharides from ___________________. 2.2 Water • Water is a good solvent – “solvent of life” • Any solution where water is the solvent is called an ___________ solution. • To understand the properties of water, you have to understand the ___________. Water molecular structure • Bonds between the oxygen and the two hydrogen atoms are _______ ________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 _________ end of one water is attracted to the _______ end of another water molecule. This attraction is called a hydrogen bond Cohesive property of water • Cohesion is when molecules of the _______ _________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 _______ in plants. Adhesive property of water • Adhesion is when a molecule is attracted to a __________ 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 ________, when it isn’t being pulled, it remains in place due to ________ 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 without changing __________ very much. • Water helps to stabilize our temperature. • Water also has a high heat of_____________, 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 ______ molecules. The vast majority of biological molecules are polar, including carbohydrates, proteins and nucleic acids. • Common aqueous solutions are __________, _________,________and _________. • Plants use water to transport material in _____ and ________. Animals use water in blood to transport materials in arteries and veins Hydrophilic and Hydrophobic • Polar molecules, such as water, are “water loving” or_____________. • Non-polar molecules are “water fearing” or hydrophobic. Hydrophobic molecules are usually made of large areas of only ________ and __________. ______ ______are hydrophobic. • ___________ can have areas that are hydrophobic and areas that are hydrophilic Solubility and Transport • Glucose: ______, very soluble in plasma • Amino acids: _____ in polarity but all soluble in plasma • Cholesterol and fats:________, low solubility, transported in plasma by blood __________ that have a polar area and a non-polar area. • Oxygen: __________, low solubility. Carried in plasma by hemoglobin of red blood cells. • Salt: ________, very soluble in plasma 2.3 Carbohydrates and Lipids • Most are very large molecules (___________) made of smaller repeating units (__________). • The monomers of carbohydrates are called ________________. • These monosaccharides can be combined by __________ _____________ reactions to form larger molecules. Monosaccharides • • • • • Classified by how many _______ they contain. Most common are: ________ (3) carbons – formula C3H6O3 _________ (5) carbons – formula C5H10O5 _________ (6) carbons – formula C6H12O6 • Notice the pattern for monosaccharides • _____________ Monosaccharide Condensation Reaction • • • • • • Two monosaccharides become a disaccharide. Two glucose = __________ Glucose + fructose = __________ Glucose + galactose = __________ A ______ 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 _______ together creates several polysaccharides. • _________: plant cell walls, rigidity/support • ________: Plants store glucose, product of photosynthesis, as starch, in roots and chlotoplasts. • __________: Animals store excess glucose as glycogen, in liver and muscle tissue. Fatty Acids • All fatty acids have a ________ group (-COOH) at one end, and a ________ group (CH3-) at the other end. • In between, what makes them different is a chain of carbons and ___________ that is usually 11-23 carbons long. Saturated Fatty Acids • Called saturated because all of the carbons have as many __________ as possible, saturated with hydrogens. • Means there are no ______ _____in the chain • Mostly _______ fat, _____ at room temp, straight chains. Monounsaturated fatty acids • Contain _____ double bond • Double bond loses two hydrogen atoms, so no longer saturated, also causes the chain to ______ at the bond. Polyunsaturated fatty acids • Have at least _____ double bonds. • Typically come from ______ (olive oil example) • Usually ________ at room temp. • Very crooked, curves chains due to the double bonds. • Double bonds are usually____, not ______ Cis vs Trans Hydrogenation • Food processors add hydrogen to remove some or all of the double bonds. • This __________ 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 _________ hydrogenated. Omega-3 fatty acids • The last carbon in a fatty acid chain, the one in the methyl group, is called the ______ 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. • ______ are a good source Omega-3 Triglycerides • Triglycerides are basically ____ in animal cells and _____ in plant cells. • The are made of one (1) _______ molecule with _______ fatty acid chains attached by condensation reactions. Energy storage • Humans and many other organisms store energy by using glucose to make_______, and making triglycerides to store energy as______. • Triglycerides can be broken down (hydrolysis) and used in the reactions of cellular respiration to make ____, just as glucose is. • Triglycerides have ______ 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 ________. • Uses both _______ and _________. • Three methods: • (1) __________ using weight and height • (2) Using a graph called a ____________ • (3) Using an on line ___________ BMI • Uses terms _____________, normal weight, overweight, or ________. • Should not be used with children or ___________ women. • ________ formula: weight (kg)/ height (m)2 • ________ form: weight (lbs)/ height (in)2 x 703 BMI 2.4 Proteins • Cells use ___ amino acids to create polypeptide chains. • Controlled by DNA, with each different chain controlled by a specific piece of DNA called a ______. • Different types of cells use different genes to make the _________ that are specific to them. • Humans have between __________ and _________ 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 ________ group. • In ________ solutions (water) the OH of the acid group will lose a H+ to the amine group. • Polypeptide chains are made at the ____________ using condensation reactions. • The sequence of the amino acids is determined by the _____ controlling the process. Levels of polypept/protein structure • Each polypeptide chain has its own 3D shape which determines it’s function. • Level 1 (primary) – ______ of the amino acids • Level 2 (secondary) – repeating pattern, either _____ or ______ sheet. Example is spider silk • Caused by _________ bonding within the main chain, not the R groups. • Usually structural • Level 3 (tertiary) ________ structure. Example: enzymes. Bonding involving the R groups • Level 4 (quaternary) 2 or more polypeptide chains bonded together. Example: _________. • A good example of why not all polypeptide chains are proteins. • Everyone has unique DNA (________), unique proteins (___________) Denaturing of proteins • The bonds that create secondary, tertiary and quaternary structure are susceptible to change due to _____ and ___, which can change the structure, therefor the _________ 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 a type of _______ 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 _______. • Within that shape is a certain area that matches a specific molecule. • The area is the ______ ____of the enzyme, the molecule it matches is called the ________. • A good analogy is lock and key. • The lock is the enzymes active site and the key is the substrate. • A certain minimum _________________is needed by the substrate when it enters the active site to supply the energy needed for the reaction. • This is called ___________ ________. • Enzymes ________ 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 __________ 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 • ______________ are the building blocks of nucleic acids • There are three types of nucleic acids, adenosine triphosphate (____), deoxyribonucleic acid (_____), and ribonucleic acid _____) • We are going to focus on DNA and RNA, the ____________ material of the cell. DNA is a polymer • DNA and RNA are __________ with the ___________ being nucleotides • Each nucleotide consists of three parts: a _________ (5 carbon) sugar, a __________ group and a single nitrogenous ______. • _________ ______ at specific locations create the appropriate structure. Nucleotide structure Nucleotide structure • The bond between the __________ group and sugar, and the bond between _______ and base are ____________ bonds. Nitrogenous bases • • • • • • The bases used in nucleotides are DNA RNA ________ _________ ________ _________ ________ _________ ________ _________ Pentose Sugar Making Polymers • DNA and RNA _________ (nucleotides) bond together to form DNA and RNA ___________. • The reaction bonding the nucleotides together is a _______________ reaction. Strands • RNA is composed of a _______ strand of nucleotides while DNA is _____ strands connected at the bases by ________ bonding • Complementary base pairing involves Adenine always attached to _________ and Cytosine always attached to ____________. • 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 _____phase of their cell cycle. • Molecules needed for the process include enzymes and free _______________ • The first step of replication involves the separation of the double helix into two strands using the enzyme ____________. • Helicase separates the strands by breaking the ___________ ______between the bases. • Each strand is now used as a __________ to create two identical DNA strands. • The separation of the strands by helicase is sometimes referred to as_____________. • Free nucleotides are added to the templates by ___ _________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 _____________________ replication because each new DNA molecule is half original and half new. Protein Synthesis • DNA controls the ___________ that are produced by the cell. • The sections of DNA that code for a certain protein are called _________. • Genes are specific codes for a specific _______ • Transcription makes __________ Transcription • Transcription begins with the DNA of one gene being unzipped by ____ ___________. • Only one of the strands will be used as a template – _________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 ________ _____ in the polypeptide chain created at the ribosome. • Every 3 bases is called a _______ • These groups of three bases that code for a specific amino acid are called _________. • 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 ____________ 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 _____ _________are inside the ribosome. • A specific tRNA with the ____ ________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 __________ bond • The first tRNA breaks loose from the amino acid chain which is being held by the ________________. • The ribosome moves down the mRNA chain to get to the next codon and the process repeats. • The last codon is a _____ _____telling the ribosome the polypeptide is finished. Polymerase Chain Reaction PCR • Developed in the ________ • Allows DNA replication to be carried out in the ____. • Used in ___________ investigations where there is only a small amount of DNA found. • Uses an enzyme from a heat loving bacteria called ____ ______________. 2.8 Cellular Respiration C6H12O6 + 6O2 6CO2 + 6H2O + 36 ATP • ________, ________ and fatty acids contain energy within their bonds. • Cells break down (metabolize) these molecules in a series of _________ catalyzed reactions called cellular respiration. • Each time a covalent bond is broken, a small amount of __________ is released. • The goal is to trap/store this released energy as ____. 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 __________ by diffusion. • A series of reactions breaks the 6 carbon glucose into two 3 carbon molecules called ___________. • This process uses ___ ATPs in the first step and creates ____ later for a net of 2 ATPs per glucose • • • • When ATP is used, it is changed into _____ When it is created, ADT converts to ATP _________ is not required for glycolysis Some organisms, called __________, 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 ______________. • Two types of fermentation, ________ and __________. • Alcohol fermentation (ex. ________) changes the 3 carbon pyruvates into a CO2 and a 2 carbon _________ molecule. • Lactic acid fermentation changes the 3 carbon pyruvates into 3 carbon lactic acid molecules. • ______________ if oxygen shows up. Aerobic respiration • Begins with glycolysis and 2 ATPs being produced. • The pyruvates enter the ______________ • Each 3 carbon pyruvate releases a CO2 and becomes a 2 carbon _____________ • Each 2 carbon acetyl-CoA enters into a series of reactions called the _______ or citric acid cycle • Each Acetyl CoA releases two _____ molecules • Each Acetyl CoA creates one ______ • Molecules are also created that go on 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 ___ are produced in a final HL step 2.9 Photosynthesis 6CO2 + 6H2O C6H12O6 + 6O2 • Converts ______ energy into chemical energy. • The most common chemical produced by photosynthesis is _________. • Plants use the pigment ___________ (green) to absorb light energy. • Chlorophyll is found in ____________ within leaves. • There are other ___________ in leaves • Photosynthesis uses _________ light from the electromagnetic spectrum. • Different pigments use different ___________. • ____ and _____ light are used the most, green is used the least. Green is reflected away • Photosynthesis occurs in two stages: • ______________ stage and _______________ Light-Dependent Reactions • Chlorophyll ( and other pigments) absorbs light energy and converts it to ___. • Light energy is also used to cause a reaction called __________ of water where water is split into hydrogen and oxygen. • The oxygen is released as a ________ product. (Yea, we can breath) • The ____ and the _____________ will be used later 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 __________at a constant but low level. • Photosynthesis rates vary drastically, depending on ____________, _________and CO2 levels. Rate of Photosynthesis • A ________ way is to measure rate of CO2 usage or O2 production. • An indirect method involves measuring the ____________ of the plant. • Light intensity: increasing light intensity will increase photosynthesis to a certain point where it will ____________due to the enzymes being maxed out. • Increasing the CO2 levels _________ 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 _____________ of the enzymes.