Weeks 1 and 2 notes
Weeks 1 and 2 notes BIO 160
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This 8 page Class Notes was uploaded by Sully Smoak on Friday September 4, 2015. The Class Notes belongs to BIO 160 at University of Tennessee - Knoxville taught by Purnima D Pinnaduwage (P) in Fall 2015. Since its upload, it has received 186 views. For similar materials see Diversity and History of Life in Biological Sciences at University of Tennessee - Knoxville.
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Can you just teach this course please? lol :)
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Date Created: 09/04/15
81915 Five Big Ideas of Biology FBl s 1 Evolution Organisms and their cellular characteristics have changed through time by selective and nonselective evolutionary processes 2 Structure and Function All living systems have smaller structural parts that impact how they func on 3 Information Flow and Storage DNA holds the information code of life How organisms use it and transfer it is the foundation of life 4 Transformation of Energy and Matter Everything living uses attains and expends matter and energy for normal cellular functioning 5 Systems Living systems are connected They interact with and influence each other in many ways You should know these and be able to relate them to what you learn in class Where do cells come from Cell theory 1All organisms are made of cells 2All cells come from preexisting cells Unicellular organisms are single cells that carry out all of the functions of life Multicellular organisms are made of many cells that specialize to perform different functions Phylogenetic trees show how species are related through evolution All living things originate from a single common ancestor We can build these trees by looking at how RNA sequences in different species are similar and different According to morphology formstructure of organisms there are 2 broad groupings of life Prokaryotes No nuclear membrane Eukaryotes have a nuclear bound membrane The theory is that Eukaryotic cells developed 15 billion years ago when cells engulfed other cells but did not digest them and those cells eventually became mitochondria and chloroplasts This is called the endosymbiosis theory 82415 In order to understand polarity which is a big theme in biology and biochemistry you need to understand Electronegativity EN 1 EN depends on the number of protons and the distance between protons and the valence shell amount of shielding 2 The more electronegative atoms are EC and N If these are present in a macromolecule it s pretty likely to be polar 3 C S and H are not as electronegative and will not result in polar bonds 4 The order of electronegativity for these atoms is OgtNgtCSH Polar molecules are hydrophilic meaning they like water since water is polar Nonpolar molecules are hydrophobic so they don t interact with water molecules pH The more H ions in water the lower the pH the higher the acidity The less H ions in water the higher the pH the solution is more basic Organic Molecules Certain functional groups make organic molecules behave in certain ways Functional groups are Amino and Carboxyl groups carbonyl group hydroxyl group phosphate group sulfhydryl group 82615 PROTEINS Building blocks of proteins are amino acids A Amino acids structure depends on their side chains the R groups B They all have an Amino group H3N on one end connected to a C in the middle followed by the carboxyl group COO on the latter end They all follow this structure what differs is the R group that is also attached to the middle C Here s my drawing of an amino acid I m not sure if I can legally sell pictures from her lecture or the textbook sorry C The side chains are what distinguish the amino acids from one another D R groups can be in one of four categories acidic basic uncharged polar non polar How to know what type of amino acid you re dealing with A If the side chain has a negative charge it s acidic because it would have lost and H making it have a negative charge B If side chain has positive charge it s basic because it has lost an OH making it have a positive charge C If side chain is uncharged does it have an O If yes it s uncharged polar If no It s just non polar If you need some examples of these there are plenty in the book on page 43 or in her lecture notes entitled ChO3Proteins Amino acids come together in a chain to form proteins They come together through peptide bonds forming when the Amino group of one Amino acid bonds with the Carboxyl group of an adjacent Amino acid When this happens the Amino group loses two of its H atoms and the Carboxyl group loses one of its 0 atoms meaning H20 is formed Because H20 leaves the system it is called a condensation reaction Another picture 0 Protein StructureVery important 0 Proteins vary greatly in size shape and other aspects of structure and this is important because Protein structure determines its function 0 Proteins can serve diverse functions because they are 0 diverse in size and shape 0 and are diverse in the chemical properties of their R side chians 0 Different protein activitiesfunctions are dependent on their shape Types of proteins include 0 TATA box binding proteins that are saddle shaped and bind DNA for transport 0 Porins that are donut shaped and form pores 0 Trypsin which has a globular shape and binds substrates 83115 Proteins have 4 basic levels of structure 1 Primary structure Unique sequence of Amino Acids that make up the protein It s just the order of building blocks that form the whole structure A single change in the sequence of amino acids will radically change the protein Sickle cell syndrome is caused by one difference in the amino acid chain 2 Secondary structure Formed by Hydrogen bonds between carbonyl group of one amino acid and the amino group of another Hydrogen bonding between sections of the same backbone result in alpha helices and beta pleated sheets Alpha helices are where the protein forms a spiral Beta pleated sheets is where the protein folds back onto itself 3 Tertiary structure Protein s tertiary structure is caused by the interactions of its amino acids R groups These include I Hbonds I Hydrophobic interactions I Van der Waals interactions I covalent disulfide bonds I and ionic bonds 4 Quaternary structure formed when two or more distinct polypeptide units come together 1 When two distinct independent polypeptides come together to form a single protein that develops the quaternary structure Protein folding is spontaneous since folded proteins are more stable Denatured proteins cannot perform their normal functions Sometimes proteins called molecular chaperones help proteins fold correctly in cells The folding is often regulated in this way Misfolding of proteins can be infectious as the proteins cannot serve their intended purpose but instead do something completely different Improperly folded forms of normal proteins are prions Mad cow disease is caused by a prion Protein function One of the most fundamental protein functions is catalysis proteins called enzymes often aid chemical reactions and processes in the cell so that they can be carried out in a timeefficient manner Enzymes perform best at certain pH levels and temperatures Nucleic Acids Nucleic acids form when nucleotides come together They do this through a phosphodiester linkage These linkages form through condensation reactions like peptide bonds Primary structure of nucleic acids is determined by the sequence of nucleotides like primary structure of proteins is dependent on sequence of amino acids The phosphodiester linkages form between the phosphates and sugars in the backbone of the molecule The links form between the 5 phosphate of one nucleotide and the 3 hydroxyl of the next nucleotide One end of the nucleotide sequence will have an unlinked 5 phosphate and the other end will have an unlinked 3 hydroxyl By convention nucleotide sequences are written in the direction of 5 gt3 9215 Differences between Proteins and Nucleic Acids Protein Polypeptide chain of Amino Acids linked by peptide bonds Starts with a NH2 terminus and it ends in a COOH terminus end Nucleic Acid Phosphodiester bonds keep the backbone which is composed of sugars and phosphate groups together The monomer of nucleic acids is nucleotides Sequences of nucleotides are written from their 5 phosphate end and with their 3 hydroxyl end If the carbons on a nucleotide contain a prime signal these carbons are present on the sugar If they have no prime they are found on the nitrogenous base Nucleic acid backbone has a negative charge because of the Phosphate groups meaning that the proteins that bind them should be basic at the binding site as basic amino acids have a positive charge Purines A and C pair with pyrimidines T and G Purines are larger and contain two rings while pyrimidines only have one ring If a nucleic acid is made up of 20 T what of it is G if it s 20 T it s also 20 A meaning there s 60 left that must be made up of G and C so they should each be 30 of the nucleic acid You need to know how to write the complement to an amino acid sequence Remember to write it from 5 gt3 DNA is held in the nucleus in eukaryotes the nucleus contains the cell s chromosomes it has a double membrane with pores to allow transfer across the membrane DNA of prokaryotes is coiled Eukaryotic DNA is linear Nuclear membrane developed when the plasma membrane folded in and surround the genetic material in the nucleus DNA replication has 2 steps 1 separate the double helix 2 the two separate strands form H bonds with complementary bases then those complements do the same to form another of the templates RNA s primary structure is the sugarPhosphate backbone Instead of Thymine as a nitrogenous base RNA has Uracil RNA s sugar is ribose not deoxyribose like in DNA The presence of the OH on ribose makes in more reactive and less stable than DNA RNA s secondary structure comes from complementary base pairing but within the same strand of RNA lt folks and forms hairpins with antiparallel RNA on the other side of the fold DNA has no tertiary structure but RNA has folds with distinctive 3D shapes Biological info flows as such DNA gtRNA gtProtein gtsome structure or function RNA can be a catalysts Ribozymes are enzymelike RNAs RNA has structural and chemical complexity it can store info and catalyze so it may be the origin of life
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