BIO 172 1st Edition Lecture 4Outline of Last Lecture I. Cells and Chemical BondsII. Properties of WaterIII. Functional GroupsIV. Proteins and Amino AcidsOutline of Current Lecture I. Four Levels of Protein StructureII. Macromolecules: Proteins and Nucleic AcidsIII. DNA ReplicationCurrent LectureFour Levels of Protein Structure: Primary Structure a linear sequence of amino acids held together by peptide (covalent) bonds. Their sequence is determined by genetic instructions.How many amino acids? 8. Color coded (below):Where is the alpha carbon? The one directly after the amino group, farthest left C.Where is the peptide bond? Between the C next to the alpha carbon, and N (color coded blue). There are 7 peptide bonds total.These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.AminogroupOne of the amino acids inthis polypeptidePolypeptides flex because groupson either side of each peptide bondcan rotate about their single bondsCarboxylgroupPeptidebondSickle cell anemia is an example of when just one Amino Acid is substituted for another (the protein or hemoglobin is altered to make the cells an abnormal shape). Change of the amino acid “Glu” to “Val.” This alteration changes how the red blood cell looks. This alters the way theyclot, and it a drastic problem where people end up losing a lot of blood.The N term (far left) is an amino group. The first black circle is the Alpha Carbon. Each Green circle is an R group. To find out how many Amino Acid are in this polypeptide, count the number of R groups. There are 9 amino acids in this primary structure.Secondary Structure: Hydrogen bonds between Carbon and Oxygen on one amino acid, and between the Nitrogen and Hydrogen on another amino acid form a secondary structure. The Hydrogen bonds make the amino acids fold. Then the protein can take shape.A Polypeptide must bend to allow Hydrogen bonding. By bending, there can be Alpha- Helices or Beta-Pleated Sheets.Secondary structure is dependent on Primary structure. Some amino acids are more likely to be involved in Alpha helices, and others more likely to form Beta-Pleated sheets.The large number of Hydrogen bonds in a secondary protein structure adds stability.(Beta-Pleated sheet)(alpha-helix) (Above) the dotted lines are Hydrogen bonds. They can either bond and generate coiled (alpha) regions, or folded (beta) regions.Tertiary Structure: One single polypeptide chain with one or more secondary structures.The one polypeptide chain and (possible) multiple secondary structures are held together by interactions between atoms in the R group. Tertiary structures have a 3-D shape.Two hydrophobic side chains interact, which helps stabilize the ionic structure- where Negative and Positive charges come together to stabilize the protein. Peptide (covalent)bonds, along with hydrogen bonds stabilize the tertiary structure protein. Below are examples of what tertiary structures can look like- multiple diverse structures.Composed of: alpha helices. Beta-pleated sheets. Disulfide bonds.CH2OHOCOHCH2CH2NH3+C-OCH2OCH2SSCH2CHCHCH3CH3H3CH3CHydrophobic interactions and van der Waalsinteractions PolypeptidebackboneHydrogenbondIonic bondDisulfide bridgeIf you were to boil this protein- all the non-covalent bonds would break. (High temperatures would disrupt hydrphobic, hydrogen, and ionic bonds) the Peptide bond and disulfide bonds would stay because they are strong!But, boiling the protein will cause it to unfold and not be able to function. A protein too heated up falls apart and cannot function.C-H bonds are HYDROPHOBIC (van der waals) bonds with other things. The Hydrogen in a C-H bond will not form a Hydrogen bond with other oxygens. Learn to recognize the side chains.Quaternary Structure: shape of a complex of multiple polypeptide chains; held together by Covalent, Ionic, Hydrogen, and/or Hydrophobic (van der waals) interactions.Two polypeptides folded into their Tertiary structure come together and interact- forming a quaternary! A) 3 polypeptide chains came together. B) More than one polypeptide folds into tertiary, and more than one interaction to form a quaternary protein.This table about the four types of protein structure is a good review:Proteins can take on many shapes:In size and shape, proteins are the most diverse class of macromolecules known. The structure of a protein helps it carry out its function.(a) Homodimer: two proteins fold into their tertiary structure and come together.(b) Homotetramer: 4 polypeptides came together to be quaternary.Macromolecules: Nucleotidesyellow: Phosphate group (5’ Carbon)Hydroxyl (O-H) on the 2’ carbon and 3’ carbon.Ribose Sugar.RNAYellow: phosphate group off 5’ carbon.DNA3’ Carbon has an O-H, but 2’ carbon has only H.Deoxyribose sugar.Bases in RNA and DNA: Either Pyrimidine or Purine.Pyrimidine: Thymine, Cytosine, Uracil.Purine: Adenine, Guanine.Uracil is not in DNA, instead, Uracil is in RNA. Thymine is, and it bonds with Adenine. Then Cytosine and Guanine bond together.In a nucleic acid, each base is attached to either a Ribose or a Deoxyribose. DNA as Genetic Material:Griffith’s Experiment.The rough colonies are NON virulent. Smooth colonies are virulent and can cause disease. A mouse dies from the smooth colonies- but then when those virulent cells are killed with heat, they cannot kill the mouse.Mix of heat-killed smooth cells with the rough cells- the mouse dies! That means the heat-killed cells have a characteristic that was transferred to the rough cells, which caused the rough cells to become smooth cells and then kill the mouse. WHAT could the characteristic be that makes the smooth colonies take over the rough?WHAT is the transforming factor that causes genes to multiply- protein, RNA, or DNA?Avery, McCarty, Macleod Experiment: They isolated the heat-killed smooth cells, and eliminated Lipids and Carbohydrate macromolecules.Used Protase to eliminate proteins. (RNA and DNA remain to possibly pass on genes).Used Rnase to eliminate RNA. (Proteins and DNA remain to possibly pass on genes).Used Dnase to eliminate DNA. (Proteins and RNA remain to possibly pass on genes).Results in the chart above: Treatment with Dnase stopped the gene transfers. Therefore DNA is required for heat-killed smooth virulent cells to transform the non-virulent cells and make the mouse die. Affirmed: take away protein or RNA, the