JANUARY 20 ● Compare and contrast the three domains of life. ○ Eukarya- eukaryotic cells. unicellular and multicellular. Contain a nucleus and internal complexities such as organelles ○ Archaea- prokaryotic cells. archaea share similar structural features with bacteria and share similar biochemical features with eukaryotes, but are neither. ○ Bacteria- prokaryotic cells. the character that separates bacteria and archaea is that bacterial have peptidoglycan in their cell walls. ● Describe the use of sequence data to determine evolutionary relationships. ○ Woese. Use rRNA to compare organisms and determine their evolutionary ancestry because rRNA ■ All organisms have rRNA ■ rRNA serves the same function in every organism ■ rRNA sequences are largely the same, meaning small changes in sequence produce a large change in evolution ● Explain why cells remain in a narrow size range within the scale of life. ○ SA to V ratio. Cannot have too much volume because there would not be enough SA to transport raw materials into the cell and waste out of the cell. ● List the functions of a plasma membrane. ○ Lets things in and out selectively. Creates an internal environment that is separate from the extracellular matrix. Does not let in toxins to the cell. ● Describe the general features of a bacterial cell. ○ Nucleoid ○ Ribosomes ○ Photosynthetic internal membrane ○ Organelles ○ Cytoskeleton ○ Plasma membrane ○ Cell wall ○ Flagella ○ fimbre JANUARY 23● Identify the major organelles in an animal cell and list their functions. ○ Nucleus - information center. Genetic information housed, copied, expressed (transcription) ■ Nuclear envelope - 2 membranes. Have numerous small pores ■ Nucleolus - produce ribosomal subunits structure responsible for synthesizing and assembling some of the RNA and protein components to form the ribosomes ■ Chromosomes - contain DNA. ● Chromatin - dispersed DNA as DNA-protein fibers. In this stage for most of the time other than when dividing ○ Rough ER - studded with ribosomes. Synthesize peptides and secretions. continuous with outside of nuclear envelope. ○ Ribosomes - protein synthesis (not really organelle). Machines. Protein synthesis. Polyribosomes are many ribosomes that are all working on one RNA molecules to produce protein ○ Peroxisome - makes peroxide as byproduct (detoxes it too) ○ Smooth ER - synthesis of lipids and steroids. Detoxes some drugs continuous with rough ER. detox chemicals. Phospholipid layer synthesis ○ Lysosomes - stores hydrolases (enzymes that digest biological molecules like proteins, lipids, carbs. Synthesized on rough ER ○ Mitochondria - powerhouse of the cell. Has its own DNA and membranes (probably was its own cell). Energy production through oxidation phosphorylation ○ Cytoskeletal elements ■ Microtubules. Microfilaments, and an intermediate filament ■ Tubules > intermediate > filaments ○ Plasma membrane - separates cell from extracellular matrix. Lipid bilayer ○ Golgi apparatus - processing and packaging secretory proteins and synthesizes complex polysaccharides. Post office. Proteins sent out. Approach from cis side and leave from trans side○ Centrioles ○ Vacuoles - temporary storage or transport ○ PLANT CELLS - CHLOROPLASTS. Photosynthesis. ■ Thylakoids - membranes within the chloroplast ■ Grana - stacks of thylakoids ■ Also have central vacuoles - storage. Mainly maintains pressure of the cell. ● Compare and contrast condensation and hydrolysis reactions. ○ Condensation reaction - monomer in, water out
○ Hydrolysis - water in, monomer out ● List the features shared by all carbohydrates. ○ Monosaccharides make up carbohydrates through condensation reaction ○ General formula of carb ■ Cn(H2O)n with H-C-OH backbone ○ Convention of carbohydrates ■ Start numbering closest to carboxyl group in straight chain and furthest right in rings ● List the biologically relevant monosaccharides and provide an example of each. ○ Aldose sugar - has aldehyde group (@ carbon 1) ■ When you circularize aldose, has 6 membered ring (one is O). ○ Ketose sugar - has a ketone group (@ carbon 2) ■ When you circularize, you get a 5 membered ring (one is O ○ Triose ■ Glyceraldehyde (based on glycerol), dihydroxyacetone ○ Pentose■ Ribose. Can circularize in alpha or beta ○ Hexose
■ Glucose, galactose, and fructose (ketose) (all isomers) ■ Circularization ● Alpha glucose (H is above) and beta glucose (H is below) ○ Isomers: have the same chemical formula, but the arrangement is different ● Explain the difference between aldose sugars and ketose sugars. ○ Aldose sugars have an aldehyde group and a ketose sugar has a ketone group. JANUARY 25 ● Describe the formation of a glycosidic linkage and classify it in the most specific terminology available. ○ The formation of a glycosidic linkage is created during a dehydration reaction and is between two monosaccharides to form a polysaccharide (carbohydrate) ○ To name: look at carbons that are bonded together and the alpha/beta of the left sugar. ● Disaccharides that we need to know: ○ Maltose - 2 glucose monomers connected with an alpha bond ○ Cellobiose - 2 glucose monomers connected with a beta bond ○ Lactose - galactose and glucose ○ Sucrose - alpha glucose and alpha fructose ● Describe the type of monomer, the type of linkage, the branching (if any), and the major functions of the following polysaccharides: ○ Starch■ Found in seeds, fruits, tubers, roots, and stems or plants, energy storage ■ Helical, unbranched or loosely branched polymers of glucose ■ Alpha-1,4-glycosidic linkages link monomers ■ Alpha-1,6-glycosidic linkages link branches ○ Glycogen ■ Found in muscle and liver cells of animals, energy storage (like starch to plants) ■ Helical, highly branched polymers of glucose ■ Monomers linked by alpha-1,4-glycosidic linkages and branches linked with alpha-1,6-glycosidic linkages ○ Cellulose ■ Most abundant compound on earth ■ Found in plant cell walls ■ Linear, unbranched polymer of glucose (beta-1,4-glycosidic linkages) ■ Unbranched cellulose is called amylose and branched helices are amylopectin ● Provide examples of the functions of carbohydrates in cells. ○ Energy sources, structural roles (exoskeletons and cell walls), cell recognition and identification. Will have oligosaccharides on outside of cells.
JANUARY 27 ● Describe the general structure of an amino acid. ○ 20 different amino acids
○ All amino acids have an H, an NH2 (amino group), a COOH (carboxyl group), and a distinctive R group (side chain) ○ In neutral solution, the COOH is an acid and the NH2 is a base ● Explain the formation of a peptide linkage. ○ Dehydration reaction ○ A peptide bond forms when the carboxyl group of one amino acid reacts with the amino group of a second amino acid ○ The alpha C is in between the carboxyl and amino group ● Compare and contrast the classes of amino acids and the consequence of being in a given class. ○ Nonpolar - polarity affects solubility ○ Polar - polarity affects solubility ○ Hydrophobic - when an amino acid is nonpolar, this means that the side chains are hydrophobic and will not react with water ○ Hydrophilic - when an amino acid is polar, this means that the side chain is hydrophilic and will react with water ○ Charged - when a side chain has either gained or lost an e ■ Negative = acidic ■ Positive = basic ○ Uncharged - if the atom is uncharged, then you need to ask if it has an O because if it does, then the O is electronegative and it will form polar covalent bonds ● List the levels of protein organization and identify the stabilizing forces at each level. ○ 1° - the linear sequence of amino acids that are connected by peptide bonds ○ 2° - structure stabilized by H bonds between the peptide backbone ■ Alpha helices and beta pleated sheets○ 3° - the 3D structure of a single polypeptide ■ H bonding ● In the middle with hydrophobic bonds ■ Hydrophobic interactions ● In the middle with H bonds ● Hydrophobic (nonpolar) side chains interact with water around the molecule and want to move to the inside of the protein ■ Van der waals ● Weakest noncovalent ● Collectively very stable, but one is very weak ■ Ionic bonding ● Most stable (noncovalent) ● Interactions between basic (+) and acidic (-) amino acids ■ Covalent bonding ● Most stable (biologically speaking) because covalent bond need an enzyme and a reaction to break them. ● Disulfide is strongest (cysteine-cysteine) ○ 4° - the 3D structure of proteins that are composed
of more than 1 polypeptide chain ○ JANUARY 30 ● Explain the process of protein denaturation and renaturation, including the use of chaperones when necessary. ○ Proteins are denatured when exposed to things that will break their H and disulfide bonds. When the exposure ends, the protein will renature.■ Can be denatured by: temperature, pH, interactions with other molecules, and modifications to original structure ○ Some proteins cannot fold on their own, so they need molecular chaperones. These chaperones help the proteins fold correctly. ○ Prions - misfolded proteins that cause other proteins to fold incorrectly ■ Spongibrain ● Compare and contrast anabolic and catabolic reactions. ○ Anabolic - create things ○ Catabolic - breaking down of things ● Categorize reactions in terms of energy transfer and change in free energy. ○ Spontaneous chemical reactions run in the direction that lowers the free energy of the system. Exergonic reactions are spontaneous and release energy. Endergonic reactions are nonspontaneous and require input of energy to proceed. ● Explain the energy of activation of a reaction and how it is decreased in the presence of enzyme. ○ Energy of activation is the energy it takes to strain the chemical bonds in substrates so they can achieve the transition state ○ The more unstable the transition state, the higher the activation energy and the less likely a reaction is to proceed ○ Enzymes decrease the activation energy because the interactions between the amino acid R groups at the active site stabilize the transition state and thus lowers the activation energy required for the reaction to proceed. ● Describe the conditions that affect enzyme activity. ○ When substrate concentrations are low, the speed of an enzyme-catalyzed reaction increases in a steep, linear fashion ○ At intermediate substrate concentrations, the increase in speed begins to slow. ○ At high substrate concentration, the reaction rate plateaus at the maximum speed ○ The speed of the reaction eventually plateaus because, even if there are a lot of substrates, all of the enzymes are busy, so it does not matter how concentrated the substrates are. ● Compare and contrast irreversible, competitive, and noncompetitive enzyme inhibition.○ Reversible - molecules bind to the enzyme covalently in order to activate it or deactivate it. This does not modify the enzyme’s primary structure ■ Competitive inhibition - the regulatory molecule binds to the enzyme’s active site in order to block substrates. ■ Allosteric regulation - the regulatory molecule binds somewhere other than the active site and changes the shape of the enzyme. This change makes the active site either available or unavailable. ○ Irreversible change - when part of the enzyme’s primary structure is cleaved from the rest of the enzymeJANUARY 20 ● Cell theory ○ Cells are the most basic component of life ○ All cells come from preexisting cells ○ All organisms are made of cells ● Morphology - form science (prokaryotic or eukaryotic) ● Phylogeny - evolutionary history ● Three domains of life ○ Eukarya ■ Eukaryotic ■ Algae, plants, animals, fungi ○ Bacteria ■ Prokaryotic ■ Ribosomes ■ Nucleoid ○ Archaea ■ Prokaryotic ■ Ribosomes ■ Nucleoid ○ Some photosynthetic species of prokaryotes have internal membrane complexes ○ Eukarya and Archaea are more closely related even though they are not both prokaryotes or eukaryotes. ○ Both eukaryotic and prokaryotic cells are packed with dynamic, highly integrated structures ● Prokaryotic cells structures ○ Nucleoid - location and structural organization of circular chromosome. Is not separated from the rest of the cell by a membrane ■ Chromosome - circular in bacterial cells. Contains large amounts of DNA (contains genes) surrounded by proteins (structural support) ■ Some have organelles - a membrane bound compartment inside the cell that contains enzymes or structures specialized for a particular function. ■ Cytoskeleton - protein fibers that give the cell shape and support. ■ Plasma membrane - contains phospholipid bilayer. Creates barrier that divides the internal environment of the cell and the extracellular matrix. The proteins that span the phospholipid bilayer and the membrane proteins do not allow toxic materials to enter the cell. ■ Cell wall - the stiff outer layer of the cell that helps keep its shape. Bacterial and archaeal cell walls are tough layers that surround the plasma membrane. ● Glycolipids - lipids that contain carbohydrate groups ■ Flagella and fimbre - ● Flagella are made of a long string of proteins that propel the cell ● Fimbre are needle like projections that extend from the surface of the cell and let it attach to other things ● Carl Woese ○ Analyzed rRNA to compare organisms ○ Why did he use rRNA? ■ rRNA can change during evolution ■ rRNA performs the same function in all organisms, but the sequence is not the same in all organisms. Which means that if a sequence is changed a little, then the two organisms are closely related ● What is the difference between prokaryotic and eukaryotic cells?
Bacteria and archaea
Location of DNA
In nucleoid (not membrane bound). Plasmids also common
Inside nucleus (membrane bound). Plasmids extremely rare
Internal membranes and organelles
Extensive internal membranes are only found in photosynthetic species. Limited organelles
Large number of organelles and many types.
Limited compared to eukaryotes
Extensive and usually found throughout the whole cell
● Explain how triglycerides serve as energy storage molecules?
● What is the difference between prokaryotic and eukaryotic cells?
○ Why did he use rRNA?
Don't forget about the age old question of when considering the differential costs versus total costs approach, the ______.
If you want to learn more check out the laetoli footprint trail is associated with which hominin species?
Don't forget about the age old question of blood type alleles
We also discuss several other topics like fau blackboard
We also discuss several other topics like uiuc hdfs
Don't forget about the age old question of alternate forms of the same gene
● Prokaryotic genome ○ Compact genomes - linear relationship between genome size and gene number (does not work for eukaryotic cells) ○ Correlation between size of genome and metabolic capabilities ○ Most genes found in one prokaryotic species are not widely shared. ○ The genomes within species are even widely and drastically different ○ Prokaryotic genomes are rearranged during evolution, so that means that even closely related species have really different gene order. ● Lateral gene transfer - when genes are transferred from one species to another. Instead of moving vertically through the generations, lateral gene transfer goes horizontal between already existing species ○ Most all bacterial and archaeal species have experienced lateral gene transfer. ○ Plasmids may be responsible for this phenomenon ● Metagenomics - aka environmental sequencing. When you catalogue genes in bacteria and archaea in a particular habitat. Study of genes, not organisms. ● Extremophiles - archaea and bacteria that live in very extreme places.● Koch’s postulates - deal with bacteria and disease (1st test of the germ theory) ● Germ theory - laid foundation for modern medicine JANUARY 23 ● Macromolecules - dry weight of the cell is mostly macromolecules. Made up of monomers ○ Proteins - most common of macromolecules. Monomer: amino acids ○ Nucleic acids - nucleotides ○ Carbs - monosaccharides ○ Lipids - fatty acids w backbone of glycerol)
● Eukaryotic cells ● Amino acids link to form proteins by dehydration reactions that form covalent peptide bonds.JANUARY 30 ● Folded molecules are more favorable than straight chains because it is more stable. ● Denatured - when proteins become unfolded. ○ Can accomplish this my exposing proteins to compounds that break H bonds and disulfide bonds ● Folding is usually accompanied by molecular chaperones ● Many peptides need help folding. ● Prions - misfolded proteins that will cause other proteins to also misfold. ● First law of thermodynamics - energy is neither created nor destroyed: it is only transferred and transformed ○ Enthalpy - the total energy in a molecule ○ Exothermic reactions - ∆H is negative ○ Endothermic reactions - ∆H is positive ○ ∆S = entropy ● 2nd law of thermodynamics - entropy must always increase in an isolated system ○ Gibbs free energy change - determine if the reaction is spontaneous ■ ∆G = ∆H - T ∆S ■ If ∆G>0, endergonic. Non spontaneous ■ if ∆G<0, exergonic. Spontaneous ● Enzymes are catalysts. FEBRUARY 1 ● Identify the components of a nucleotide. ○ A phosphate group ○ A 5 carbon ring ○ A nitrogen base ■ Purines (G, A) ■ Pyrimidines (C, U in RNA, T in DNA) ● Compare and contrast the basic properties of DNA and RNA. ○ DNA - A, G, C, T ■ Sugar = deoxyribose ○ RNA - A, G, C, U ■ Sugar = ribose ● Describe the functions of DNA and RNA. ○ DNA ○ RNA ● Explain the formation of a phosphodiester linkage. ○ A bond between a hydroxyl on the sugar component of one nucleotide and the phosphate group of another nucleotide (condensation reaction)○ Joins the 5 C on the sugar of one nucleotide to the 3 C of the sugar of another ○ 5 -> 3 direction ● Explain why lipids are not as easily categorized as the other macromolecules in a cell. ○ Because it is a catchall term for carbon containing compounds that are found in organisms and are largely nonpolar and hydrophobic ○ Grouped together based on physical property - hydrophobic and unsoluble in water ■ Insolubility based on high proportion of nonpolar C-C and C-H bonds compared to polar functional groups ● Describe the structure and nomenclature of fatty acids and their condensation into triglyerides and phospholipids. ○ Fatty acid - simple lipid consisting of a hydrocarbon chain bonded to a carboxyl functional group ○ Fats - nonpolar molecules composed of 3 fatty acids that are linked to a 3C molecule called glycerol (called triglycerides). Dehydration reaction occurs between a hydroxly group of glycerol and the carboxyl group of fatty acids. The glycerol and fatty acid molecules join via an ester linkage ○ Steroids - family of lipids with bulky 4 ring structure ○ Phospholipids - consist of glycerol that is linked to a phosphate group with 2 hydrocarbon chains of either isoprenoids or fatty acids ● Explain how triglycerides serve as energy storage molecules.