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 Eukaryotes 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. cytoskeleton Limited compared to  eukaryotes Extensive and usually  found throughout the  whole cell Overall size small large

● 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 ______.
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Don't forget about the age old question of blood type alleles
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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.

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