1. What are the main organelles in cells and their basic functions?

Cell membrane :defines the periphery of the cell, separating its contents from the surroundings. The membrane is a barrier to the free passage of inorganic ions and most other charged or polar compounds.

Nucleus: contains the genes (chromatin)Site of most DNA synthesis and repair.RNA synthesis

Nucleoid: Contains single, simple long-circular DNA molecule.

Ribosomes: Protein synthesis from an RNA message.

Golgi Complex: processes, packages and targets proteins to other organelles or for export. Also involved in formation (biogenesis) of lysosomes, secretory vesicles (hormones, blood plasma proteins, digestive enzymes).

Mitochondria: oxidizes fuel to produce ATP : Powerhouse of cell, perform cellular respiration, Urea and heme synthesis, contain own genome, circular mtDNA.

Endoplasmic Reticulum (ER):

2. Know the structural hierarchy in the molecular organization of cells. (Lipids, proteins, carbohydrates, and nucleic acids)

3. Know the common functional groups of biomolecules. What is stereoisomers, chiral center? What are the naming systems for geometric isomers? (cis/trans, R-/S-, D-/L-, systems)

3 D structures: StereochemistryStereoisomer- molecules with the same chemical bonds but differing spatial arrangement.

Cis/trans isomerism (Geometric isomerism) is a form of stereoisomerism describing the relative orientation of functional groups within a molecule. Chirality: 1 Chiral Carbon = 2 Stereoisomers(n)Chiral Carbons = 2n stereoisomers

Naming Conventions:By Configuration R- and S- By optical activity: (+)- and (-)-By configuration: D- and L- 9 (configurational standard Glyceraldehyde)

Enantiomers: stereoisomers that are mirror imageDiastereomers: Pairs of Stereoisomers that are not mirror imagesof each other.

Know free energy(G), entropy (S) and enthalpy (H), and their relationship: dG= dH-TdS. What is the difference between endergonic and exergonic, endothermic and exothermic? How to calculate equilibrium constant of a chemical reaction? The equation of K and dG?

Basic Thermodynamics:Free energy G:The component of the total energy of a system that can do work at constant temperature and pressure.G=H-TS

Entropy S:The randomness or disorder of the components of a chemical system.

Enthalpy H

G= H-TS

Endergonic vs Exergonic: Endergonic reactions require an input of energy, and their G values are positive.Exergonic;

Endothermic vs Exothermic:G= H-TSHow to calculate the equilibrium constant:Keq = [C]ceq Ddeq K and G

What is ATP, ADP, and AMP

ATP: adenosine triphosphateADP: adenosine diphosphateAMP: adenosine monophosphate

Know the concepts: Metabolism: The entire set of enzyme-catalyzed transformations of organic molecules in living cells; the sum of anabolism and catabolism.

Catabolism: The phase of intermediary metabolism concerned with the energy yielding degradation of nutrient molecules.

Anabollism: The phase of intermediary metabolism concerned with the energy-requiring biosynthesis of cell components from smaller precursors.

What is central dogma from DNA to protein?

Chapter 2: WATER

Part I:

What properties make water the best solvent for life? What is the geometric and molecular structure for water? What is the electric dipole for water? What is hydrogen bonding? What are requirements? Why is carbon not able to do hydrogen bonding?

Know the interaction among water molecules due to electric dipole. (What is longer? Why is weaker in comparison to the other?) What makes hydrogen bonds weak or strong (generally)?

Know the non-covalent weak interactions/bonding (there are 4). Review over colligative properties; the ones mentioned in class are boiling point, melting point, and osmotic pressure. For osmotic pressure, understand the 3 subtypes (hyper-, isotonic, and hypo-).

Fact: Multiple hydrogen bonds are added as a whole that increases the amount of energy to break the bond.

Between butane, and butanol, butanol has a much higher boling point. Explai why this occurs.

Know how many hydrogen bonds are possible for one water molecule in ice and liquid.

Fact: The two most common functional groups involve in ionic interactions are carboxylic group, and amino group.

Ina solid form of NaCl it is readily soluble in water because of what? (hint: Entropy as a solid vs entropy in aqueous solution)

Fact: polarity determines solibility

Make sure to understand very well the entropy concept!

Hydrophobic interactions(involving non-polar molecules): thermodynamics- low solubility is explained through entropy; water near hydrophobic solute is highly ordered (-dS)

Part II:

What is a buffer solution? What does it consist of?review pH, pOH, Ka, and how to calculate them. Make sure to understand the Hopping effect of H+.

Quiz Questions Q1: How many hydrogen bonds a CH3-O-CH3 molecule can make with itself? What about with water?

Q2. Atoms in the molecule, if held together by what bonds create the strongest chemical linkages?

Q3: Why maintenance of pH is important in biological systems?

Q4: Which of the following will be most/ least soluble in water?

Q5: How many hydrogen bonds can one ammonia molecule for with water moleculs?Draw formations)

chapter 3: Amino acidsPart I