PHYC452Biophysics:Schedule/BioChem

Here is a list of concepts and vocabulary that we have learned.

Basic Components of the Cell
Know the basic description and function of each.
 * Membranes
 * Cytoplasm
 * Cytosol
 * Organelles
 * Nucleus
 * Mitochondria
 * Endoplasmic Reticulum
 * Golgi
 * Lysosome

Basic Molecular Components of Cell
Know the basic structure and function of each.
 * Nucleotide
 * Amino Acid
 * Fatty Acid
 * Lipid
 * Polypeptide
 * Polynucleotide
 * RNA
 * DNA
 * Histone
 * Nucleosome
 * Chromatin Fiber

Protein Synthesis

 * In Transcription, RNA Polymerase produces mRNA
 * In Translation, the ribosome uses mRNA and tRNA to produce polypeptides
 * The Primary Structure is the chemical sequence of amino acids
 * The Secondary Structure is the three dimensional structure after the folding of subsections into structures such as alpha helix and beta sheets.
 * The Tertiary Structure is the three dimensional structure after complete folding.
 * The Quaternary Structure is the three dimensional structure of a complex of folded sub units.

Biochemistry
A few very useful links to Molecular Biology of the Cell:

[http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=nucleotides&rid=mboc4.box.217 2-6. A Survey of the Nucleotides]

[http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=nucleotides&rid=mboc4.figgrp.220 Figure 2-28. A small part of one chain of a deoxyribonucleic acid (DNA) molecule.]

The 20 Amino Acids Found in Proteins

Know the basic concept and approximate strength of each in KT in water. Know the basic structure or concepts of the following:
 * Covalent Bond
 * Ionic Bond
 * Hydrogen Bond
 * Van der Walls interaction
 * The basic structure of the sugars glucose, ribose, and deoxyribose including 1' to 5' positions.
 * The chemical structure of an Amine group and a Carboxyl group.
 * Condensation and hydrolysis reactions.
 * The structure of a phosphate
 * Nucleotides consist of a Base, Sugar and Phosphate
 * Bases are either Pyrimidines (one ring) or Purines (two rings)
 * The sugar is either ribose in RNA or deoxyribose in DNA
 * Bases are linked to the Sugar at the 1' position
 * Phosphates are linked to the sugar at the 5' position
 * Polynucleotides are formed when phosphates of one nucleotide bind to the 3' position of another nucleotide.
 * Nucleotides bind to their complementary base with hydrogen bonds. G-C uses 3 H-bonds, A-T(U) uses 2 H-bonds.
 * Amino Acids contain an Amino group, Carboxyl group and a reactive group.
 * The reactive group gives the specificity of the amino acid. 20 are produced and used in living organisms.
 * Polypeptides are formed by peptide bond, combining the amino group of one amino acid the carboxyl group of another.
 * The N-terminus of a protein corresponds to the free amino group at one end.
 * The C-terminus of a protein corresponds to the free carboxyl group at one end.
 * Adenosine triphosphate is the nucleotide Adenosine with two extra phosphates linked sequentially to the first. ATP is the main energy carrier of the cell, and can give energy on conversion to ADP (Adenosine diphosphate).