Honggie's personal DIARY

AP Bio.
Hongdao Nguyen
Chapter 5.4-5.5

Proteins have many structures resulting in a wide range of functions:
- Proteins accounts for more than 50% of the dry mass of a cell
- speed up chem reactions, structural support, storage, transport, cellular communications, movement, and defense against substance
- enzymes- proteins regulate metabolism by action as catalysts chem agents that selectively speed up chem reactions the cell without being consumed by the reaction (can perform funct. over and over again)
- proteins are the most structured sophisticated molecules known

Polypeptides:
- are polymers constructed from the same set of 20 amino acids
- polymers of acids= polypeptides
- protein consists of one or more polypeptides folded and coil specifically

Amino Acid Monomers:
- Amino acids are organic molecules possessing both carboxyl and amino groups
- center of amino acid is asymmetric C atom called Alpha C
- pattern: amino group, carboxyl, H atom, and variable group/ R group (may be simple as a H atom, or a carbon skeleton with various funct groups)
- acidic amino acids: those with side chains that are generally neg in charge owing to presence of carboxyl group which dissociates at cellular pH
- basic amino acid: have amino groups in their side chains that are generally pos charge.  (both are hydrophilic)

Amino Acid Polymers:
- when 2 acids are positioned so that the Carboxyl group is one adjacent to the amino group of the other, an enzyme can cause then to join by catalyzing a dehydration reaction, with the removal of a water molecule= peptide bond
- attached to polypeptide backbone are diff kinds of appendages, side chains of the amino acids
- polymers are diff by linking a limited set of monomers into diverse sequence

Determining the Amino Acid Sequence of a Polypeptide:
- Sanger tried to determine sequence of proteins by: using protein-digesting enzymes  (and other) that break polypeptides at specific places rather than completely hydrolyzing the chains= chromatography
- hydrolysis with diff agent breaks the polypep. at diff sites
- then searched for overlapping sequences- reconstruct overlapping sequences of letters; recog. Primary structure of insulin

Protein Conformation and Function:
- a functional protein is not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into a molecule
- why cell synthesized a polypeptide- chain folds spontaneously, folding is driven and reinforced by formation of a variety of bonds btwn parts of the chain
- many proteins are globular (roughly spherical) while others are fibrous in shape
- a proteins funct. Depends on its ability to recog. And bind to some other molecule
- morphine, heroin, and other opiate drugs are able to mimic endorphins and bind to those in the brain
- ability of a receptor protein to identify and associate w a particular pain-relieving signal molecule- is an emergent prop.

4 Levels of Protein Structure:
- we can recog. 3 superimposed levels of structure. The 4th level arises when a protein consists of 2 or more polypeptide chains
- Primary Structure: its unique sequence of amino acids.    
    -Precise primary structure of a protein is determined not by random linking but by inherited genetic     info. The order of letters in a very long word.
- Secondary Structure: have segments of their polypeptide chains repeatedly coiled or folded in patterns that contribute to the proteins overall formation.
    -Coils and folds result of H bonds bten repeating polypeptide backbone. 
    -O and N- Neg charge, H- weakly pos charged. ____ helix, a     delicate coil held together by H     bonding btwn every 4th amino.
    -Many also has ____ pleated sheet: two or more regions are connected by H bonds btwn parts of the     2 parallel polypeptide backbones sheets make up the core for globular proteins
- Tertiary Structure: superimposed on the patterns of the secondary structure.
    -Rather than involving interactions btwn backbone, this is the overall shape of a polypeptide resulting     from interactions btwn the R groups .
    - One misleading type: hydrophobic interaction: as folds  into its funct. Conformation bc it clusters     at the core of the protein out of contact with water.
    - When not close together, Van Der Waals holds them together. Disulfide bridges: conformation of a     protein that may be reinforced by covalent bonds.
- Quaternary Structure: the overall protein structure that results from the aggregation of these     polypeptide subunits.
    - Ex collogen, has a large triple helix- suits bc it girders connective tissues, bone, tendons etc. each     subunit has a no polypeptide component, called heme, with an iron atom that binds O2

 Sickle- Cell Disease: A Simple Change in Primary Structure:
- sub of a amino acid of valine for the normal one, glutei acid, at a particular position in the primary strucutre of hemoglobin can cause sickle-cell disease.
- the red blood cells are crystallized, deforming some of the cells into a sickle shape.- the cell can clog tiny blood cessels, impeding blood flow

What Determines Protein Conformation?:
- polypeptide chain of a given amino acid sequence can spontaneously arrange itself into a 3-D shape determined and maintained by the interactions responsible for secondary and tertiary structure
- also depends on the phy and chem conditions of the proteins enviro. - pH, salt concentration, temp, etc.- maybe denature (unravel)- which makes it inactive.
-proteins become denatured if they are transferred fro an aqueous envir. To a organic solvent (others= disrupt the H bonds, ionic bonds, disuflide bridged)
- denaturation results= excessive heat (ex, high fevers can be fatal bc proteins in blood becomes denatured by high temp)
- protein will ften return to its functional shape when denaturing agent is removed
- sequence of amino acids determines conformation- where an ___ helix can form, where ___ pleated sheets can occur, where disulfide bridged are located, wher ionic bonds can form etc.

The Protein- Folding Problem:
- bc proteins go through several intermediate states on their way to a stable conformation,  looking at a mature one does not reveal the stages
- chaperonins: protein molecules that assist in the proper folding of other proteins. They work by keeping the new polypeptide segregated from “bad influences” in the cytoplasm enviro. While it folds
- X-ray crystallography: an important methods used to determine a protein’s 3-D structure.. Another method= nuclear magnetic resonance (NMR) spectroscopy… which does not require protein crystallization.

Nucleic Acids Store and Transmit Hereditary Information:
- gene: programs the amino acid sequence of a polypeptide, consists of DNAà nucleic acids

The Roles of Nucleic Acids:
- Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA): molecules that enable organisms to reproduce their complex components fro one generation to the next.
- DNA provides directions for its own replication.. Directs RNA synthesis, and RNA controls protein synthesis
-  each chromosome contains one long DNA molecule, with thousands of genes.
- when a cell reproduces itself by dividing, its DCA is copied and passed along
- DNA does not directly involved in running operations of cell
- actual sites of protein synthesis are ribosome’s, DNA remains in nucleus. M-RNA conveys genetic instruction for building proteins from nucleus

The structure of Nucliec Acids:
- polymers= polynucleotide.. Consists of monomers called nucleotides- composed of 3 parts: nitrogenous base, a pentose, and a phosphate group

Nucleotide Monomers:
- pyramiding has a 6-membered ring of C and N atoms. Members are: cytosine, thymine (found in DNA), and Uracil (found in RNA_
- Purines are larger with a 6-membered ring fused to a 5-membered ring purines are: adenine, and guanine (both found in DNA and RNA)
- pentose connected to the N base is Ribose in RNA, and deoxyribose in DNA, only diff btwn these sugars= Deoxyribose lacks an O atom on the second carbon in the ring

Nucleotide Polymers:
- adjacent nucleotides are joined by covalent bonds called phosphodiester linkages btwn the -OH group on the 3 C and the phosphate on the 5 C of the next-  repeating backbone.
- 1 free end has a phosphate and the other has a hydroxyl= DNH strand has a built-on directionality along its sugar-phosphate backbone
The DNA Double Helix:
- RnA molecules consist of a single polynucleotide chain, contrastingly, DNA molecules have 2 polynucleotide that spiral around, forming a double helix
- 2 sugar backbones run opp 5-3 directions from each other, referred to as ant parallel
- sugar-phosphate backbons are on the outside o the heliz. Held together by H bonds btwn paired bases.
- A pairs with T and G pairs with C . two strands are complementary.- makes copying genes possible
- for cell division: each of 2 strnds of DNA molecules serves as a template to order nucleotides into a new complementary strand - result in two identical copies

DNA and Proteins as Tape Measures of Evolution:
- genes and their products (proteins) document the hereditary background of an organism

The Theme of Emergent Properties in the Chemistry of Life: a Review:
- unusual behavior of water, results from interactions of the water molecules.
- reduces complexity and diversity of organic compounds to the chem characteristic of C: structural arrangement of C skeleton and funct groups
- small molecules to large molecules