Theromodymamic Laws

I. the total amount of energy in the universe is constant. Energy cannot be created or destroyed vut only converted from one form into another. If an object or process gains an amount of energy, it does so at the expense of a loss in energy somewhere elesin the universe


II. the entropy of the universe increases with any change that occurs.  DS_universe  > 0

III. absolute zero is removal of all thermal molecular motion

In any chemical reactions, the output of energy will exceed the input of energy. Just like investing money into an account, a portion of money is used to make more money as in chemcial reactions the energy is put into something that will yield more energy in the end as a result. 
For example, cellular respiration shown in the diagram. The first part of the reaction is an anatabolic process which energy is used as activaion. Free energy is put into to break glucose and later combined with oxygen to produce carbon dioxide, water and ATP for body function.  The second part of the reaction is a catabolic process. Through the process, the reaction yields greater free energy than the free energy used for synthesis them. More energy means more entorpy. While the reaction is in progress the energy is released and result in the total free engergy less than 0.  Thus, DG< 0.

 
ex. glucose+ oxygen = carbon dioxide + water

4 Macromolecues

Carbohydrate

-Amylopectin

-Monomer: glucose

-1° Bonding: glycosidic
-Function: energy source

 

-contains carbon, hydrogen, oxygen atoms in 1:2:1 ratio

-contain an aldehyde (functional group at the end) or a ketone (functional group inside)group and one or more hydorxyl group

-simplest carbohydrates are monosaccharides

            Examples: galactose, glucose, fructose 

            -glucose is an energy source

            -sugars are linear with five or more carbons but are readily to form cyclic structures when           dissolved in water

-disaccarides have two covalently linked monosaccharides

         Example: sucrose (glucose and fructose), Lactose (galactose and glucose), Maltose (glucose+ glucose)

-polysaccharides are composed of thousands of monosaccharide subunits held together by glycosidic linkages

           Examples: amulopectin, amylose

          -some are straight chains, others are branched

          -two important functions are energy storage and structural support

             Cellulose (polymer b-glucose)top holding hands; Starch (polymer a-glucose) bottom holding hands

Lipids

-Triglycerid

-Monomer: glycerol + fatty acid

-Hydrophilic vs. Hydrophobic(tail)

-1°  Bonding: ester

-Function: energy storage, membrane structure, hormones, vitamins

-hydophobic molecules composed of carbon, hydrogen, and oxygen

-insoluable in water but soluble in other nonpolar substances

-used for energy storage, building membranes, and other cell parts, chemical signalling molecules

-fatty acids with many carbon-carbon double bonds are called polyunsaturated fatty acids        

Divided into four families:

 fats

-most common fat in plants and animals are triglycerides

               -contans three fatty acids and a molecule of glycerol

-saturated fatty acids have single bonds – more stable

-unsaturated fatty acids have one ore more double bond – less stable – break more easily 

  phospholipids

-composed of a glycerol molecule attached to two fatty acid (hydrophobic), and a highly polar phosphate group (hydrophilic)

-tail and head, respectively

- form spheres, micelles, when added to watter (heads dissolve in watter, tails mix with one another in the center)

Steroids

-compact hydrophobic molecules, four hydrocarbon rings, several functional roups

Eg. Cholestrol, testosterone, estrogens

Protein

-Four-stranded parallel  ß-sheet (gold), for a helicaes (red) and a single 316 helix (purple)

-Low molecular wight

-Monomer: 157 amino acid

-1°  Bonding: peptide

-Function: signal transduction, cell cycle regulation, differenciation

-variety of roles, strctural building blocks, involved in almost everything the cell do

-amino acid polymers folded into specific 3-D shapes

-contains carboxyl and amino group 

-proteins have four levels of structure

Primary structure

-the sequence of amino acidss in the polypeptide strand

Secondary Structure

-portions of polypeptide chain forms coil due to hydrogen bond between oxygen of the carboxyl group and hyrogen of an amino group  

-Beta sheets – two parts of the polypeptide chain lie parallel to one another

Tertiary Structure

-contains both beta sheets and helix

Quaternary Structure

-composed of more that one tertiary protein

A change in 3-D shape of proteins caused by changes in temperature, pH, ionic concentration, or other environmental factors is called denaturation (cannot carry out is biological functions)

 

 

Nucleic Acid

-deoxyribonuleic acid

-Monomer: nucleotides

-N-Base: A, T, G, C

-1°  Bonding: phosphodiester

-Function: inheritance, genetic, protein synthesis

 

DNA

-contains sugar deoxyribose, phosphate group, nucleotides (A,C,G,T)

-hydrogen bond between the two strands between nitrogenous bases

-phosphodiester linkage between phosphate group of one nucleotide and the sugar of the next

RNA  

-contains ribose instead of deoxyribose, nucleotide U instead of T

Replication

DNA Replication
-DNA replicate semi-conservatively. During DNA replication, base pairing enables existing DNA strands to serve as templates for new complementary base pairs.
-On each of the upper and lower strand will have many lagging and leading strand. To be more specific at each replication bubble there is one lagging and one leading strand on the DNA itself. 

Replication Enzymes
       DNA Helicase           Primase-RNA Primer    DNA polymerase I     Single Stranded Binding Protein   
 DNA Polymerase III             DNA Ligase                   DNA Gyrase


1) DNA Helicase- Unwind the double helix by breaking the hydrogen bonds between complenmentary base pairs that hold DNA strand together.

2) Gyrase- Massage the unwinding DNA to release any tension.

3) Single Stranded Binding Protein- Bind to exposed single stranded DNA and block hydrogen bonding to prevent the two strand of DNA anneal back.

4) Primase- is an enzyme synthesis RNA Primer, which is the initiation sequence for replication.

5) Polymersase III- build complementary strand using the template strand/ catalyze the elongation of new DNA at a replication fork/grab deoxyribonucleoside trisophate as new strand building up using the template strand. As it is add from the 3' to 5' the leading strand will replicate continuously and the lagging strand will replicate along with the unzipping process of DNA. On the lagging strand there are many different fragments of replicated DNA, Okazaki  fragments, from 3's to 5's due to the prevention of degration of DNA.

6) Polymerase I- remove the RNA Primer from the replicated DNA of the leading and lagging strand.  And replace these RNA Primers with appropriate deoxyribonucleotides.

7) Ligase- act as glue to join the Okazaki fragments of the lagging strands and gaps between pieces of DNA at the end of replication fork.

8) Polymerase I & Polymerase III- proofread the finish replicated DNA.