entropy

Entropy is chaos, disorder, randomness.
According to the second law of thermodynamics, everything that happens in the universe leads to more disorder, everything increases in complexity over time.
Disorder puts energy in a usable form (free energy), sometimes a system may seem like it's getting more organized but more work is required, leading to even more chaos.

Law of Thermodynamics

The 3 Laws of Thermodynamics are:

1. Conservation of mass-energy: Energy can neither be created nor destroyed, they can only be converted from one form to another
2. Law of Entropy: all spontaneous events act to increase the total entropy (measurement of disorder/chaos)
3. Absolute Zero: absolute zero is removal of all thermal molecular motion

Second Law of Thermodynamics with reference to metabolic processes:

Living organisms constantly use anabolic processes to build highly ordered structures such as proteins, DNA, and membranes.  These are endergonic reactions which are not spontaneous and uses up energy.  This seems to violate the second law of thermodynamics by decreasing the amount of disorder and increasing the free energy.  However, in reality, every 'order' created by anabolic processes are actually followed by an even greater disorder caused as these catabolic processes release energy.  The overall (net) free energy is less than 0, more disorder is created, which supports the second law of thermodynamics.  

macromolecules

Deoxyribonucleic Acids

• It is a polymer made up of nucleotides (adenine, thymine, cytosine, guanine), ribose sugar, and phosphate.
• It contains phosphodiester bonds, hydrogen bonds, and glycosyl bonds.
• The functional groups in this macromolecule are carbonyl and hydroxyl groups.
• Functions: contains genetic material for inheritance and replication, protein synthesis, and reproduction
• Characteristics: it has a double helix shape with the two strands running antiparallel to each other.

Carbohydrates

(maltose)

• Empirical formula: (CH₂O)_n 
• Carbohydrates may be classified into three groups: monosaccharides, oligosaccharides, and polysaccharides.
• Simple sugars can have spatial arrangement of their atoms, forming isomers with different chemical properties (e.g. glucose, galactose, and fructose)
• Monosaccharides are monomers that can undergo condensation reaction to form dimers (e.g. maltose, sucrose), or polymers.  
• Bonding between the monomers are glycosidic linkage (covalent bonds), the condensation reaction also produces a biproduct of water
• Function: energy storage, structural support, building materials, cell surface markers for cell-to-cell identification and communication
• Characteristics of Carbohydrates (polymers): can be straight chain or branched
• Examples: fructose, glucose, sucrose maltose, lactose, amylose, amylopectin, cellulose, glycogen, chitin

Proteins

(keratin)

• Amino acid polymers folded into specific 3-D shapes.  Its structural characteristics determine its function.
• An amino acid is an organic molecule with a central carbon atom attached to an amino group, a carboxyl group, a hydrogen atom, and an R chain.
• Monomers of protein polypeptide bonds to form polypeptide chains into polymers through condensation reaction
• Functions: signal transduction, cell cycle regulation, differentiation, structural building blocks
• Characteristics: may be polar, nonpolar, or charged, low molecular weight
• Examples: keratin, fibrin, collagen

Lipids

(cholesterol)

• Hydrophobic molecules composed of carbon hydrogen, and oxygen.
• They are polar molecules
• Lipids can be divided into four families: fats, phospholipids, steroids, and waxes.
• Triglycerides are lipids containing three fatty acids attached to a single molecule of glycerol
• Glycerol reacts with fatty acids through a condensation reaction between the hydroxyl group of glycerol and the carboxyl group of a fatty acid.  The bond is called an ester linkage. (esterification)
• Functions: energy storage, membrane structure, hormones, vitamins
• Examples: cholesterol (steroids), testosterone, butter, cutin, beeswax

DNA Replication

• DNA replication is a semiconservative process, in which there is one parent strand and one daughter strand in the replicated DNA.
• Each parent strand is a template for ordering nucleotides to make a new complimentary strand
• There are many sites of replication on a strand of DNA called "replication bubbles", with replication forks on each ends.
• The strands in the double helix are antiparallel, so one strand runs in 5' -> 3' direction, while the other runs in 3'->5' direction
• A new DNA strand can only elongate in the 5'->3' direction

The process:

1. DNA helicase unwinds the double helix
2. DNA gyrase (bacterial enzyme) relieves the tension (produced from unwinding of DNA)
3. Single-stranded binding proteins (SSBs) keeps separated strands of DNA apart
4. Primase (RNA polymerase) makes primer, which signals Polymerase III to make complementary strand
5. DNA Polymerase III then grabs nucleotides to make complementary strands of DNA
6. One of the parental strand (3'->5' into the fork), the leading strand (growing towards the fork) can form a continuous complimentary strand (only need one single primer as the fork continues to separate and the new strand continues to elongate)
7. The lagging strand (5'->3' into the fork) has to be copied away from the fork in Okazaki fragments, in order to elongate in the 5'->3' direction (it also needs a new primer for each fragment)
8. DNA Polymerase I then replaces the RNA primer with DNA
9. DNA ligase join all the gaps that are present on the daughter strands

Five Famous Geneticists

Erwin Chargaff

(1905-2002)

Year of Fame: 1947

Publications that make him Famous: Chargaff's Rules

Contribution to the world of Genetics: His rules on the complimentary base pairs helped Watson and Crick to find the double helix structure of DNA.  His lab also researched on the metabolism of amino acids, lipids, etc.

Arthur Kornberg

(1918-2007)

Year of Fame: 1957

Publications that make him famous: In 1956, he isolated the first DNA polymerizing enzyme (now known as DNA polymerase I).  This won him the Nobel prize in 1959.

Contributions to the world of Genetics: His discovery of the DNA polymerizing enzyme later on became the crucial steps in gene splicing and other techniques in genetic engineering.  It also contributed to the drug-making to treat cancers, AIDS, and other viral infections.

In 1967, he and his team "created life in a test tube" - they produced the active inner core of a virus in a lab.

Rosalind Franklin

(1920-1958)


Year of Fame: 1958 (after her death)


Publications that make her famous: Her discovery that the sugar-phosphate backbone of DNA lies on the outside of the molecule, instead of inside.  She also found that the structure of DNA has two strands, not three.  These were published by her supervisor, Maurice, without her consent.  She also had publications on the structure of an entire virus, called the Tobacco Mosaic Virus.


Contributions to the world of Genetics: Her discovery about the DNA's structure using X-ray crystallography made it possible for Watson and Crick to make the DNA double helix structure.




Barbara McClintock

(1902-1992)


Year of Fame: 1983 (First woman to win the Nobel Prize, unshared!)


Publications that make her famous: Genetic structure of maize: "A cytological and genetical study of triploid maize", "A Correlation of Cytological and Genetical Crossing-Over in Zea Mays"...


Contributions to the world of Genetics: Her theory that genes are transportable on and between chromosomes have helped her proof that genes are responsible for turning physical characteristics on and off.  She also developed the technique for visualizing maize chromosomes and demonstrated many fundamental genetic ideas such as crossing-over during meiosis to exchange genetic information.


Kary Banks Mullis

(1944- )


Year of Fame: 1993


Publications that make him famous: The invention of the polymerase chain reaction (PCR), which won him the Nobel Prize.


Contributions to the world of Genetics: He invented a method (PCR) for amplifying DNA, which is used in medicine, biotechnology, forensics, and genetics.  He also developed a revolutionary approach cause the immune system to react instantly to fight invading toxins and pathogens (Altermune LLC).  It is currently focusing on Influenza A and drug resistant Staphylococcus aureus.