Hydrogen Peroxide Lab Results - Concentration of Substrates

Procedure:

1. 2mL of hydrogen peroxide and 8mL of water were added into a 10mL graduated cylinder to create a hydrogen peroxide solution of 20% concentration.
2. Step 1 was repeated to make solutions of 30%, 40%, 50%, and 60% concentrations of hydrogen peroxide.
3. Overflow pan was filled with tap water.

4. A 1L graduated cylinder was filled with water and inverted into the pan. The volume of air inside the graduated cylinder was recorded.
5. 5 disks of filter paper that were immersed in beef liver were placed at the bottom of a 20mL Erlenmeyer flask. The flask was capped with a rubber stopper that has a funnel and tubing.
6. The end of the tube was put into the overflowing pan and inserted into the 1L graduated cylinder. The 20% hydrogen peroxide solution was pured into the funnel. The funnel opening was immediately blocked and the flask was shaken to allow mixing of the hydrogen peroxide and the liver.
7. New volume of gas in the 1L graduated cylinder was recorded. The initial volume was subtracted from this recording to calculate the amount of oxygen gas displaced. 

8. Steps 4-7were repeated for 30%, 40%, 50%, and 60% solutions of hydrogen peroxide. 

Data Table:

Sources of Errors:

• inconsistent amounts of reactants and enzymes used
• O2 gas may have escaped
• leftover water in the flask due to rinsing after each trial may influence result

The Second Law of Thermodynamics

The second law of thermodynamics states that energy spontaneously tends to flow only from being concentrated in one place to becoming diffused or dispersed and spread out. It is also called the law of entropy. Entropy measures the spontaneous dispersal of energy: how much energy is spread out in a process, or how widely spread out it becomes — at a specific temperature.

While quantity of matter or energy remains the same (First Law), the quality of matter/energy deteriorates gradually over time. Usable energy is inevitably used for productivity, growth and repair. In the process, usable energy is converted into unusable energy. Thus, usable energy is irretrievably lost in the form of unusable energy. 

Examples of the second law include:

• the increase in the volume of a gas
• the spontaneous mixing of different gases and liquids
• heating a substance
• the addition of a small amount of solute into a solvent
• spontaneous exothermic reactions

Macromolecules

There are four types of macromolecules that make up all living matter: carbohydrates, lipids, proteins, and DNA.

They are all composed of long complex chains of molecules (polymers) made up of simpler, smaller subunits (monomers). They are joined together in a process known as dehydration, in which a covalent bond is formed between two monomers, releasing a water molecule.

Carbohydrates:

• Carbohydrates are made up of sugars and their polymers. Simple sugars  are chains of hydrocarbons of varying length that possess a hydroxyl (OH) group on each carbon.
• Glucose and galactose are two types of monomers that form a hexagonal ring because of its aldehyde structure. Fructose forms a pentagonal ring because of its keytone structure.
• Carbohydrates are essential for both energy storage and structure. Starch is the chief energy source for plants and glycogen is the main energy source for animals.Cellulose in plants and chitin in invertebrate animals help to provide structure and support.

Lipids:

Lipids ccan be divided into three main categories: fats, steroids, and phospholipids.

• A fat (tryglyceride) is composed of a glycerol molecule (a short hydrocarbon) bonded to three fatty acids through dehydration synthesis.
• If there are no double covalent bonds between the carbons of the fatty acids, the fat is said to be saturated, because the maximum number of hydrogens are bonded to the carbon skeleton. IF the fatty acid has any double bonds, it is said to be unsaturated.
• Phospholipids are composed of a glycerol molecule bonded to two fatty acids and a phosphate group. This phosphate group is polar although the rest of the molecule is hydrophobic.
• Steriods are made of four interconnecting carbon rings and cholesterol is the most common steroid.
• Lipids are excellent sources of energy, insulation, and, in the case of the dual nature of the phospholipid, they are crucial elements of membranes.

Proteins:

Proteins have many levels of structure.

• Their primary level of structure is the sequence of amino acids linked together in a peptide chain. There are only 20 amino acids, each with a hydrogen, an amino group (NH2-), a carboxyl group (COO -), and an R group.
• The secondary level of structure in proteins is the bending of this peptide chain into either an alpha helix (coil) or a beta sheet (plaited sheet) as a result of hydrogen bonding.
• The tertiary structure is based on the folding of the secondary structure caused by interactions between amino acid side chains. These include ionic and covalent bonds, disulphide bonds, and hydrophobic interactions.
• A protein's quaternary structure is based on the interaction between many peptide chains. 

DNA:

• DNA is composed of a nitrogenous base, a five-carbon sugar (a pentose), and a phosphate group.
• There are five nitrogenous bases: adnine, guanine, thymine, uracil, and cytosine. Adenine only binds with thymine, guaning only binds with cytosine. Thymine is only found in DNA and uracil is a substitude for thymine in RNA.
• The pentose in RNA is ribose and deoxyribose in DNA. A phosphate group is linked to the sugar via a phosphodiester bond and the three nucleotides have become a nucleic acid.  
• DNA holds the generic information necessary for protein synthesis and RNA carries this information to the actual site of protein production.

DNA Replication

Roles of enzymes:

-Helicase: moves along a double-helical DNA, breaks the hydrogenbonds between two strands, unwinds the helix, and creates a replication fork.

-Single-stranded binding proteins: anneal to each single-stranded DNA immediately after it is unwinded by helicase to prevent it from reannealing.

-Gyrase: relieves the tension created by the unwinding of DNA at the replication fork by cutting the strands, letting them to rotate, and reconnecting them.

-Primase: builds short segments of RNA (primers), which are used by DNA polymerase III for elongation.

-DNA polymerase III: adds appropriate deoxyribonucleoside triphosphate to the 3' end of a parent strand, thereby creating a daughter strand in the direction of 5' carbon to 3' carbon. In each replication bubble, there is one leading strand and one lagging strand; the leading strand replicates towards the replication fork, the lagging strand replicates away from the fork. The leading strand is built continuously, whereas the lagging strand consists of many short segments of DNA called Okazaki fragments.

-DNA polymerase I: replaces the RNA primers in each Okazaki fragment and in the leading strand with corresponding DNA.

-DNA ligase: connects the Okazaki fragments by creating a phosphodiester bond.

-DNA polymerase I and DNA polymerase III also proofread the entire sequence, and fix any mistakes that were made in the replication process.

Here's a link that explains the replication process step-by-step.
A youtube video that gives an overview of the replication process.

Five Famous Geneticists

Thomas Hunt Morgan

(1866-1945)

Year of Fame: 1933

Publications that made him famous: "for his discoveries concerning the role played by the chromosome in heredity"

Contribution to the world of Genetics: Morgan was able to demonstrate that genes are carried on chromosomes and are the mechanical basis of heredity. These discoveries formed the basis of the modern science of genetics. He was the first person to be awarded the Nobel Prize in Physiology or Medicine for his work in genetics.

 Arthur Kornberg

(1918-2007)

Year of Fame: 1959

Publications that made him famous: "for [his] discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid"

Contribution to the world of Genetics: Arthur Kornberg spent decades isolating and purifying the enzymes that run the machinery of the cell. He and Severo Ochoa were the first to identify the enzyme catalyzing the synthesis of DNA, polymerase I.Kornberg's approach - isolating enzymes in the chemist's lab and analyzing them within their biological context - was a crucial component in understanding the molecular biology of the cell.

Marshal Warren Nirenberg

(1927-2010)

Year of Fame: 1968

Publications that made him famous: "for [his] interpretation of the genetic code and its function in protein synthesis"

Contribution to the world of Genetics: After a postdoctoral fellowship at the National Institutes of Health (NIH) in Bethesda, Maryland, he joined the staff as a research scientist. There he developed the procedure for deciphering the genetic code in living cells. He demonstrated that in protein production, each sequence of three chemical units—known as triplets or codons—in genetic material forms the arrangement for a specific amino acid. In 1961, he announced his discovery of the code for one amino acid. By 1966. Nirenberg had deciphered the code for the 20 amino acids involved in protein production.

Barbara McClintock

(1902-1992)

Year of fame: 1983

Publications that made her famous:"for her discovery of mobile genetic elements"

Contribution to the world of Genetics: McClintock studied chromosomes and how they change during reproduction in maize. Her work was groundbreaking: she developed the technique for visualizing maize chromosomes and used microscopic analysis to demonstrate many fundamental genetic ideas, including genetic recombination by crossing-over during meiosis—a mechanism by which chromosomes exchange information. She produced the first genetic map for maize, linking regions of the chromosome with physical traits, and demonstrated the role of the telomere and centromere, regions of the chromosome that are important in the conservation of genetic information.

 Werner Arber

(1929- )

Year of fame:1978

Publications that made him famous:"for the discovery of restriction enzymes and their application to problems of molecular genetics"

Contribution to the world of Genetics: He, Daniel Nathans,and Hamilton O. Smith together discovered restriction enzymes that break the giant molecules of DNA into pieces small enough to be separated for individual study, but large enough to retain meaningful amounts of the genetic information of the original substance. He also observed that bacteriophages cause mutation in their bacterial hosts and undergo hereditary mutations themselves.