Intro-Biochemistry

Biochemistry: 

Biochemistry

Biochemistry: 

Biochemistry the science dealing with the chemical composition and chemical reactions happening within and between the living cells of all organisms (the mammals, the vertebrates, the plants, etc.)

Branches of Biochemistry : 

Branches of Biochemistry Main Branches Other Branches Molecular Biology - Biotechnology Cell Biology - Genetic Engineering Immunology -Cytology Genetics

Applications of Biochemistry : 

Applications of Biochemistry Ames Test - a test that is used to determine whether a substance will affect (mutate) the structure of DNA. In this test salmonella bacteria is exposed to the chemical under question (food additives, for example), and changes in the way the bacteria grows are measured. Many substances that cause mutations in these bacteria also cause cancer in animals and humans. Indeed, this test is used today to screen chemicals for their potential ability to cause cancer in humans.

Pregnancy Testing: 

Pregnancy Testing There are two types of pregnancy tests – one uses a urine sample and the other a blood sample. Both detect the presence of the hormone human chorionic gonadotropin (hCG). This hormone is produced by the placenta shortly after implantation of the embryo into the uterine walls and accumulates.

Breast Cancer Testing : 

Breast Cancer Testing Most breast cancer is not hereditary, but in 5-10 percent of cases, there is a heredity linkage. The vast majority of these cases is due to mutations in two genes: Breast Cancer-1 gene (BRCA1) and the Breast Cancer-2 gene (BRCA2), which were discovered in 1994 and 1995, respectively. Females who inherit a mutation in either one of these genes have a greatly increased chance of developing breast cancer over their lifetime. Positive tests for these mutations allow the individual to schedule increased screening tests at a more frequent rate than the general population.

Prenatal Genetic Testing: 

Prenatal Genetic Testing - refers to testing the fetus for potential genetic defects. Tests commonly are performed on blood or tissue samples from the fetus. This may involve amniocentesis – collection of a sample of amniotic fluid that contains cells from the fetus—or collection of blood from the umbilical cord. Tests such as these are used ot detect chromosomal abnormalities such as Down syndrome or birth defects such as spina bifida.

PKU Screening : 

PKU Screening Phenylketonuria (PKU) is a metabolic disorder in which the individual is missing an enzyme called phenylalanine hydroxylase. Absence of this enzyme allows the buildup of phenylalanine, which can lead to mental retardation.

Genetic Engineering : 

Genetic Engineering - involves taking a gene from one organism and placing it into another. The recipient may be bacteria or a plant or an animal. One of the most well-known examples of genetic engineering involves the hormone insulin. Diabetes use to be treated with insulin derived from pigs or cows, and although very similar to human insulin, these animal-derived insulin’s were not identical and caused problems for some individuals. Biochemists solved this problem by inserting the gene for human insulin into bacteria. The bacteria, through the process of translation, created human insulin.

Cloning: 

Cloning In 1996, Dolly the sheep was cloned—the first mammal ever cloned from adult animal cells. The cloned sheep was, of course, genetically identical to the original adult sheep. This clone was created by taking cells from the udder of a 6-year-old ewe and growing them in the lab. They then took unfertilized eggs and stripped the genetic material from them. Finally, they inserted the genetic material grown in the lab into these cells and implanted them into the uterus of another sheep. And Dolly was born. Since Dolly, many other animals have been successfully cloned. However, there is worldwide debate on the idea of cloning a human, which will surely continue for decades.

Gene Replacement Therapy: 

Gene Replacement Therapy - a modified or healthy gene is inserted into the organism to replace a disease-causing gene. Commonly a virus that has been altered to carry human DNA is used to deliver the healthy gene to the targeted cells of the patient. This process was first used successfully in 1990 on a 4-year old patient who lacked an immune system due to a rare genetic disease called severe combined immunodeficiency (SCID). Individuals with SCID were prone to life-threatening infections. They lead isolated lives, avoiding people and commonly taking massive doses of antibiotics. Scientists removed white blood cells from the patient, grew them in the lab, and inserted the missing gene into the cells. They then inserted this genetically altered blood back into the patient. The process allowed the child to develop normally and even attend school, but the treatment must be repeated every few months.

Chemistry of Life: 

Chemistry of Life Elements, Atoms and Molecules Elements are made of atoms. Elements cannot be broken down into simpler substances (this is not referring to subatomic particles). Atoms=uncharged particles Molecules=compounds made of two or more elements Ex: H2O

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Covalent Bonds and Ionic Bonds Covalent bonds -occur when molecules share electrons. Example:H2O Oxygen Hydrogen + WATER is covalently bonded hydrogen and oxygen. Ionic bonds -occur when electrons are transferred between atoms.

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-results in one positive ion (cation) and one negative ion (anion). -ionic bonds do not form molecules. -the exist in a crystalline lattice. -ions are more stabilized because their outer energy level becomes full. Ion -atom with a charge that has gained or lost electrons.

Common Elements in Organisms: 

Common Elements in Organisms H, C, O = most common Hydrogen forms one covalent bond Oxygen forms two covalent bonds Carbon forms four covalent bonds -can also form long chains with other carbon atoms.

Other Common Elements: 

Other Common Elements Nitrogen -part of amine groups in amino acids and other proteins Calcium -needed to make the mineral that strengthens bones and teeth Phosphorous -part of the phosphate groups in ATP and DNA molecules Iron -needed to make hemoglobin and thus to carry oxygen in the blood

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Sodium -used in neurons for the transmission of nerve impulses and maintaining electrical potential across membranes. Potassium -same general functions as sodium. Homework Outline the properties of water and how they are useful to living organisms as coolants, for metabolic reactions and transport. Thermal properties Cohesive properties Solvent properties

Homework: : 

Homework: 1. Outline the properties of water and how they are useful to living organisms as coolants, for metabolic reactions and transport. 2. Thermal properties 3. Cohesive properties 4. Solvent properties

Water : 

Water Water is polar. Polarity is caused by unequal sharing of electrons. The oxygen is attracting more electrons than the hydrogen atoms. Oxygen becomes slightly negative. Hydrogen becomes slightly positive.

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The polarity of water causes it to form hydrogen bonds with other water molecules. Hydrogen bonds are formed by the attraction of polar ends of water molecules (negative end attracts positive end). Hydrogen bonds are not chemical bonds; they are attractions of forces (electrons are not transferred or shared).

Thermal Properties of Water: 

Thermal Properties of Water Heat capacity or specific heat - amount of energy required to raise the temperature by 1°C. 1. Water has a large heat capacity. 2. It can release or absorb a lot of heat without changing its temp. 3. Organisms with large amounts of water have more stable temps.

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Heat of vaporization -amount of energy needed to evaporate 1.0g of water (540cal/g). 1. This is useful for humans when we sweat. 2. The water that we perspire evaporates. 3. The water on our skin absorbs 540 cal/g of heat from our bodies, then it evaporates. This is what cools us off

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Heat of fusion - amount of energy required to change 1.0 g of a solid to a liquid. Boiling point - 100°C 1. The b.p. of water is high compared to many other fluids. 2. For water to boil all hydrogen bonds must be broken. **Water can evaporate at temperatures below the boiling point. Hydrogen bonds are still broken.

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Freezing Point – 0°C 1. As water becomes solid it loses density, causing it to float. 2. Water freezes at the surface first. 3. The surface ice insulates the water underneath, keeping it from freezing. This allows aquatic organisms to survive the winter.

Cohesive Properties of Water : 

Cohesive Properties of Water Cohesion -water is attracted to water 1. It is caused by hydrogen bonds. 2. It is responsible for surface tension. A sphere exhibiting surface tension is caused by cohesion. Adhesion -water’s attraction to other substances.

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Cohesive properties of water are especially important for plants. 1. Capillary action -describes how water is able to move up the xylem. 2. Capillary actions in plants is directly related to transpiration 3. Cohesion keeps the water molecules intact . 4. Adhesion attaches water to the xylem walls.

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Water’s polarity allows it to dissolve most solutes (Water is the universal solvent.) The positive side of a water molecule will attract the negative side of another molecule (and vice versa) Example: Sodium chloride dissolves easily in water because it is charged. Butters/oils/waxes will not dissolve in water because they are non-polar.

Solvent Properties of Water : 

Solvent Properties of Water Water as a transport medium Blood’s plasma is about 90% water. Many minerals and ions are dissolved in our blood, thus making water necessary for nutrient transport. Water is also necessary for nutrient transport in plants.

Water and Metabolic Processes: 

Water and Metabolic Processes All metabolic processes require water. Digestion Assimilation Cellular respiration Metabolism

Organic Compounds: 

Organic Compounds Organic compound -any molecule containing carbon. - found in living systems. - carbon pairs most frequently with O, H and N. carbon often uses covalent bonds to pair with other atoms. Example: Methane (CH4)

Proteins: 

Proteins the most important of all biological compounds. derived from the Greek proteios, meaning “of first importance”. Many types of proteins exist and they perform a variety of functions, including the following roles:

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Structure – In plants, cellulose is the main structural material. For animals, it is structural proteins which are the chief constituents of skin, bones, hair and nails. Two important structural proteins – collagen and keratin. Catalysis – Virtually all the reactions that take place in living organisms are catalyzed by proteins called enzymes. Without enzymes, the reactions would take place so slowly as to be useless.

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3. Movement – Muscles are made up of protein molecules called myosin and actin. 4. Transport – ex. hemoglobin (protein in the blood that carries oxygen from the lungs to the cells in which it is used and carbon dioxide from the cells to the lungs. 5. Hormones – ex. insulin, erythropoietin and human growth hormone.

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6. Protection – ex. fibrinogen (a protein that is responsible for blood clotting). 7. Storage – ex. casein (in milk) and ovalbumin (in eggs) store nutrients for newborn mammals and birds. Ferritin (protein in the liver that stores iron). 8. Regulation

2 major types of proteins:: 

2 major types of proteins: 1. Fibrous proteins – insoluble in water and are used mainly for structural purposes. 2. Globular proteins – more or less soluble in water and are used mainly for nonstructural purposes.

Amino Acids: 

Amino Acids - an organic compound containing an amino group and a carboxyl group. Alpha amino acids – the 20 amino acids commonly found in proteins. The most important aspect of the R groups is their polarity. On that basis we can classify amino acids into four groups:

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1. Nonpolar – hydrophobic (they repel water). 2 . Polar but neutral – hydrophilic (attracted to water). 3. Acidic 4. Basic This aspect of the R groups is very important in determining both the structure and the function of each protein molecule.

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Chiral – from the Greek cheir, meaning “hand”; an object that is not superposable on its mirror image. Achiral – an object that is superposable on its mirror image. Zwitterions – from the German word zwitter, meaning “hybrid”; compounds that have a positive charge on one atom and a negative charge on another.

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An amino acid has –COOH and –NH2 groups in the same moleule. Amino acids are zwitterions not only in water solution but also in the solid state. They are therefore ionic compounds – that is, internal salts. All of them are solids with high melting points ex. glycine melts at 262C), just as we would expect for ionic compounds.

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The 20 common amino acids are also fairly soluble in water, as ionic compounds generally are. If they had no charges, we would expect only the smaller ones to be soluble. If we add an amino acid to water, it dissolves and then has the same zwitterionic structure that it has in the solid state. Let us see what happens if we change the pH of the solution, as we can easily do by adding a source of H3O+, such as HCl solution (to lower the pH), or a strong base,

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such as NaOH (to raise the pH). Because H3O+ is a stronger acid than a typical carboxylic acid,it donates a proton to the – COO- group, turning the zwitterion into a positive ion. This happens to all amino acids if the pH is sufficiently lowered – say, to pH 2.* Addition of OH- to the zwitterion causes the –NH3+ to donate its proton to OH-, turning the zwitterion into a negative ion. This happens to all amino acids if the pH is sufficiently raised – say, to pH 10.*

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Isoelectric point (pI) – the pH at which a molecule has no net charge. Amphiprotic – a compound that is both an acid and a base. Buffer solution – a solution that neutralizes both acid and base. Amino acids are therefore amohiprotic compounds and aqueous solution (a solution in which the solvent is water) of them are buffers.