Biochemistry

Atoms

Atoms

• consists of protons and neutrons and surrounded by electrons

• many share electrons in shells as molecules are most stable when their shell is complete

Complete Shell Equation

2N^2

Combining Atoms

• chemical reaction occurs whenever a chemical bond is formed, rearranged or broken

Ions

• atoms that have a charge because of an unequal number of protons and electrons

Molecules

• two or more atoms that share electrons

Compunds

• contain atoms of 2 or more elements

Free Radicals and Their Effects on Health

• an atom or molecule with an unpaired electron in its outer shell that is unstable, highly reactive and destructive to nearby molecules

• generation of free radicals is increased when exposed to UV light, X-rays, chemical and certain normal metabolic processes

• effects can be partially offset by antioxidants

Chemical Bonds

• forces that hold together the atoms of molecules and compounds

• likelihood depends on the number of valence electrons

• atoms of the most biologically diverse elements do not have eight valence electrons

Formation of Methane

4H+C>CH4

• carbon has 4 valence electrons that form with hydrogens 4 valence electrons to make it complete

Energy Flow in Chemical Reactions

• Chemical reactions either use or release energy that was present in the chemical bonds

• can be exergonic or endergonic

Exergonic

• spontaneous chemical reaction where there is a net release of energy

Endergonic

• nonspontaneous chemical reaction where energy is absorbed from the surroundings

What determines whether energy is released or absorbed?

• the change in potential energy in the chemical bonds

Organic Compounds

• contain carbon

• are usually large molecules

Inorganic Compounds

• do not contain carbon and include water, salts, acids and bases

Water Qualities

• boiling point: 100°C

• Freezing point: 0°C

• Density: 1g/cm^3

• High heat capacity making it resistant to temperature changes

• High heat/energy required to vaporize/boil

• High surface tension as water molecules stick together

Water as a Solvent

• negative side associates with positive end of solute molecule

• Positive side associates with negative end of solute molecule

Salts

• contain positive ions (cations) other than H+

• Contain negative ions (anions) other than OH-

• Typically dissociate readily in water

Salts to Know

• NaCl (sodium chloride)

• CaCo3 (calcium carbonate)

• KCl (potassium chloride)

• CaPO4 (calcium phosphate)

Acids

• release H+ ions sin large amounts

• Are proton donors

• pH of 0-6.9

• Example is HCl found in the stomach

Bases

• accept H+ ions and are called proton acceptors

• pH of 7.1-14

• examples are bicarbonate found in blood and ammonia found in waste products

Buffers

• living cells and tissues are very sensitive to changes in pH and need to maintain a constant pH of 6.5 to 7.2

• regulation is completed by molecules that resist abrupt changes in pH

What makes carbon so special?

• carbon forms bond with many other carbon atoms

• large number of shapes and sizes

• unique structure and function

Macromolecules

• carbohydrates

• lipids

• proteins

• nucleic acids

Carbohydrates

• sugars and starches

• contains carbon, hydrogen and oxygen

• only make up 2-3% of total body mass

• provide energy

• glucose produces ATP

Monosaccharides

• simple sugars

• general formula is (CH2O)n

Glucose

• formula is C6H12O6

• type of monosaccharide that can be absorbed directly into blood

• does not require digestion

• important when looking at diabetes

Diasaccharides

• formed when 2 simple sugars join together

• glucose + fructose > sucrose

• 2 carbohydrates form one carbohydrate

Lactose

• formed by glucose and galactose

• disaccharide

Maltose

• formed by 2 glucose molecules

• disaccharide

Polysaccharides

• many simple sugars linked together

• form in ways most carbohydrates are found

Homopolysaccharides

• many molecules of one sugar

• such as glycogen, starch and cellulose

Heteropolysaccharides

• most of these contain only 2 types of sugars and are associated with proteins

• such as glycoprotein

Glycogen

• most important homopolysaccharide in humans

• used for the storage of glucose

• made and stored primarily in the liver, skeletal muscle and cardiac muscle

• storage varies dramatically with diet, exercise and stress

Starch

• equivalent storage product of humans found in plants

• most common carbohydrate in human diets

• large amounts in wheat, potatoes, rice and corn

• made by leaves during the day and used as an energy source at night

• also used for nonfood purposes

Lipids

• contain carbon, hydrogen and oxygen (lower proportion than carbohydrates)

• make up 18-25% of total body mass

• macromolecules made of fatty acid monomers

• used for structural support for the cell, energy storage, protection of body organs and cell signalling (steroid hormones for chemical messages)

• nonpolar

• includes triglycerides, phospholipids, steroids and waxes

Fatty Acids

• simplest lipids that can be broken down to produce ATP

Triglycerides

• neutral fats

• fat when solid and oil when liquid

• large molecules used for storage that is found just below the skin

Phospholipids

• modified triglycerides that contain phosphorus

• found in cell membranes

Steroids

• structurally different than triglycerides

Cholesteral

• type of lipid (steroid) that is essential for human life

Proteins

• basic structural material of the body that has many functions

• 12-18% of total body mass

• contains carbon, oxygen, hydrogen and nitrogen

• some may also contain sulphur

• composed of amino acids

Amino Acid Functional Groups

• amine group (common)

• organic acid group (common)

• unique group

Amino Acids

• link to form peptides

• 20 common ones

• either obtained from nutrition (essential) or synthesized by the body (non-essential)

Essential Amino Acids

• Leucine

• Isoleucine

• Valine

• Histidine

• Lysine

• Methionine

• Phenylalanine

• Threonine

• Tryptophan

Non-Essential Amino Acids

• alanine

• arginine

• asparagine

• aspartic acid

• cysteine

• glutamic acid

• glutamine

• glycine

• proline

• serline

• tyrosine

Dipeptide

• two amino acids

Tripeptide

• three amino acids

Primary Structure

• amino acids in polypeptide chains

Secondary Structure

• polypeptide chains form spirals or sheets

Tertiary Structure

• spirals or sheets folded up

Quaternary Structure

• two or more chains combine to form function protein

Enzymes

• proteins that acts as catalysts to speed up biochemical reactions

• not used up during the reactions

• reduce the energy needed to start the reaction

Nucleic Acids

• largest molecules in the body

• composed of carbon, oxygen, hydrogen, nitrogen and phosphorus

• DNA and RNA

Nucleotides

• structural unit of nucleic acids

• adenine and guanine are purines with 2 ring bases

• cytosine, thymine and uracil are pyrimidines with 1 ring bases

DNA

• found in the nucleus

• replicates itself and is found in nearly all cells

• provides information for building proteins

RNA

• usually found outside the nucleus

• works for DNA by carrying out orders for protein synthesis

• different types of RNA carry out different parts the building process

• single strands of nucleic acids

Adenosine Triphosphate (ATP)

• provides energy that is directly used by cells

Cellular Respiration

• exergonic reaction

• glucose in oxidized

• oxygen is reduced