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Biochem notes
Basic chemistry review: ch 3
Chemical nature of life
• Living things are made of atoms and
molecules
• Life is the product of complex chemical
reactions
Remember?
• Atoms: simplest form of matter
• Elements: types of atoms (92 natural)
• Molecules: bonded atoms with new
properties--H2O is nothing like H or O
• Compounds: types of molecules
To know
• Symbols of elements: C, H, He, O, N, S,
P, Na, Cl, K, Mg, Fe, I, Hg, Ca, Si
• Formulas of compounds: H2O, NaCl,
CO2, CO, O2, N2, H2, CH4, NH3,
C6H12O6, SiO2
Atomic structure
– Nucleus
• Protons: mass of 1AMU, charge +1
• Neutrons: mass of 1 AMU, Charge 0
– Electrons in orbits: almost no mass, charge -1
• Chemical reactions
– C6H12O6 + O2
CO2 + H2O + ENERGY
– CH4 + O2
CO2 + H2O + ENERGY
• Bonds: hold atoms together to form molecules
– Ionic: between charged ions, weak, dissolve in water
• NaCl
– Covalent: shared electrons, strong.
• H2O
– Hydrogen: between water molecules
• Ions: charged atoms (gained or lost electrons)
• Solutions: molecules dissolved in water
• Isotopes: fat atoms (extra neutrons)
The most amazing molecule: water
• A polar molecule: one end is + one is – Universal solvent
• Doesn’t mix with or dissolve oils because oil is non-polar!
– Surface tension
– Cohesion and adhesion
• High specific heat: heats and cools slowly (cooler by
the lake in Duluth)
• High latent heat: extra energy to melt or evaporate
(sweat cools)
• Ice floats!
Adhesion
• H2O molecules form H bonds with other
substances
– capillary action
– meniscus
– water climbs up fiber
• ex. paper towel
Acidity (acid or base)
• Acids add H+ ions to water
–
–
–
–
Taste sour
Feel wet
Lemon
Turns litus paper red
• Bases add OH- ions to water (hydroxide)
–
–
–
–
Tastes bitter
Feels soupy
Baking soda
Turns litmus paper blue
• Acids and bases neutralize each other
– OH- + H+ = H2O + a salt
• pH scale measures acidity
strong1----------------------7--------------------------14 strong
Acid
water
base
Organic compounds
• Contain C, H, O and sometimes N, P, S
– Carbon forms the backbone of all biochemicals
– Carbon is the smallest element that forms 4 bonds--the
maximum
• Macromolecules--big
• Polymers--made of smaller molecules called
monomers (proteins are made of amino acids)
• Like legos! The units can be used to make lots of stuff
• REMEMBER:
CARBON, CARBON, CARBON
Macromolecules
• Smaller organic molecules join together
to form larger molecules
– Macromolecules: big molecules
– polymers made of monomers
• 4 major classes of macromolecules:
– Carbohydrates: sugars and starch
– Lipids: fats and oils
– Proteins: muscle and cell parts
– nucleic acids: DNA and RNA
Composition of cells
• 70% water--universal solvent
• 15% protein--structural fibers,
hormones, enzymes
• 10% lipids (fats)--energy storage
• 4% Nucleic acids (DNA & RNA)--store
information/genetic code
• 1% Carbohydrates (energy)
Carbohydrates
• Carbohydrates are composed of C, H, O
• carbo - hydr - ate
Glucose: C6H12O6 (1:2:1)
• Function:
–
–
–
–
energy
energy storage (plant starch)
raw materials (Plants make everything from glucose)
structural materials
• Monomer: sugars
• Polymer: starch
Carbohydrates: types
• Sugars
– Glucose (monomer/monosaccharide)
– Sucrose (disaccharide)
– There are many more. They end in “ose”
• Starch (polymer)
– Energy storage in plants (food starch): “complex
carbohydrates”
– Structural material in plants: cellulose in cell wall
– Glucose balance in animals (glycogen in livers)
Carbohydrates: uses
• Energy--plants store solar energy in glucose
molecules (in the C-H bonds)
– All cells use respiration to release this energy and make ATP
for metabolism. Even plant cells!
– Plants use starch for long term energy storage
• Structural material--starch
– Cellulose in plant cell walls
– Chitin in bug exoskeletons
• Cell recognition for immune system
Lipids: fats, oils, waxes
• Animals store energy in fats
• Fats also insulate and pad organs
• Steroid hormones--testosterone,
estrogen
• Cell membrane (cholesterol)
• Made of fatty acids (monomers) and
glycerol
types
• Membrane lipids.
• Saturated--often bad for you
– Animal fats
– More solid at room temp
– Maximum of C-H bonds
• Unsaturated--less worser
– Plant oils
– Liquid
– Not as many C-H bonds
*Hydrogenated (margarine)--forcing more hydrogen into a plant oil to
make it saturated! Think margarine.
• Cholesterol--used for steroids and in the cell
Proteins
• Really big
• Thousands of amino acids joined by peptide
bonds.
• The order of the amino acids, the number of
amino acids, and the folded shape of the
protein matter.
• There are only 20 amino acids
• Some are “essential” and must come from
your diet.
Protein functions
• Structural fibers in skin, tendon, ligaments,
hair, nails
• Hormones--most
• Enzymes--these speed up chemical
reactions so they happen fast enough to
keep you alive
• Neurotransmitters--let nerve cells talk to
each other.
Nucleotides
• There are four nucleotides--the
monomers
• Cytosine, quinine, adenine, thymine
• millions are in a molecule of DNA
• Thousands are in a gene
Enzymes are Catalysts
• Catalysts: substances that speed up
chemical reactions without being
affected by the reactions themselves.
• Enzyme: a protein that increases the
rate of reactions by lowering the
activation energy.
All Chemical reactions
• Require activation energy--energy to get
them started
• Require alignment of molecules involved
• Spontaneous combustion doesn’t really
happen
Enzymes
• Enzymes are biological catalysts
• Catalysts and enzymes speed reactions
up without being used up
• Chlorophyll is the catalyst for
photosynthesis
• Many enzymes are used for digestion
(duh)
How they work
• Enzymes lower activation energy
• Most biological reactions would happen to
slowly to keep you alive without enzymes
• Unless you were on fire. This is also not
good.
• *High fever (107 F) unfolds enzymes so they
won’t work--”denaturing.” This will kill you.
Lock and Key Model
• Enzymes have an active site
• The active site “fits” the substrate and
facilitates the reactions
• The substrate is the stuff an enzymes
works on--like the food in your gut.
Complex reactions
• Many metabolic reactions are complex
• They require many steps and many
enzymes/catalysts
• These are called biochemical pathways
• Or cascade reactions
• Blood clotting, digestion, respiration,
photosynthesis