Download Chemistry of Life Chap 5

The Chemistry of Life – Chap5
Universe is made of matter, energy and space-time.
Matter: All things are made of Matter. Matter exists in 3 states: Solid, Liquid and Gas.
Matter is formed of 92 basic kinds called elements. An element has atoms of only 1 kind.
Element Hydrogen has the smallest atoms and element Uranium has the largest atoms.
Atom
Atom: The smallest part of a substance to retain its properties. The smallest is Hydrogen and the
largest is Uranium.
Nucleus: An atom is formed of a very small central dense part called Nucleus having protons and
neutrons.
Proton: It has + particles called a Protons. It determines Element.
Neutron: Atoms have in their nucleus a neutral particle called a Neutron. It determines Isotope.
Electron: Around the nucleus is a large hollow area in which really small – particles called Electrons
move very fast around the nucleus. Electrons in the outermost shell determine chemical properties.
Chemical Bonds
Covalent Bond is formed by sharing an electron pair between 2 atoms. These are strongest bonds.
Equal shared covalent bonds like H – H, O = C =O have no charge on atoms. H2, O2, CO2
Unequal shared covalent bonds like H – O – H have partial charges over atoms. This produces weak
bonds called H-bonds, for example H2O molecules.
Ionic bond is present between 2 ions formed due to complete transfer of electron/s. this produces
higher unit charges and strong bonds.
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Recap 1 Chemistry
------------exists in 3 states solid, liquid and gas.
Matter is formed of 92 -----------, Hydrogen to Uranium.
--------are positive charged particles in nucleus and determine ---------------are negative charged particles orbiting around nucleus and determine --------------are neutral particles present in nucleus and determine --------------- -------means water molecules are attracted to ions and polar molecules.
2 atoms with same # of protons but different # of neutrons are different ------------.
---------bonds are formed between different water molecules due to their polar nature. (weak
bonds)
-------bonds are formed due to complete transfer of electron/s from 1 atom to another. (strong )
--------bonds are formed due to shared electron pair between 2 atoms. (very strong bonds)
Acids, Bases, Salts, Buffers
Acids are chemicals that produce H+, like HCl
Bases accept H+ and may produce OH- ions, like NaOH
Salts: Acids and bases react to form salts; salts produce ions other than H+ or OH-. Like NaCl, table
salt
pH scale is used to measure the concentration of H+ in any solution. It is a - log scale. It means the
stronger the acid the lower its pH.
pH scale varies from 0 – 14.
pH 7 is neutral; represented by pure water.
Acidity increases from 7  0 by 10 for each digit
Alkalinity increases from 7  14 by 10 for each digit.
Buffers are chemicals that minimize changes in pH.
Radioactive Isotopes
Radioactive isotopes have a constant rate of decay, half-life period.
Tracers: decay very rapidly and are used in body for diagnosis – for example cancer.
Dating Earth / rocks / fossils: have very long half life, scientists use fraction of radioactive isotope to
determine the age.
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RECAP-2 Chemistry
------- produce H+; ----------accept H+ .
------- are formed due to reaction between acid and base.
pH of pure water is ---strong acid is ---and strong base is ------------resist fast changes in pH.
Anything with mass, occupies space is ----------# of Protons indicates ------------ -------------# of Protons + # of neutrons = ----------- -----------Chemical behavior is determined by # of-----------Element is determined by # of ---------------------Isotope is determined by # of ------------------Radioactive isotopes are used as -------------- and
----------- of fossils.
Organic molecules
Organic Molecules always have C and H. O is also present in most organic molecules.
Some examples include CH4 = methane, C6H12O6 = Glucose and CH3COOH = Vinegar
Is CO2 organic or inorganic? What about H2O?
Organic molecules have a core of C and H atoms.
Functional groups are small groups of atoms attached to the core – NH2, - COOH, - OH
Organic Molecules
Organic molecules may have 1 or 2 or many unit structures in them.
Monomer = 1 unit, glucose, amino acids
Dimer = 2 units – maltose have 2 glucose units and a dipeptide has 2 amino acids.
Polymer = many units,
Starch has hundreds / thousands of glucose units
a protein has hundreds of amino acids and
a nucleic acid has thousands to millions of units.
Carbohydrates
Monosaccharide (mono=one, saccharide=sugar) are sugars formed of single units of C3 to C7. Most
common examples are glucose and fructose. These are monomers.
C3 = Glycerol, C5 = Ribose and Deoxyribose, C6 = Glucose and Fructose
Disaccharide (di=2) and Oligosaccharides (oligo=few).
Glucose + Glucose Maltose + H2O
Glucose + Glucose Sucrose + H2O Sucrose is commercial sugar
Lactose is a disaccharide milk sugar of glucose and galactose.
Polysaccharides: Starch, Glycogen, and Cellulose are all polymers of Glucose. Starch is food storage
molecule of plants and Glycogen does the same for animals and fungi. Cellulose is a polymer of
slightly different glucose is a building material in cell walls. Cellulose is the most abundant organic
molecule in biosphere.
Lipids or Fats
All lipids are Hydrophobic (hydro=water, phobic=repulsion). These are compounds of C,H and O.
True fats are formed of a molecule of Glyecrol a 3C alcohol and 3 long chain fatty acids called
triglycerides.
Fats are solid at room temp and are rich in saturated fatty acids.
Oils are liquids at room temp and are rich in unsaturated fatty acids.
Phospholipids are special lipids in which phosphate replaces one of the 3 fatty acids in fat molecule.
They have ionic part usually an amine attached to phosphate. 2 long chains of fatty acids are
attached to glycerol. Ionic part is Hydrophilic (philic=loving) and fatty acid tails are Hydrophobic. This
dual nature helps them create and maintain Cell membranes.
Steroids are lipids formed of 4 fused rings. Most common examples include Cholesterol present in
blood and attached to membranes. Steroid hormones include sex-hormones and adrenal-hormones.
Recap 3 Chemistry
1. Organic molecules always have ----- and ------ elements.
2. ----- ------ are small groups of atoms (– NH2, - COOH, - OH) attached to the core.
3. Glucose + glucose  Maltose + H2O; is an example of ---------4. Maltose + H2O  Glucose + Glucose; is an example of --------5. ------ is a monosaccharide sugar but ------- is a disaccharide sugar.
6. A -------- sugar is formed of 2 units. Sucrose is formed of 1 glucose and 1 fructose.
7. ----- and ------- are energy storing polysaccharides.
8. Starch is a polymer of ---------- units.
9. A True fat molecule is formed from 1 ---- and 3 ---- ---- molecules.
10. Fats have ------ fatty acids in them but oils have -------- fatty acids.
Proteins
Proteins are polymers of 20 kinds of Amino Acids. Glycine, Alanine, Lysine and Methionine are some
examples.
Each amino acid has a carboxylic (acidic) group and an amino group.
Carboxylic group of one amino acid joins with the amino group of second amino acid to form a
covalent bond called a Peptide bond. Many amino acids join together with peptide bonds to form a
Polypeptide.
A polypeptide has only primary structure a fixed # of amino acids with a specific arrangement.
A polypeptide undergoes regular coiling to form a Secondary Structure which mostly undergoes a 3dimensional unique irregular coiling resulting in a structure. Most proteins are globular and have a
tertiary structure. Most fibrous proteins have a secondary structure.
Nucleic Acids DNA and RNA
Nucleic Acid: are acidic substances found in nucleus of cells.
2 basic types: DNA = Deoxyribose N.A. and RNA = ribose N.A.
Nucleic acids are polymers of units called Nucleotides.
Each nucleotide is formed of: a) a pentose sugar Ribose or Deoxyribose b) a Phosphate c) one of 4 Nbases, both have 3 common bases Adenine, Guanine and Cytosine. In DNA Adenine always bonds to
Thymine and Cytosine to Guanine. A-T and C-G are called Complementary bases.
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DNA
Sugar is Deoxyribose
N-bases include Thymine
Genetic material
Double Helix
Most lies in nucleus
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RNA
Sugar is Ribose
N-bases include Uracil
Executes protein synthesis
Single chain may be coiled
Most lies in cytoplasm
DNA Structure
DNA is a ladder like molecule formed of 2 antiparallel chains.
The main chain is formed of alternating Deoxyribose and Phosphate molecules.
The side chains are formed of N-bases of opposite chains held together by H-bonds.
The 2 chains are twisted around each other resulting in a Double Helical Structure.
ATP the Energy Currency of Cells
ATP: Adenosine Triphosphate is a nucleotide formed of 5 molecules.
Ribose a pentose (5C) sugar
Adenine a N-base formed of 2 fused rings (purine)
3 Phosphates that is why a Triphosphate. It can lose 3rd phosphate to become ADP + Pi and releases
energy used in most cell functions.
Adenine + Ribose = Adenosine
Recap 4 Chemistry
1. Proteins are polymers of -------- -----------.
2. A -----------covalent bond joins 2 amino acids in a protein.
3. ------ kinds of amino acids form proteins in living things.
4. Hemoglobin has quaternary structure and has ---chains.
5. DNA has pentose sugar --- but RNA has --- pentose sugar.
6. 4 N-bases present in DNA are -----------.
7. Unique N-base present in RNA is ------------.
8. DNA has --- chain/s and RNA has ----chain/s.
9. In DNA N-bases always pair as --------- and -----------.
10. ATP molecule has 1 N-base---, 1 pentose sugar-----, and 3-------groups.