BASIC CHEMISTRY

1
BASIC CHEMISTRY
2
MATTER

• Anything possessing mass and taking up space
• Tangible
• Can exist in various forms
• Solid
• Liquid
• Gas
• Comprised of many elements

3
ELEMENTS

• Substance that cannot be broken down into simpler
  substances by normal chemical means
• Approximately 100 different elements exist
• Each denoted by a symbol
• e.g., carbon (C), hydrogen (H), etc.
• e.g., NOT water (H2O), glucose, sodium chloride,
  etc.

X
Sodium Chloride (NaCl)
Sodium (Na)
Chlorine (Cl)
4
ELEMENTS

• 96 of the mass of living matter is comprised of
  just four elements
• Carbon (C)
• Hydrogen (H)
• Nitrogen (N)
• Oxygen (O)
• Many other elements arealso important
  componentsof living matter

5
ATOMS

• Smallest unit into which an element can be
  subdivided while retaining its properties
• Comprised of smaller subatomic particles
• Protons charge mass 1 amu
• Neutrons no charge mass 1 amu
• Electrons - charge mass ltltlt 1 amu
• (1 atomic mass unit (amu) 1 Dalton 1.7
  10-24 g)

6
ATOMIC STRUCTURE

• Protons and neutrons form the nucleus of an atom
• Electrons are present outside of the nucleus

Helium (He) Atom
7
ATOMIC NUMBER

• Atoms of different elements possess different
  numbers of protons
• The number of protons in an atom is its atomic
  number
• The atomic number defines the element

1
2
3
8
ATOMIC MASS

• Protons and neutrons have significant mass
• The number of protons neutrons in an atom is
  termed its atomic mass or mass number
• The mass of electrons is negligible
• The atomic mass is slightly variable for many
  elements

1
4
7
9
ISOTOPES

• Atoms of the same element possessing different
  atomic masses
• Due to different numbers of neutrons
• Identical chemical behavior

1
2
3
H
H
H
1
1
1
10
ISOTOPES

• Some isotopes are stable
• e.g., 1H, 2H, 12C, 13C, etc.
• Some isotopes are unstable
• e.g., 3H, 14C, 32P, 35S, etc.
• Radioactive
• Decay at a constant rate into more stable forms
• May transform into another element
• e.g., 14C ? N
• Time required for half of a radioactive sample to
  decay is termed the radioisotopes half-life
• e.g., 14Cs half-life 5000 years
• Important research tools

11
ELECTRON SHELLS

• An atoms electrons are placed in 1 or more
  electron shells
• Represent energy levels of electrons
• First shell must be completely filled before
  electrons can be placed in the second shell, etc.
• The first shell can hold 2 electrons
• The next few shells can each hold 8 electrons

12
CHEMICAL BONDS

• Atoms can be joined to each other via chemical
  bonds
• A molecule consists of two or more atoms joined
  together by chemical bonds
• A compound consists of atoms of two or more
  different elements held together by chemical
  bonds
• Ions (charged atoms) are not molecules, but are
  often included in discussions of small molecules

13
CHEMICAL BONDS

• Making and breaking chemical bonds involves the
  exchange or rearrangement of electrons
• Atoms are most stable when their outermost
  electron shell is completely full
• Atoms will tend to react such that their
  outermost electron shell is completely full

14
CHEMICAL BONDS

• How would you expect F and Cl to react?
• Li and Na?
• He, Ne, and Ar?

15
IONIC BONDS

• Na tends to lose an electron to form Na (sodium
  ion)
• Cl tends to gain an electron to form Cl-
  (chloride ion)
• The interaction between ions of opposite charge
  is termed an ionic bond
• Atoms of both elements present in fixed ratio
• compound

16
COVALENT BONDS

• Electrons are not always gained or lost
• Electrons can be shared
• Sharing is always in pair(s) of electrons
• The sharing of a pair of electrons is termed a
  covalent bond

17
COVALENT BONDS

• Electron sharing may be equal or unequal
• Equal sharing ? no charge separation
• Nonpolar covalent bonds
• Unequal sharing ? charge separation
• Polar covalent bonds
• Electronegative atoms such as oxygen tend to
  attract electrons and thus possess partial
  negative charges

18
BOND COMPARISON
19
HYDROGEN BONDS

• Attraction between a hydrogen atom possessing a
  partial positive charge and another molecule
  possessing a partial negative charge
• Much weaker than covalent and ionic bonds
• 1/20 as strong
• Many weak bonds can add up to a significant
  force
• Transient
• Constantly breaking andreforming

20
CHEMISTRY OF WATER

• Most prevalent molecule within living organisms
• Crucial to life
• Polar covalent bonds
• Participate in H-bonds
• Water molecules interact with each other
• Water is held together by these H-bonds
• Cohesion
• Water attaches to other ions molecules by
  H-bonds
• Adhesion

21
COHESION ADHESION

• Cohesion adhesion allow transport against
  gravity
• Movement of blood into capillary tubes
• Capillary action
• Transport of water in plants

Xylem vessels in plants
22
SURFACE TENSION

• Surface tension results from cohesion
• Difficult to break the surface of water
• e.g., water strider, skipping rocks, etc.

23
WATER AS A SOLVENT

• Water is a powerful solvent
• Interacts with other polar or charged molecules
  and ions
• Many molecules and ions dissolve in water
• Most chemical reactions in organisms occur
  dissolved in H2O

24
DISSOCIATION OF WATER

• Most water molecules exist as H2O (H-O-H)
• A fraction of water molecules exist is a
  dissociated state
• H-O-H ? H OH- (hydrogen ion hydroxide ion)
• (H actually reacts with H2O to form H3O)
• In pure water, H 10-7 mol/L
• In pure water, OH- 10-7 mol/L
• H OH- 10-14 mol/L
• H is not always equal to OH-
• As H ?, OH- ?, and vice versa

25
ACIDS BASES

• An acid is a substance that increases H
• Typically ionizes to form H
• e.g., HCl ? H Cl-
• As H ?, OH- ?
• A base is a substance that decreases H
• Frequently ionizes to form OH-
• e.g., NaOH ? Na OH-
• As H ?, OH- ?

26
pH

• Power of hydrogen
• Quantitative measure of H
• -log10H
• e.g., H of 10-7 mol/L ? pH 7
• e.g., H of 10-6 mol/L ? pH 6
• e.g., H of 10-2 mol/L ? pH 2
• e.g., H of 10-8 mol/L ? pH 8
• e.g., H of 10-12 mol/L ? pH 12

27
BUFFERS

• Significant changes in pH can be damaging to
  cells and organisms
• Inactivated cellular components
• Altered nutrient availability
• A buffer is a substance or system able to resist
  significant pH changes
• Absorbs excess H or OH- ions
• Typically contains a weak acid or weak base

28
BIOLOGICAL MACROMOLECULES
29
CELL COMPOSITION

• 70 95 water
• Most of the remainder of the cell is composed of
  organic molecules
• Four major classes of biological macromolecules
• Carbohydrates
• Lipids
• Nucleic acids
• Proteins
• Molecules containing both carbon and hydrogen

30
MACROMOLECULES

• Assembled from various smaller subunits
• Most are polymers, a series of repeating subunits
  
• Assembled via condensation reactions
• a.k.a., dehydration reactions
• Disassembled via hydrolysis reactions

31
CARBOHYDRATES

• Sugars and their polymers
• General formula (CH2O)n
• CHO ratio 121
• Possess polar covalent bonds
• Form H-bonds
• Generally interact favorably with water

32
ROLES OF CARBOHYDRATES

• Short-term energy source
• Monosaccharides (e.g., glucose, fructose)
• Disaccharides (e.g., sucrose, lactose)

33
ROLES OF CARBOHYDRATES

• Longer-term energy source
• Starch (in plants)
• Can be hydrolyzed into sugar monomers
• Glycogen (in animals)
• Can be hydrolyzed into sugar monomers

34
ROLES OF CARBOHYDRATES

• Structural roles
• Chitin
• Present in fungal cell walls
• Present in insect exoskeletons
• Not easily hydrolyzed

• Cellulose
• Present in plant cell walls
• Not easily hydrolyzed
• Comprises half of organic carbon on earth

35
ROLES OF CARBOHYDRATES

• Cell communication
• Glycoproteins and glycolipids on cell surface

36
LIPIDS

• Not polymers
• Comprised almost exclusively of C and H
• Non-polar bonds ? no H-bonding
• Hydrophobic
• Generally interact poorly with water
• (Oil and water dont mix very well)

37
ROLES OF LIPIDS

• Energy storage
• Fats and oils
• Triacylglycerols
• Fatty acids glycerol
• Saturated vs. unsaturated
• Which is better in your diet?

38
ROLES OF LIPIDS

• Membrane components
• Phospholipids
• Similar to fats
• Glycerol
• Two fatty acids
• Phosphate
• (Inositol, choline, etc.)
• Amphipathic
• Hydrophobic region
• Hydrophilic region

39
ROLES OF LIPIDS

• Membrane components
• Phospholipids
• Aggregate in water-rich environments
• Micelles
• Phospholipid bilayers
• Form basis of cell membranes
• Hydrophobic regions are hidden from water
• Hydrophilic regions are in contact with water

40
ROLES OF LIPIDS

• Membrane components
• Cholesterol
• Steroid
• Amphipathic
• Membrane antifreeze
• Prevents membrane solidification at low
  temperatures

41
ROLES OF LIPIDS

• Cell communication
• Steroid hormones
• Cholesterol is the precursor for all steroid
  hormones
• Involved in a variety of body functions
• e.g., reproduction
• e.g., water regulation
• e.g., salt regulation
• e.g., sugar biosynthesis

42
PROTEINS

• Polypeptides (almost synonymous)
• Comprise over 50 of dry weight of most cells
• Polymers of amino acids
• 20 different amino acids
• Different R groups
• Very diverse in structure and function

43
PROTEINS

• Amino acids are covalently linked via
  condensation reactions
• Amino group of one reacts with acid group of
  another
• Peptide bonds
• All proteins are made by assembling the same 20
  amino acids in different orders to different
  lengths

44
ROLES OF PROTEINS

• Structural
• e.g., collagen, elastin, keratin, etc.

45
ROLES OF PROTEINS

• Movement
• e.g., actin, myosin, tubulin, etc.

46
ROLES OF PROTEINS

• Transport
• e.g., hemoglobin, lac permease, etc.

47
ROLES OF PROTEINS

• Chemical messengers
• e.g., hormones, neurotransmitters
• Receptors
• Respond to chemical messengers

48
ROLES OF PROTEINS

• Storage
• e.g., ovalbumin, casein, etc.

49
ROLES OF PROTEINS

• Defensive
• e.g., antibodies, fibrin

50
ROLES OF PROTEINS

• Enzymes
• Biological catalysts
• Speed up the rate of a chemical reaction
• As much as 10,000 times
• Not consumed in this reaction
• Highly specific

51
PROTEINS

• Humans can make tens of thousands of different
  proteins
• All use the same 20 amino acids
• Different orders
• Different lengths
• How many distinctly different tripeptides can be
  made using these 20 amino acids?

52
ESSENTIAL NONESSENTIAL

• All organisms require all 20 amino acids
• The bacterium Escherichia coli can normally
  synthesize all 20 amino acids from precursor
  molecules
• Humans can produce 10 amino acids from precursor
  molecules
• Non-essential amino acids
• Humans lack the ability to synthesize the
  remaining 10 amino acids
• Essential amino acids
• Must be acquired from diet
• Humans can produce 12 amino acids from
  precursor molecules, but the precursor molecules
  for the production of two of these 12 amino acids
  are themselves essential amino acids (met ? cys,
  phe ? tyr)

53
PROTEIN STRUCTURE

• Protein function is related to its structure
• Various levels of protein structure
• Primary structure
• Secondary structure
• Tertiary structure
• Quaternary structure

54
PROTEIN STRUCTURE

• Primary structure
• Linear sequence of amino acids
• Genetically determined
• Will ultimately affect secondary structure, etc.
• Lysozyme is depicted
• 129 amino acids long
• How many different ways can 129 amino acids be
  assembled into a protein?

55
PROTEIN STRUCTURE

• Secondary structure
• Formed by regular H-bonding at regular intervals
  along polypeptide backbone
• a-helices
• b-pleated sheets (b-sheets)
• Charges in primary structure can alter secondary
  structure

56
PROTEIN STRUCTURE

• Tertiary structure
• Formed by bonding between R-groups
• Covalent bonds
• Disulfide bridges
• Ionic bonds
• H-bonds
• Hydrophobic interactions

57
PROTEIN STRUCTURE

• Quaternary structure
• Interactions between separate polypeptide chains
• Not all proteins possess multiple polypeptide
  chains
• Not all proteins possess quaternary structure
• Collagen and hemoglobin are depicted

58
PROTEIN STRUCTURE
59
PROTEIN STRUCTURE
60
PROTEIN DENATURATION

• 3-D protein conformation critical to function
• Altered conformation ? compromised function
• Denaturation
• Factors affecting protein conformation
• Temperature
• pH
• Salt concentration
• Etc.
• Denaturation often irreversible
• It is difficult to un-hardboil an egg

61
NUCLEIC ACIDS

• DNA
• Deoxyribonucleic acid
• Polymer of deoxynucleotides
• Genetic material of all cellular life and of some
  viruses
• Organized into genes
• Blueprints for proteins

• RNA
• Ribonucleic acid
• Polymer of nucleotides
• Genetic material of some viruses
• Intermediates in gene expression
• Components of ribosomes
• Some possess enzyme-like activity
• Ribozymes

62
GENE EXPRESSION

• DNA is organized into units called genes
• A gene is a blueprint for a protein
• RNA is an intermediate in gene expression
• DNA ? RNA ? protein

63
(DEOXY)NUCLEOTIDES

• DNA monomers are termed deoxynucleotides
• RNA monomers are termed nucleotides
• Nucleotides and deoxynucleotides are composed of
  three parts
• Pentose sugar
• Nitrogenous base
• Phosphate

64
PENTOSE SUGARS

• Both DNA and RNA possess a pentose sugar
• Ribose in RNA
• Deoxyribose in DNA
• Lacks the 3 OH group possessed by ribose

65
NITROGENOUS BASES

• Both DNA and RNA possesses four nitrogenous bases
• Adenine
• Guanine
• Cytosine
• Thymine (DNA only)
• Uracil (RNA only)

66
PHOSPHATE GROUPS

• One or more attached to the 5 carbon of
  (deoxy)ribose
• Triphosphates used in polynucleotide synthesis
• Only one is incorporated into a DNA or RNA
  chain

67
POLYNUCLEOTIDES

• Nucleotides joined via condensation reactions
• 3 OH and 5 phosphate group OH
• New nucleotides added to 3 end of growing
  polynucleotide chain
• Two strands of double-stranded polynucleotides
  are NOT covalently linked
• Interact through H-bonds

68
DNA

• Most DNA and some RNA is double-stranded
• Nitrogenous bases project from backbone of
  alternating sugar and phosphate groups
• Interact through H-bonds

DNA double helix