Biological Molecules

1
Biological Molecules
2

• Quick chemistry review

3
BONDS

• ATOMS
• Made of particles called protons, neutrons,
  electrons.
• Element atom with a certain number of protons,
  etc.
• Isotope atom with the wrong number of
  neutrons, . RADIOACTIVE
• ION atom which has gained or lost an electron,
  and is . charged. Positive charge lost an
  e-. negative charge gained an e-.
• Atoms like to have a set number of electrons 2,
  then multiples of 8. If they dont have enough
  or too many theyll form bonds, and/or become
  ions!

4
BONDS
Hydrogen
     
Oxygen
Carbon
5
BONDS

• IONIC between two ions
• not as strong
• comes apart easily, e.g. soluble in water
• think of it as charged and ready to react!
• COVALENT shared electrons
• very strong
• most common in biological matter
• can be POLAR or NON POLAR
• think of it as sharing gives strength!

6
Polar vs. Nonpolar Bonds

• Polar charged surface
• electrons are shared unevenly
• Prefer other polar molecules
• Soluble in water, which is also polar
• Think of it as a charged situation, looking for
  action!
• Nonpolar no residual charge
• electrons are shared evenly
• Prefer nonpolar molecules
• Soluble in oils
• Think of it as a fair, balanced situation, .
  unreactive, stable, mellow molecule

7
Molecular Rules of Attraction

• Charged molecules have ionic or polar covalent
  bonds.
• e.g. water, salt
• Uncharged molecules have non polar covalent
  bonds.
• e.g. oils
• CHARGED MOLECULES ARE ATTRACTED TO CHARGED
  MOLECULES.
• specifically charges/polarity is attracted to
  - charges/polarity
• UNCHARGED MOLECULES ARE ATTRACTED TO UNCHARGED
  MOLECULES.

8
Hydrogen Bond
H in a polar covalent bond, has a slight
charge. H bond Weak attraction of that H for
another electronegative atom. - Results in
surface tension of water, capillary action!
9
WATER

• WATER!!!
• Good solvent (polar molecule), which forms
  hydration spheres.
• Human body is largely water!

10
Water is a good SOLVENT
11
Hydration spheres
12
WATER

H
OH-
H2O
Water molecule
Hydroxide ion
Hydrogen ion
A few water moleculesnaturally dissociate
13
pH
LIFE
Log scale
SeaWater
Bleach
OvenCleaner
LemonJuice
Blood
Ammonia
WATER
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
Neutral
BASIC Lots OH-
ACIDIC Lots H
14
Buffers

• System of molecules and ions that act to prevent
  changes in H.
• In blood bicarbonate system.

15
Acids and bases

• Acid
• Molecule that can release protons (H).
• Base
• Negatively charged ion that can combine with H,
  and remove it from solution.

16
FORMING MOLECULES

• Condensation Synthesis
• remove water
• new molecule (cooking!)

Hydrolysis - add water - break up a molecule
17
FORMING MOLECULES
Condensation Synthesis
Hydrolysis
18
Stereoisomers
Stereoisomers Exactly the same atoms arranged in
same sequence, but they differ in spatial
orientation. D-isomers right-handed. L-isomers
left-handed. Enzymes are specific we can
utilize only certain stereoisomers! only L-amino
acids and D-sugars.
19

• Biological Macromolecules

20
Biological macromolecules

• Monomer one subunit
• Polymer large molecule, made of many monomers

21
Biological macromolecules

• Monomer Polymer
• amino acids (20 types) ---gt Proteins
• sugars ---gt Carbohydrates
• nucleotides (4 types) ---gt Nucleic Acids
• fatty acids ---gt Lipids

22

• Proteins

23
Structural Proteins
24
Proteins

• Proteins are amino acid polymers.
• Many roles!!!
• Enzymes
• Hormones
• Structure
• Signaling
• Transport
• DO-ERS

25
Amino Acids

• Small molecules 20 kinds
• 1 amino group
• 1 carboxyl group
• 1 "R" group
• Joined by peptide bonds to form polypeptide
• Different sequence makes different protein

26
Generic AminoAcid 20 Different R Groups
Carboxylic AcidGroup
AmineGroup    
R
R Group
27
Glutamic Acid
AmineGroup  
Carboxylic Acid     Group
Glutamic AcidR Group
28
Arginine
Carboxylic Acid     Group
AmineGroup  
Arginine R     Group
29
Phenylalanine
Carboxylic Acid     Group
AmineGroup  
PhenylalanineR Group
30
Leucine
Leucine R     Group
31
Cysteine
Cysteine R     Group
32
Proteins

• Protein structure, known as configuration, is
  intrinsic to its function.
• - shape
• - chemistry (possible bonds)

33
Illustration ofProtein Structure
Primary
Tertiary
Quaternary
Secondary
34
Levels of Protein Structure

• Like describing a knot by starting with the
  strands of the rope
• Primary The sequence, polypeptide chain
• Secondary Coiling of the chain alpha helix,
  beta sheets
• Tertiary Coiling of the coil
• Quaternary Two or more chains together

35
Proteins
36
Proteins

• Peptide polypeptide (short chain)
• Protein long polypeptide
• Denaturation heat, pH unravels protein down to
  primary structure

37
Proteins

• Glycoproteins protein, plus CH
• Lipoproteins protein, plus lipids

38

• CARBOHYDRATES

39
CARBOHYDRATES

• C, H, and O
• ose
• MONOSACCHARIDE
• Mono- means one
• Simple sugars e.g. GLUCOSE
• Usually with 5 or 6 carbons
• Soluble in water
• Taste sweet

Deoxyribose
40
CARBOHYDRATES

• DISACCHARIDES 2 sugars
• Made through?!

Sucrose Water
41
CARBOHYDRATES

• POLYSACCHARIDES more than 2!
• Important in metabolism.
• Sometimes used for cell I.D.
• Store energy.

42
Plant Starch (Amylose)
Spiral polymer of glucose
Glucose
43
Cellulose
44
Cellulose
45
Chitin

• Arthropods exoskeletons, fungal cell walls
• Like cellulose, but with nitrogen
• Strong, very resistant to digestion

46
Glycogen
47
CARBOHYDRATES

• Eat starch, break it down -gt glucose, synthesize
  -gt glycogen (in liver)

48

• Nucleic Acids

49
Nucleic Acids

• Nucleotides monomers
• NUCLEIC ACIDS nucleotide polymers
• DNA Genes, blueprint
• RNA Messenger, to make proteins.

50
Nucleotides

• Also
• energy carrier ATP (monomer)
• chemical messenger cAMP

51
NucleotideStructure
Phosphate Group
NitrogenousBase
Varies DNA ATCG RNA AUCG
Sugar
52
Nucleic Acids

• Nucleotides can be joined together into a chain
  (polymer!).

Result is DNA, RNA Sugar-phosphate
backbone. Bases like ladder rungs in DNA double
helix.
53
DNA
54
DNA vs. RNA
DNA deoxyribose sugar, phosphate, ATCG RNA
ribose sugar, phosphate, AUCG DNA double
stranded RNA single stranded
55

• Lipids

56
Lipids

• i.e. FATS
• Slippery-oilies
• Nonpolar insoluble in water
• Mostly C and H

57
Lipids

• Very heterogeneous group
• Some are polymers of FATTY ACIDS
• Fatty-acid types Oils waxes
• Nonfatty-acid types steroids

58
Fatty Acids

• FA Hydrocarbon chain with a carboxyl (COOH)
• Most fats 3 FA monomers glycerol
• Triglycerides are in beef, vegetable oils,
• butter, etc.

59
Fats
Unsaturated - One or more CC double bonds -
Usually vegetable fats -
Liquid at room temperature (RT)
Saturated - No CC double bonds - Usually
animal fats - Solid at RT
60
UNSATURATED FAT
FATS
Vegetable oils Better for you!!!
61
News flash
HYDROGENATED OILS
Also known as TRANS FATTY ACIDS
- Created by unsaturated-gt saturated
- Solid at RT
- Such as margarine
- Found in almost all processed foods
soup, crackers, cookies
- belly spread heart attacks
BAD FOR YOU!!!
62
TriglycerideFormation
Triglyceride
Glycerol
RemoveTheseWaters
Add 3FattyAcids
3 Waters
63
Lipids

• Phospholipids - mostly in membranes
• Soap-like

64
Phospholipids
PolarHead
Glycerol
Fatty Acid Tails
Hydrophobic (non polar!)
Hydrophilic (polar!)
65
Phospholipids (micelle)
66
Steroids

• Some hormones
• Cholesterol
• Natural substance
• Hormone precursor
• Found in membranes
• Essential for life!!!

67
Steroids
Cholesterol