Lecture 2 BIOL L100 Indiana University Southeast David Partin, Instructor

1
Lecture 2BIOL L100 Indiana University
SoutheastDavid Partin, Instructor
2
Todays Plan

• Lecture 2 Basic Chemistry Biochemistry
  (Chapters 2 3)
• Video clip
• One-Minute Paper
• Lab

3
Chapters 2 3

• Basic Chemistry Biochemistry

4
Did you say CHEMISTRY??I thought this was
BIOLOGY class!

• Chemistry and Biology are interconnected, no
  doubt about it.
• Chemistry is the study of the interactions of
  matter.
• Biology is the study of living things. Remember
  from last lecture that BOTH living AND non-living
  things are made up of matter.

5
What is matter?

• Anything that
• Takes up space
• Has mass
• So this includes living AND non-living things.

6
What is matter made of?

• Living and non-living matter
• Both are made of elements.
• Elements cannot be broken down to substances with
  different properties.
• So an element cant be broken down?? NO! I didnt
  say that!
• Elements can be broken down to atoms, but each of
  the atoms will have the same properties! (i.e.
  the same number of protons)
• 92 natural elements (additional man-made elements
  are on the periodic table).

7
Elements

• Examples of elements include
• Oxygen
• Carbon
• Hydrogen
• Gold
• Silver
• Potassium
• Magnesium
• Lead
• Helium
• Lithium

• The most common elements found in living
  organisms
• Carbon
• Oxygen
• Nitrogen
• Hydrogen
• Phosphorus
• Sulfur

8
Periodic Table of the Elements (excerpt)
9
What are elements made of?

• An element consists of atoms of the same kind.
  (i.e. The same number of protons, or atomic
  number.)
• For example, every atom that has 6 protons is the
  element CARBON.
• Every atom that has 7 protons is NITROGEN.
• Every atom that has 8 protons is OXYGEN. Etc.

10
Atomic structure

• Atoms are made of sub-atomic particles
• chart, p21

11
Structure of an Atom
12
Atomic Structure

• All atoms of the same element have the same
  ATOMIC NUMBER (aka, number of protons).
• Does it make more sense now?
• Any questions?

13
Atoms combine to form compounds.

• When atoms of 2 (or more) elements form bonds
  together, the new combination is called a
  COMPOUND.
• We will briefly discuss 3 types of bonding
• Ionic bonds
• Covalent bonds (polar nonpolar)
• Hydrogen bonds

14
Ionic Bonds

• Ion a charged atom (can be or -)
• Ionic bonds are fairly weak, and are formed by
  the attraction between a positively charged atom
  and a negatively charged atom.
• Example NaCl, p.24

15
Ionic Bonds
16
Covalent Bonds

• Covalent bonds are strong.
• 2 atoms literally share an electron
• Nonpolar both atoms share equally
• Polar one atom has a stronger pull on the
  electron
• Examples (page 25) O2, H2, CH4
• Compare the covalent bond diagrams on p25 with
  the ionic bond diagrams on p24.

17
Covalent Bonds
18
Hydrogen Bonding

• The polarity in a water molecule causes the
  HYDROGEN atoms of one water molecule to be
  attracted to the OXYGEN atoms of another water
  molecule.
• Very weak bonds, but there are so many! So, as a
  collective force, they can be quite strong.

19
Structure of Water Hydrogen Bonding
20
Summary of atomic bonds

• Covalent strong
• Ionic weaker
• Hydrogen bonds weakest (individually), but
  strong collectively.

21
Chemistry of Water

• Why should we study water in Biology?
• Living things are made of 70-90 water.
• Water is essential for all organisms.

22
There are 6 properties that make water special
(and make it useful to living organisms)!

• High heat capacity
• High heat of vaporization
• Solvent properties
• Cohesive adhesive nature
• High surface tension
• Solid is less dense than liquid.

23
Chemistry of WATER

• 1. High heat capacity Water heats up cools
  down slower than most liquids. Holds heat longer
  than most. This buffers the amount of
  evaporating and freezing that go on in the
  environment.
• 2. High heat of vaporization Evaporation
  requires a lot of energy. Sweating helps to
  reduce body heat. Body heat is used as energy to
  evaporate water. Critter loses body heat, water
  gains it and evaporates.
• 3. Solvent properties Molecules dissolve in
  water, which allows them to move around more and
  interact. Water facilitates all chemical
  reactions in the body.

24
Chemistry of WATER

• 4. Cohesive adhesive nature Water molecules
  move freely, but stick together (hydrogen bonds).
  Great for transporting nutrients in plants, and
  circulation in animals.
• 5. High surface tension This is another effect
  of hydrogen bonds. Water is tough!
• 6. Solid is less dense than liquid Ice floats!
  Bodies of water freeze from the top down.

25
(No Transcript)
26
(No Transcript)
27
Biochemistry where chemistry and biology meet
head-on

• Living things require millions of chemical
  reactions within the body, just to survive.
• Metabolism all the chemical reactions occurring
  in the body.
• Organic molecules
• usually associated with living things.
• Always contain CARBON.
• large molecules, many atoms
• Always have covalent bonds.

28
Macromolecules of Cells

• Macro large
• 4 types of macromolecules in cellular biology
• 1. Carbohydrates
• 2. Lipids
• 3. Proteins
• 4. Nucleic Acids

29
Macromolecule 1 Carbohydrates

• Sugars and groups of sugars
• Purposes energy and structure
• Monosaccharide (1 sugar)
• Disaccharide (2 sugars)
• Polysaccharide (many sugars)

30
Macromolecule 1 Carbohydrates

• Monosaccharide 1 sugar molecule, quick energy
  (e.g. glucose, fructose, D of DNA, etc.)

31
Macromolecule 1 Carbohydrates

• Disaccharide 2 sugar molecules linked. (e.g.
  glucose fructose sucrose)

32
Macromolecule 1 Carbohydrates

• Polysaccharide many sugar molecules linked
  together for energy storage or structure.
• Examples
• Glycogenglucose polymer stored for future energy
  needs. Found in liver, muscle and sperm, etc.
• Celluloseglucose polymer used to form fibers for
  plant structures. Humans cant digest (fiber).
  Most abundant organic molecule on Earth!
• Chitinglucose polymer for exoskeletons of some
  crustaceans insects.

33
Polysaccharides
34
Polysaccharides
35
Macromolecule 2 Lipids

• Insoluble in water (think oil water)
• Multipurpose molecules long-term energy storage,
  structural purposes within the cell, cell
  signaling purposes, protection, insulation,
  prevention of water loss.
• 4 types 1-triglycerides, 2-phospholipids,
  3-steroids, 4-waxes

36
Macromolecule 2 Lipids

• 4 types of lipids 1-triglycerides,
  2-phospholipids, 3-steroids, 4-waxes
• Triglycerides fats and oils
• Purpose long-term energy storage, insulation

37
Triglycerides
38
Triglycerides
39
Macromolecule 2 Lipids

• 4 types 1-triglycerides, 2-phospholipids,
  3-steroids, 4-waxes
• Phospholipids
• Purpose STRUCTURE. They are the primary
  component of the cell membrane.

40
Phospholipids
41
(No Transcript)
42
Macromolecule 2 Lipids

• 4 types 1-triglycerides, 2-phospholipids,
  3-steroids, 4-waxes
• Steroids totally different structure than fats.
  Classified as lipids because of their
  insolubility in water.
• Purpose (1) structure cholesterolpart of the
  cell membrane. (2) signaling cholesterol
  molecules are modified to form sex hormones.
  (e.g. testosterone, estrogen, etc.)

43
Steroids
44
Macromolecule 2 Lipids

• 4 types 1-triglycerides, 2-phospholipids,
  3-steroids, 4-waxes
• Waxes solid at room temperature. Used mainly by
  plants, but also bees, some furry animals and
  humans.
• Purpose protection, prevents water loss

45
Waxes
46
Macromolecule 3 Proteins

• Greek proteios first place. IMPORTANT!
• Probably the most complicated of all biological
  molecules.
• Serve the most varied purposes

47
Collagen
48
Antibodies
49
(No Transcript)
50
(No Transcript)
51
actin myosin
52
Macromolecule 3 Proteins

• The building blocks of proteins are AMINO ACIDS.
  20 total
• There are millions of different proteins, and
  they are all built from different combinations of
  the 20 amino acids.
• Amino acids join together by peptide bonds to
  form peptides.
• Many peptides linked together form polypeptides.
• Proteins can be made of one or more polypeptide
  chains.

53
(No Transcript)
54
Macromolecule 3 Proteins

• The function of a protein is largely determined
  by its shape.
• Primary structure amino acid sequence of the
  polypeptide
• Secondary structure hydrogen bonding between
  amino acids causes the polypeptide to form a
  helix or b sheet
• Tertiary structure further twisting and folding
  that results in the final 3D shape of the
  polypeptide
• Quaternary structure some proteins (but not
  all) are formed from 2 or more polypeptide chains
  interacting. Each of them has its own 1, 2 3
  structure. (e.g. Hb)
• Protein folding diseases! (Mad Cow, Alzheimers,
  Cystic Fibrosis, p53 in cancer)

55
Levels of Protein Organization
56
Levels of Protein Organization
57
Levels of Protein Organization
58
Macromolecule 4 Nucleic Acids

• Nucleotides building blocks of nucleic acids.
• Each nucleotide contains (a) phosphate molecule,
  (b) nitrogenous base, and (c) 5-carbon sugar
• Several types of nucleic acids, including
• DNA deoxyribonucleic acid
• Genetic material, double stranded helix
• RNA ribonucleic acid
• Genetic material, single stranded
• ATP adenosine triphosphate
• High energy compound

59
Nucleotide Structure
60
RNA
61
DNA
62
(No Transcript)
63
BIG PICTURE Chemistry is essential for
life Biology and Chemistry are inextricably
intertwined!
64
Video Clip

• Protons, neutrons, electrons
• Ionic bonds

65
Lab Overview

• Page 12 in your lab manual
• Control/Variables
• 1 ___________________________
• 2 ___________________________
• 3 ___________________________
• 4 ___________________________
• Add ingredients, make bubbles
• Measure dataHOW??

66
Thanks for your attention!

• Write your One Minute Paper
• Scientific Method Lab

Preparation for next class Read Ch4 Ch5 in
the textbook.