Essential Chemistry for Biology

1
Chapter 2

• Essential Chemistry for Biology

2
AIDS A Matter of Chemistry

• 1981 CDC followed a disease in young men with
  very rare diseases
• failing immune system - ? T-helper cells
• diseases that normal healthy individuals fought
  off
• 1982 called AIDS (acquired immunodeficiency
  syndrome)
• 1984 caused by HIV which targets T-helper cells
  due to protein on outside of virus that
  recognizes the proteins on the T-cell, causes
  T-cell death
• Must understand some chemistry to study biology
• cells are bags of chemical reactions

3
HIV Infection
4
Matter

• Elements and compounds
• Occupies space and has mass solid, liquid or
  gas state
• Composed of elements substances that cant be
  broken down into other substances
• Elements form compounds such as NaCl or H2O
• compounds in living organisms contain several
  different elements

5
Periodic Table

• 92 naturally occurring elements

6
Composition of Cells

• 96 is C, N, H and O
• 4 are ions that help cells to function
• There is also a need for small amounts of trace
  elements
• gt0.01 of Fe, Mn, I, etc
• I is used for preventing goiter enlargement of
  the thyroid gland

7
Atoms

• Building blocks of elements
• Smallest unit that still maintains the properties
  of the element
• Made up of subparticles
• proton positive charge
• neutron no charge
• electron negative charge

8
Helium

• 2 protons and 2 neutrons are tightly packed in
  the nucleus of the atom
• 2 electrons orbit around the nucleus and held
  there by the charge

9
Elements

• Vary by number of protons they possess
• Atomic number number of protons
• Mass number number of protons number of
  neutrons
• 1 atomic mass unit mass of protons/neutrons
• electrons hardly has mass (1/2000 of proton)

10
Isotopes

• Same number of protons but different number of
  neutrons causes mass to be different
• C-12 99 of all carbon
• C-13 most of the final 1
• C-14 minute quantities unstable or
  radioactive nucleus decays, gives off particles
  and energy
• C-12 and C-13 are much more stable and stay
  intact
• Use in biological research cells can take up
  and we can see by radiation they emit
  uncontrolled exposure can be harmful to organism
  especially in DNA
• 1986 radiation plant blew up in Chernobyl,
  Urkraine killed 30 in weeks and increased risk
  of cancer to 1000s
• natural exposure such as to radon gas can
  increase risk of lung cnacer

11
Isotopes in Medicine

• Use C-11 in a molecule of PIB (binds to
  beta-amyloid protein)
• PET scan can detect the isotope as it attaches to
  the Alzheimer protein
• Leads to early detection of Alzheimers and other
  diseases

12
Electron Arrangement

• Determines how atoms interact when close to
  others
• Electrons vary in amount of energy based on
  distance from nucleus, further away greater
  energy
• Orbit nucleus in electron shells varying number
  of shells dependent on number of electrons,
  outer shell has most energy in elements of
  concern for biologists
• 1st shell as 2 electrons and 2nd and 3rd have 8
  electrons

13
Properties of Atom

• Determined by outermost electron shell
• H, C, O and N are reactive because outer shell is
  not full
• He is inert as its outer shell has 2 electrons
  and is full

14
Chemical Bonding and Molecules

• Reactions deal with atoms giving up or sharing an
  e- with another atom
• transferring or sharing e- in the outer shell
  creates a chemical bond
• 2 types of bonds
• ionic which requires a transfer of an e- to
  create a full outer shell
• covalent which requires the sharing of one or
  more e- to complete the outer shell

15
Ionic Bonds

• Na and Cl are electrically neutral but both want
  to have their outer shell complete
• Na transfers its lone e- to Cl
• Na gets a charge because it has 11 protons and
  only 10 e-
• Cl gets a charge because it has 17 protons and
  18 e-
• and charge cause the Na and Cl to interact
• Naming ionic compounds the negative ion usually
  ends in ide
• chlorine becomes chloride

16
Covalent Bonds

• Share 1 or more pairs of e- to form a molecule
• Compound is made of more than 1 element
• Number of covalent bonds is dependent on number
  of e- in the outer shell
• H 1 O 2 N 3 and C 4

17
Water Is Special

• There are 2 H and 1 O in each molecule
• The sharing of the e- in the covalent bond is
  unequal because of the larger nucleus in O and
  the 2 pair of e- that are not participating in a
  bond
• water is POLAR because of this meaning that
  within the molecule, there is a charge

18
H-Bonds or Interactions

• The e-being pulled towards the nucleus of O give
  it a ?- charge and the H a ? (H acts mostly as a
  proton)
• The charges form an interaction between the ?-
  and the ? similar to an ionic bond but it is
  called a H-bond

19
H-Bond

• Can form only between the H attached to a O or N
  and an additional O or N
• need the ?- of the O or N to interact with the ?
  of the H on O or N
• NEVER BETWEEN THE HYDROGEN ON A CARBON

20
Chemical Reactions

• Changes in chemical composition of mater
• Break bonds in reactants and make new ones in
  products explosive reaction
• Must be able to account for each atom as we know
  they cant be created or destroyed

21
Importance of Water

• Cells in body range from 70-95 water
• Earth is ¾ water which allows it to be habitable

22
Properties of Water

• The polarity of water and the ability to form
  H-bonds give it very special properties
• cohesive nature
• moderates temperature
• floating of ice
• functions as a very diverse solvent

23
Cohesion of H2O

• Cohesion is the ability to stick together due
  to H-bonds, stronger than other solvents
• helps pull H2O up against gravity
• surface tension

24
Moderation of Temperature

• H-bonds make H2O more resistant to change than
  other liquids
• Temperature intensity of heat
• Heat amount of energy to move atoms/molecules
  in a body of matter
• To heat water, you must first break the H-bond
  and eventually the molecules speed up,
  temperature hardly changes until this starts to
  happen can store a vast amount of heat in the
  H2O, opposite happen when H2O cools can release
  heat while cooling with only a few degrees drop
  in temperature
• Earths water help regulate climate by storing
  heat during warm periods and releasing heat
  during cold periods

25
Temperature

• Moderate temperature by evaporative cooling
• Why sweating is important on very hot days even
  when exercising

26
Floating Ice

• Most liquids move molecules closer together as
  they cool but as temperature drops in water, the
  H-bonds move apart and make ice less dense than
  water so it floats
• Helps to keep the world from freezing solid if
  oceans froze and sank, then eventually all the
  water would be ice

27
Solvent of Life

• Solution mixture of something dissolved in a
  liquid
• Solvent the liquid
• Solute substance dissolved
• Aqueous solution if water is solvent fluid of
  organisms
• Water is good solvent because of its polarity
  uses the ? and ?- charges to aid in dissolving
  salts and polar molecules like sugar

28
Acids, Bases and pH

• H2O can dissociate into H (essentially a proton)
  and OH- (hydroxyl group)
• Balance between these is critical for life and
  chemical properties in an organism
• Acids compounds that release or donates a H
  into the solution such as HCl
• Bases compounds that gain a H from the
  solution, may also release a OH- groups

29
pH Scale

• Measure of H
• Logarithmic scale used to determine acidity and
  alkalinity
• each unit is a 10-fold change in the H
• pH 2 has 100 times more H than pH 4
• pH 7 is neutral, pH 1-6.9 is acidic, pH 7.1-14 is
  basic

30
Buffers

• Even small changes in pH may be harmful to an
  organism
• Buffers can accept H or donate them to a
  solution to keep the pH constant

31
Acid Rain

• Causes damage to an ecosystem
• The rain picks up the H from the air and end
  up with a pH of 2-3