CBG exam 1 ; Chapter 2 - Essential Chemistry for Biology

Atoms → an Organism

1.     Atoms (carbon, hydrogen, oxygen, etc.) make up molecules

2.     when molecules come together they create macromolecules (proteins, carbohydrates, glucose, lipids, nucleic acids / DNA & RNA)

3.     these come together to make organelles (mitochondria, endoplasmic reticulum, nucleus)

4.     these come together to make cells (blood cells, liver cells, etc.)

5.     these come together to make tissues (connective tissue, nervous tissue, muscle tissue, epithelial tissue)

6.     this come together to make your organs (heart, kidney, brain, etc.)

7.     this comes together to make your organ system, coming together to make an organism (you).

à      Electrons = negatively charged, circle around the nucleus

à      Protons & Neutrons = within the atom / inside the atom

à      Valence electrons: based on which row the element is in

à      Noble electrons: already have their outer most shell filled

o   The elements on the periodic table that are on the right side

 

Elements & Molecules

¨     Atoms - building blocks of molecules

¨     Elements - types of atoms

o   92 natural elements

¨     Molecules - composed of two or more atoms

¨     Compounds - molecules composed of more than one element

¨     Emergent properties - characteristics that arise when multiple components interact to form a larger system

 

25 elements essential for life

·      96% of living matter made of 4 elements.

o   Oxygen O

o   Carbon C

o   Hydrogen H

o   Nitrogen N

·      Most of remaining 4% just 7 elements

·      Remaining > 0.1% are “Trace Elements”

 

Essential trace elements

·      Just because they’re a small percentage doesn’t mean you don’t need it

 

Atomic structure

·      Characteristics of particles

o   Location

o   Atomic number = number of protons in the atom

o   Atomic mass = nucleus = protons + neutrons

o   Atomic charge = number of electrons compared to protons + neutrons ?

 

·      Within the first orbital you can have at most 2 electrons

·      Within the second orbital you can have at most 8 electrons

 

·      Chemical Inertness: An atom is chemically inert when its outer electron shell is full, making it stable and unlikely to react with other atoms. This is characteristic of noble gases, which are in Group 18 of the periodic table.

 

Structure of typical atoms

Rule 1

·      Neutral atoms have equal number of protons and electrons

Rule 2

·      Typically, atoms have equal number of protons and neutrons

 

Structure of typical Nitrogen Atom

Exceptions to rules

Exception to rule 1

·      Ions = unequal protons and electrons (electric charge)

o   Can have an added electron or one less electron

Exception to rule 2

·      Variable isotopes = Abnormal number of neutrons (more or less neutrons)

 

Properties of common atoms (know these common atoms & their properties)

Element

Abbreviation

Atomic number

Mass number

Valence number

Hydrogen

H

1

1

1

Carbon

C

6

12

4

Nitrogen

N

7

14

3

Oxygen

O

8

16

2

 

Four chemical bonds

Atoms want to fill up their outer most shell to make it “happy”, the same reason you would want to form bonds with other people

·      Strong chemical bonds

o   Covalent bonds

·      Weak chemical bonds

o   Ionic bonds

o   Hydrogen bonds

·      Other interactions

o   Hydrophobic interactions

 

Covalent Bonds

             

 

 

Non-Polar and Polar Covalent Bonds

·      Non-polar covalent = Equal sharing of electrons

·      Polar covalent = unequal sharing of electrons

       

o   Oxygen = Shaq           Hydrogen = Kevin Heart

o   Bond gets pulled away from hydrogen because ?

 

Properties of covalent bonds

·      Sharing pair of electrons

·      Strongest of chemical bonds

·      Valence number

·      Single, double, and triple bonds

·      Important for shape of molecules

·      Nonpolar / polar forms

 

Ionic bonds

·      Complete sharing of electrons

o   Example: You only have $2 so you give the robber all of your $2

(Attraction between positive ions and negative ions)

·      Both Na and Cl have 8 electrons on their outermost shell so they’re both happy since its full

 

Hydrogen Bonds

·      The thing that connects one water molecule to another water molecule

o   Holds multiple hydrogen bonds together

o   Is a weak bond / weak interaction

§  Easy to break apart a water molecule

·      Attraction between a hydrogen with a partial positive charge and an electronegative atom (linked to less electronegative atom)

·      Requires polar bonds

·      Outside of oxygen, nitrogen and fluoride can also bond to form ...?

·       (explain the positive and negative bonds?) (this slide in general)?

 

Hydrophilic vs Hydrophobic Molecules

¨     Hydrophilic (Water loving) - Polar molecules that form hydrogen bonds with water

o   Things that mix well with water

¨     Hydrophobic (Water hating) - Non-Polar molecules that do not form hydrogen bonds with water

o   Things like oil that do not mix well with water

¨     Amphipathic - Both a hydrophobic and hydrophilic region

 

Þ   Hydrophobic Interactions

 

 

Chemical Reactions
(Rearranging Chemical Bonds)

       2H2   +   O2     ®     2H2O

(not going to really get tested on chemical reactions)

 

Water and Life

Four special Properties:

  1. Cohesion/Adhesion

  2. Temperature Moderation

  3. Significance of Floating Ice

  4. Solvent Properties

Other issues

·      pH

 

 

 

Þ   Cohesion /Adhesion

When you have gazillions of water molecules come together, it creates surface tension, due to cohesion

à      Cohesion: interactions with the same type of molecule

à      Adhesion: interacting with other types of molecules / water molecules stick to other molecules

à      Surface tension: A resistance or force created that prevents the water from being broken up

o   The greater force you’re putting on the surface tension, (like when doing a belly flop), the more tension and force there will be, compared to a smaller surface area (like when you’re diving) you’re breaking through the suraface tension with a smaller surface area

 

Þ   Temperature Moderation

   

à      High Specific Heat: (the measurement of heat) The amount of heat it takes for a liquid to rise 1 degrees Celsius; water has a higher specific heat so it takes more energy and longer to ride compared to ethanol that has a lower specific heat so it takes a shorter amount of time to rise

o   Water can absorb a lot of heat

à      Evaporative cooling: Generating a lot of heat, water in body absorbs a lot of the heat, once it evaporates and is turned into a gas state a lot of the heat is released

o   Seen when sweating or a dog panting

 

 

 

 

Þ   Floating Ice

   

à      Ice is less dense than water so it allows it to float on water

à      Water expands when it freezes because of the bonds

 

Þ   Water’s Solvent Properties

à      hydrophilic molecules dissolve in water

 

 

 

 

Þ   Disassociation of Water

H+ = proton

 

Buffers

Carbonic Acid - buffer in our blood

         In response to

           rise in pH

H2CO3                     H+    +     HCO3-

        In response to

         a drop in pH

 

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