L1. Introduction

The Tree of Life 

The cell theory and the theory of evolution by natural selection imply that all species are descended from a single common ancestor at the root of a family tree of all organisms - the tree of life. 

Phylogeny 

I. Reading a phylogenetic tree

1. The evolutionary relationships between organisms can be determined by comparing genetic information.

ex) Humans and dogs have more similar genetic information compared to snakes.

2. Nodes represent evolutionary divergence of ancestral species. 

 

II. A major distinction among organism Eukaryotes vs Prokaryotes 

1. Eukaryotic cells have a membrane-bound nucleus

2. Prokaryotic cells do not have a membrane-bound nucleus 

* Eukaryotes and prokaryotes differ in many other ways (transcription, introns, other organelles)

III. Organisms can be unicellular or multicellular

1. Bacteria = unicellular prokaryote

2. Paramecium = unicellular eukaryote

3. Flowering plant = multicellular eukaryotes

 

IV. Comparing Bacteria, Archaea and Eukaryotes

1. Archaea and bacteria are both prokaryotes. 

2. Archaea and bacteria have similar cellular organization. 

However, archaea share some features with Eukarya.

Archaea more closely related evolutionarily to Eukarya to Bacteria. 

=> Archaea and Eukarya share the closest common ancestor. (phylogeny tree)

 

Basic Atomic Structure

1. An atom is the basic unit of matter. 

2. Atoms are composed of: 

(1) Protons: positively charged particles

(2) Neutrons: neutral particles

(3) Electrons: negatively charged particles

3. (1) Protons and neutrons are located in the nucleus. 

(2) Electrons are found in orbitals surrounding the nucleus. 

 

I. Types of chemical bonds in cells

1. Covalent: polar and nonpolar covalent

(1) Covalent bonds involve the sharing of electrons between atoms. This holds the two atoms together. 

(2) Polar (more electronegative atom has stronger pull) covalent bonds: unequal

• When two atoms have significantly different electronegativity, they form a polar covalent bond

• Polar covalent bonds in water molecule
• Ex) N-C, O-H, N-H, O-C

Electrons are not shared equally, so partial charges exist on the O and H atoms 

(3) Nonpolar covalent bond: equal share

 

Nonpolar covalent bond in hydrogen molecule

(electrons are shared equally) 

• Ex) C-C, H-H, C-H 

*  C and H have slightly different electronegativity. C-H is non-polar, but the non-polarity is small enough that it acts in practice as a n-p bond. 

 

2. Non-covalent: ionic bonds, hydrogen bonds, Van der Waals forces

(1) Ionic bonds

• Various elements have valence electron numbers that favor either a loss of an electron or gain of an electron. 
• Ionic bonds are the result of full charge interactions between atoms or molecules.

(2) Hydrogen bonds

• Hydrogen bonds form as a result of the partial charges that are found in molecules with polar covalent bonds (H-bonds do not have to involve a H) 

• Ex) H2O 

(3) Van der Waals interactions 

• Van der Waals occur between non-polar molecules
• Positive and negative charge in a molecule with nonpolar covalent bonds creates weak interactions when molecules are very close. 
• Both hydrogen bonds and Van der Waals interactions are charge interactions. 
• H-bonds are much stronger due to a larger charge difference. 

 

II. Relative strength of interactions 

1. (1) Methane is gaseous at room temperature because it is a non-polar molecule and can’t make strong charge interactions. 

(2) Water is liquid at room temperature because hydrogen bonds hold the molecules together. 

(3) Salt is a solid at room temperature because the large number of full ionic bonds hold the molecules together strongly. 

2. Covalent bonds are much stronger than any of the other interactions. 

Covalent bonds > ionic > H-bonds >> Van der Waals interactions 

3. The strength of the bonds combined with the number of bonds determines how stable something is. 

Review 

I. Questions 

1. (1) Which group can for a hydrogen bond with a hydrogen atom on water?

 

(2) Which group can for a hydrogen bond with an oxygen atom on water?

 

2. (1) If Van der Waals interactions are relatively weak, why would a group of hydrophobic molecules stick together in an aqueous environment instead of interacting with water molecules?

(2) Water is a liquid at 20 degrees C. Why does it convert to a solid below 0 degrees C?

(3) How do polar covalent bonds affect the properties of water?

 

II. Concepts 

1. Why are Archaea and Eukarya more closely related to each other than Bacteria and Eukarya?

2. How does one determine phylogenetic relationships?

3. What do the “branches” in a phylogenetic tree mean?

4. What is the relationship between polar vs n-p covalent bonds and electronegativity and electron sharing?

5. How does polar vs n-p covalent bond affect the charge of the atoms involved?

6. Why are the strength of bonds ionic>h-bonds>>Van der Waals?

7. How do covalent bonds compare in strength to ionic bonds?

8. Why do you think water is liquid at 20 C and solid at 0 C?

 

III. Terms 

Phylogeny, bacteria, archaea, eukarya, prokaryote, eukaryote, atom, proton, neutron, electron, covalent bond (polar / non-polar), ionic bond, hydrogen bond. 

 

[Quiz 1] 

Q1. Which type of covalent bond creates charge differential on the atoms involved?

•   Ionic 
•   H-bonds 
•   Polar covalent 
•   Non-polar covalent 

 

Q2. Which of these is true?

•   None of the answers are correct 
•   As pH increases, [H+] increases. 
•   As pH increases, [H+] decreases. 
•   As pH decreases, [H+] decreases. 

 

Q3. What's the key difference between Prokaryotes and Eukaryotes?

•   No nucleus vs nucleus 
•   No photosynthesis vs photosynthesis 
•   Unicellular vs Multicellular 

 

Q4. Which best describes a covalent bond?

•   Two atoms are chemically attracted to transient hotspots of charge 
•   Two atoms share a pair of electrons 
•   Two atoms are bond because they have opposite charges 
•   One atom donates an electron to another atom, so that one has a +1 charge and the other a -1 charge 

 

Q5. Of the bonds shown, which is the strongest?

•   H-bond    
•   Van der Waals 
•   Ionic 

 

Q6. Which node represents the most recent common ancestor for all eukaryotes?

 

•   2 
•   4 
•   3 
•   1 
•   5 

 

Q7. If an atom has a charge of +2, which of the following must be true?

•   It has fewer electrons than it has protons 
•   It has fewer protons than it has electrons 
•   It has at least three valence electrons 
•   It has two more protons than neutrons 

 

Q8. Which statement is FALSE?

•   Neutrons have a -1 charge 
•   Electrons have a -1 charge 
•   Protons have a +1 charge