BIOL 411 Study Guide - Final Guide: Hydrogen Bond, Peptide Bond, Chemical Polarity
Bio411 notes
Biology 411.01
1/29/16
Chapter 1:
• Diversity evolved in response to the diversity of environments on earth
• Environments present challenges that species may respond to through adaptive genetic
changes
o fitess = suial
• These adaptive changes are random, nothing conscious
• There are universal biological similarities, especially at the molecular level
o For example, genetic code (DNA/RNA) and the way it is expressed (transcription,
translation)
o This suggests that life arose once, all organisms evolved from that one primordial
life
o “haed featues tell ou he a ogais eoled, relatively
• In the light of evolution, life is what the genome surrounds itself with to survive
o Ex. By this definition, viruses are alive because they have a genome that
surrounds itself with what it needs to survive
Where did life come from?
• First self replicators (first genomes)- first things that were able to make more of
themselves
o 2 things needed for the origin of life
▪ 1. Template or information (DNA)
▪ 2. Catalysis (protein)- makes the replication process fast enough for for
accumulation to occur
• Which came first DNA or protein? Neither, probably RNA because
it contains instructions and catalysis so it can accumulate
o Darwinian evolution:
▪ Arose by mutation
• Catalysis: an increase in the rate of reactions, leads to accumulation because synthesis is
faster than degradation
o The first molecule needed catalytic ability- RNA is a molecule that can do this
(Chech discovered this)
o Catalysis is determined by shape and free OH (hydroxyl) group
▪ Proteins are good because they can take on any shape and can have
hundreds of amino acids
▪ Base pairing gives RNA a secondary/tertiary structure
▪ Every time a mutation occurred in RNA that gave it an ability to survive
better- it survived- this lead to Darwinian evolution
2/1/16
• ‘NA has a fee hdol goup that DNA doest hae in the positio
find more resources at oneclass.com
find more resources at oneclass.com
o This helps to explain why RNA is a good catalyst
• Primary structure of RNA is just a long, string
o Secondary (2D) and tertiary (3D) structure of RNA is formed by regions within
the molecule that are complementary and will come together
• How did we transition to a DNA genome-protein catalyst world?
o RNA is capable of performing all of the reactions of protein synthesis
▪ Transition from RNA world→RNA-protein world→DNA-protein world
• DNA genomes are better than RNA genomes, so DNA survived
What you need to know:
Understand the 2 things needed for 1st genome to survive (instructions, complementary
base-pair template of RNA, catalytic ability, mutation)
Features of RNA that make it a good catalyst
RNA making copies of itself lead to mutations that made better enzymes→DNA world
Chapter 2: Atoms and elements, electrons, orbitals, and valence electrons, molecules and
bonds
• Electronegativity: how elements share electrons
o Oxygen is an electron hog, hydrogen is electronegatively weak, so they wont
share electrons equally, i.e. water is polar
▪ Large differences in electronegativity→polar bonds
o Electronegativity increases as you move right on the periodic table
▪ Because more protons, therefor greater pull towards the nucleus on the
electrons
o Electronegativity increases as you go up the periodic table
▪ The electrons are closer to protons, therefor greater pull
▪ As you go down, the number of electron shells increases- electrons are
further and further out, so there is less pull
2/3/16
• Atom: protons, neutrons (nucleus), and electrons
• Electrons shells
o First shell- maximum 2 electrons (1s orbital)
o Second shell- maximum 8 electrons (2s and 2p orbitals)
• Coalet od: atos shae a eleto pai i a oleula oital alee
electrons)
• Polar bond: between two atoms of different electronegativity
o Water has 2 polar bonds, O is an electron hog (high electronegativity value [E])
• Hydrogen bond: association of a hydrogen atom (w/ partial positive charge) and an
electronegative atom (w/ a partial negative charge)
o Only H bonded with O, N, or F will form a hydrogen bond
find more resources at oneclass.com
find more resources at oneclass.com
o Water molecules stick together with hydrogen bonds, hydrogen bonds with
oxygen
o The bases are bonded together by hydrogen bonds in DNA and RNA
▪ Allows DNA and RNA to replicate
• Water is a polar molecule
o Polar molecules are hydrophilic- likes water
o Nonpolar molecules are hydrophobic- doest like ate
o There are aqueous and nonaqueous phases
• Membranes are nonpolar, hydrophobic environment- helps mask/shield themselves
from water
• Proteins are made of long chains of amino acids, as amino acids are added the protein is
folding (instructions for folding usually given by the amino acids), one of the major
dies of potei foldig is a egio of opola aio aids that fold do ecause
they want to escape water
o hdophoi effet
• Aids: poto doo, aids ill elease potos H+ ito the aueous solutio, oe
H+ in the solution
o Low pH
• Bases: accepts protons, so there are fewer H+ ions in the solution
o High pH
• pH: the measure of the proton content (hydrogen ion concentration) of a solution
expressed as the negative log of the hydrogen ion concentration
o Ex: 10-4 ions, log10-4= -4 (negative)= 4
• Carbon:
o Carbon based life form
o 4 valence electrons, so 4 covalent bonds
o 6 electrons total
o Forms 4sp3 hybrid orbitals so the electrons can be as far away as possible from
each other
o Tetrahedral bond and angles (109.5 degrees)
2/5/16
• The organic molecules of life-macromolecules- Linear polymers of subunits liked by
covalent bonds (polymer- large molecular chain of similar subunits)
o Nucleic acids- subunit: nucleotides, bond: phosphodiester
o Proteins- subunits: amino acids, bond: peptide
o Carbohydrates (often branched)- subunits: sugars, bonds: glycosidic
▪ Polysaccharides
o Lipids (not polymers)
• Proteins: linear (no branches) polymer of amino acids joined by peptide bonds
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
In the light of evolution, life is what the genome surrounds itself with to survive: ex. By this definition, viruses are alive because they have a genome that surrounds itself with what it needs to survive. Where did life come from: first self replicators (first genomes)- first things that were able to make more of themselves, 2 things needed for the origin of life, 1. Understand the 2 things needed for 1st genome to survive (instructions, complementary. What you need to know: base-pair template of rna, catalytic ability, mutation) Chapter 2: atoms and elements, electrons, orbitals, and valence electrons, molecules and bonds. Features of rna that make it a good catalyst. Nh, sh= generally polar, ch= generally nonpolar) *he said if asked on a test it will be an obvious one: *know how to draw 2 amino acids and put them together joined by a peptide bond.
