Themes in Biology
- Organization and Emergent Properties
o Reductionism
§ Reducing complex systems to simpler components that are easier to study
- Many emergent properties reflect structure function relationships
Genetic information
- Thousands of genes are found on a single chromosome
- How is this expressed into proteins?
- How is this passed on/transmitted?
Transformation of energy and matter
- How does energy flow?
- How is energy converted?
- How are chemicals cycled?
Organisms Interacting (ecology)
- How do organisms interact with each other?
- How do organisms interact with other species?
- How do organisms interact with their environment?
Evolution is a unifying theme of biology
- What is evolution?
o Natural selection -> adaptations
o The role of randomness
- Evolution explains the unity and diversity of life
Life and Evolution
- Diversity of life
o Domains are divided into kingdoms
§ Kingdom Plantae
§ Kingdom Fungi
§ Kingdom Animalia
o Protist is not a kingdom anymore
o Tree of life
§ Hypothesis of relationships
· Three domains
o Bacteria
§ Single cell, no nucleus
o Archaea
§ Single cell, no nucleus
o Eukaryota
§ Has a nucleus
§ Metazoans = multicellular animals
§ Protists are eukaryotes that are not plants, fungi or animals
- Unity of life
o Similarities across levels of hierarchy
§ Organisms share characteristics at different levels
· Molecular
o All life uses the same genetic language (DNA/RNA)
· Cellular
o Many different animals have similar immune cells
· “vestigial” organs are functional in some species
o Appendix
· Some structures seen only in development
· All birds have feathers and a beak
o Not all used in the same way
· Homology: similarity due to shared ancestry
o Mammalian limbs have the same bone pattern
· Analogy: similar function, evolved independently
- Descent with modification
o Descent
§ Traits or structures are passed down (and inherited)
o Modification
§ Those traits start to differ in the formation of new species
o Descent with modification = evolution
Natural Selection
Darwin’s Influences
- Binomial nomenclature
§ Organizes life into species
· Taxonomy
o System of classification
· Taxon/ taxa
o Group
§ Example
· Canis lupus
o Canis is the Genus, always capitalized
o Lupus is the species, not capitalized
§ Binomial = 2 part
§ Nomenclature = name
o King = kingdom
o Philip = phylum
o Came = class
o Over = order
o For =family
o Garlic = genus
o Shrimp = species
- Humans use selective breeding in agriculture
o Selective
§ Choosing which individuals breed next generation
- Small gradual changes can explain Earth’s present geology
o Charles Lyell – geologist
o Processes that alter Earth are slow and constant
o Small changes + long time = big changes
§ Valleys can be created by gradual erosion
o Present is a link to the past
Darwin’s Contribution
- Darwin’s Journey
o HMS Beagle hired to chart coast of South America
o Darwin hired as a naturalist -> observe, record new plant/ animal life
o Read Lyell’s book and observed geology
Natural Selection
- On the origin of species
o Selective breeding can cause changes over generations
o Natural selection is similar but nature chooses
Observation 1
- Individuals vary in their traits (variation)
o Inference 1
§ Individuals best suited to their environment are more likely to survive and reproduce
Observation 2
- More offspring are produced than survive
o Inference 2
§ Over time, more individuals in a population will have advantageous traits
Natural selection must happen if:
- Variation exists that leads to differences in fitness
- Variation has genetic basis
Does not create new traits, only works on traits that already exist
(natural selection requires variation with a genetic basis that impacts fitness)
Support for Evolution
Direct observation
- Soapberry bugs
- MRSA
Homology (descent with modification)
- Anatomical
o Reptile lower jaw made of multiple bones
o Mammalian lower jaw made of a single bone (other bones are reused for hearing)
- molecular
History
- fossil record
Phylogenetic Trees
- “phy” means tribe
monophyletic (clade)
- ancestral species and all descendants
o homology
paraphyletic
- ancestral species and some descendants
o not all of the descendants
polyphyletic
- distantly related species and no common ancestor
o analogy
Chemical Bonds
Elements of life
- elements can combine to create emergent properties
- elements
o substance that cannot be broken down by chemical reactions
- compound
o two or more elements combined into a fixed ratio
- CHNOPS (97.6)
o Carbon
o Hydrogen
o Nitrogen
o Oxygen
o Potassium
o Sulfur
- Trace elements
o Required, but in small amounts
§ Less than 0.01% of our mass
· Ex: iron (Fe)
- Atoms contain protons, neutrons, and electrons
o Atom
§ Smallest unit that still retains properties of an element
o Nucleus
§ Center of atom
o Protons
§ Determines the element name/ atomic number and mass
o Neutrons
§ Determines mass
o Electrons (-)
§ Determines bonding
· Electrons can “jump” levels to absorb/ release energy
o Excited electrons “jump up” and store potential energy
o Relaxed electrons “fall down” and release energy
§ Valence electrons are involved in bonds and chemical bonds
· Valence electrons are the outermost layer of electrons
o 1st shell is complete with 2 electrons
o 2nd shell is complete with 8 electrons
o 3rd shell is complete with 8 electrons
Covalent and ionic bonds
- Reactions occur when atoms “help” each other become stable
o Atoms are stable with full valence shells
- Covalent bond
o Sharing electrons
- Ionic Bond
o Called “salts”
o A full transfer of an electron from one atom to another
§ Solvent can get between attraction
· Less stable than a covalent bond, attractive forces are not strong
Hydrogen Bonds
- Covalent bonds can be polar or nonpolar
o Nonpolar covalent bond
§ Electrons are shared equally, symmetry
o Polar covalent bond
§ Electrons not shared equally
· Partial charge develops
- Partial negative of one molecule is attracted to the partial positive of another molecule
o Between water molecules (for this class)
§ Cohesion
· Water sticks to itself
§ Adhesion
· Water sticks to other things
Organic Compounds
Building blocks
- Valence
o Number of unpaired electrons
o What determines “valence” numbers
§ Number of “valence electrons”
§ Shell
- Carbon
o Most of life is made of water and organic molecules
§ Organic
· Carbon=based
o Properties of carbon
§ Small
§ Valence = 4
§ Electroneutral (nonpolar)
· Glucose has 6 carbons
-
- Monomers and polymers
o Monomer (meaning one)
§ Small molecule that is part of a longer, repeating chain
o Polymer (meaning many units)
§ Chain of connected monomers
o Dehydration reaction
§ Synthesizing a polymer
o Hydrolysis
§ Breaking down of a polymer
Organic molecules
- Carbohydrates
o Monomer: monosaccharide
o Dimer: disaccharide
o All multiples of CH2O
o Energy in electrons from hydrogen
o Many form rings
o Glycosidic linkage connects monosaccharides
o Starch and Glycogen are polysaccharides of glucose
§ Useful for storing glucose
o Glycogen is extensively branched
§ Useful for quick release of glucose
o Cellulose is also a polysaccharide, but humans can’t digest it
§ Hydrogen bonds keep molecules of cellulose together
§ Fiber
· Put together in such a way that hydrogen bonds form between strands of polysaccharides
- Lipids
o Don’t form true polymers
o Mostly hydrocarbons
§ Leads to non-polarity (non-polar = hydrophobic)
o Categories of lipids
§ Fats (triglycerides)
· Contain three fatty acid tails
o Glycerol acts like the “head” and connects three fatty acid tails
o Long carbon chains make triglycerides nonpolar
o Single or double bonds in fatty acids determine structure/ function
§ Unsaturated fats have double bonds between carbons
§ Saturated fats only have single bonds between carbons
§ Phospholipids
· Contain a charged phosphate group
o Two fatty acid tails (nonpolar)
o Glycerol
o Phosphate group (polar)
o Hydrophilic head
o Hydrophobic tail
o Essential for making cell plasma membrane
§ Steroids
· Cholesterol is an important component of animal cell membranes
o Precursor for other hormones
o hydrophobic
- Proteins
o Proteins are made of one or more polypeptide chains
§ Polymer: polypeptide
§ Monomer: amino acid
· 20 unique amino acids
· Order and properties of amino acids determines shape
§ Peptide bonds link amino acids together
· Dehydration
§ > 50% of dry mass of most cells
o Amino acids are identical except for the side chain (R)
§ Different amino acids have different side chains
§ Functionality comes from side chain
· Mostly carbon = nonpolar (hydrophobic)
· Polar groups = hydrophilic
· Acids/ bases = hydrophilic
o Proteins have three/ four levels of structure
§ Primary structure
· Order of amino acids in polypeptide
§ Secondary structure
· Polypeptide twisting and bending due to H bonds
o Alpha helix
o Beta sheet
§ Tertiary structure
· Shape due to side chains interacting
o Hydrophilic side chains
o Hydrophobic side chains
o Covalent bonds
§ Quaternary structure
· Two or more polypeptide chains mixing/ entangling with each other
o Physical and chemical conditions affect protein structure
§ Changes in pH, salt, and temperature can denature a protein
§ Denatured protein is biologically inactive
§ Some changes are irreversible
- Nucleic Acids
o Made of monomers called nucleotides
§ Three parts
· Nitrogen containing base
o Pyrimidine
§ C, T, U
o Purines
§ A, G
· A five-carbon sugar
o Deoxyribose
· One to three phosphate groups
o The part of the nucleotide without a phosphate group is called a nucleoside
o Polymers
§ Polynucleotides
· Phosphodiester linkage
o DNA
§ Provides instructions for protein synthesis
o RNA
§ Controls protein synthesis
Five groups add charge to carbon chains
- Hydroxyl
o OH like water (H2O)
- Carboxyl
o Acid -> loses an H+
- Amino Group
o Base -> gains H+
- Sulfhydryl
o Similar to OH but SH added instead
- Phosphate Group
o Important for cellular energy (ATP)
§ Add a positive charge