bio test one

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   1^st shell is complete with 2 electrons

o   2^nd shell is complete with 8 electrons

o   3^rd 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