1)Organize 

2)Metabolism 

3)Respond to stimuli 

4)Reproduce (growth of oganism & population)

5)Evolution (adaptation & mutation) 

1) Geological age/fossil record (allow dating~only have what we fin though)

2)Physical structure (not always reliable~you look the same .. likely same ancestor)

3)Genetic similarities (more acurate - molecular clock~DNA changes at a relatively constant frequency over time)

Classification schemes - 

Whittaker's 5 kingdom system (1970s)

1)Monera - all prokaryotes

2)Protists - all eukaryotes

3)Fungi - all eukaryotes

4)Plants - all eukaryotes

5)Animals - all eukaryotes 

Classification schemes -

3 Domain system (Woese 1990)

-Prokaryotes

-Originally labelled as extremophiles

i)high heat ii)low pH iii)high salt

-Prokaryotes

-very diverse metabolically

-can live anywhere & use anything as nutrients 

-Large cells

-Often multicellular

-Some you can see & some you cannot 

Comparisons of 3 different domains:

Chemistry of life?

Water is polar (due to dipoles) - unequal distribution of charge

O² is a strongly electronegative atom - steals e^- & creates a unequal distribution in a convalent bond

-interact based on particle charges 

Carbon is a backbone because:

i)it can form bonds with 4 other atoms

ii)can bond to another carbon

iii)can form double & triple bonds 

Monomers 

(Macromolecule) 

-a single sub unit or building block of a polymer 

ie. amino acids are monomers of proteins 

Polymers 

(Macromolecules)

-chain of monomers consisting of similar/identical subunits, must be built and broken by cell

ie. DNA is a polymer of nucleotides 

-polymers are more biologically important because combinations can be made whereas monomers are all single

~ Polymers ~

synthesis 

(condensation reactions/dehydration)

-add monomers to a growing polymer(forming a convalent bond)

→requires energy

→releases H₂O

ie. protein translation

~ Polymers ~

breakdown

(hydrolysis reactions)

-cleavage of covalent bonds

-release energy

-often spontaneous but slow

→sped up by enzymes 

ie. cellular respiration 

~ Carbohydrates ~ 

(polysaccharides/sugars)

Function & Structure

-energy storage 

-cell structure

-cell-to-cell recognition 

~ Carbohydrates ~ 

(polysaccharides/sugars)

Monomers 

-monosaccharides 

-multiples of CH₂O (3-7 carbon long)

 ie) glucose 

-central energy source in cell

-linear or ring

~ Carbohydrates ~ 

(polysaccharides/sugars)

Disaccharides

-Formed by covalent bonds

-glycoside bond btw 2 monosaccharides

-glycosidic bond type

-glyco (sugar)

~ Carbohydrates ~ 

(polysaccharides/sugars)

Polysaccharides

-polymers of multiple monosaccharides (100-1000 units)

 1)Starch- polymer of glucose, nutritional polysaccharide, energy storage, alpha1-4 glycosidic bond, same orientation, in plants 

2)Cellulose- polymer of glucose, structural polysaccharide, beta 1-4 glycosidic bond, alternating form or glucose, enzyme that breaks alpha1-4 cant digest beta1-4

3)Glycogen- nutritional polysaccharide, storage form of energy in animals(liver/muscles)

4)Chitin- structural polysaccharide, exoskeleton of insects 

-not true polymers

-hydrophobic (water fearing)

-non polar

-fatty acid structure: chain of HC ~16-18C long

:electrons are equally shared

:nonpolar

:no dipoles

:hydrophobic 

-aggrigate (clump) away from water

-3 fatty acid attached to a 3C gycerol backbone

-storage form of energy in animals

-lengthof hydrocarbon tail (14-22C)

-diff in frequency of C=C

:saturated fats , no C=C, solid at room temp., pack tightly together

:unsaturated fats, 1 C=C in fatty acid tail, C=C causes kink in HC bond, liquid at room temp.

-function in cell membrane

-2 HC chains attached to glycerol, fill a phosphate on3rd carbon of glycerol

-phosphate head is negative charge

-polar + hydrophilic (water loving)

-HC tails are non polar (hydrophobic)

-amphipathic- contain both hydrophilic and hydrophobic 

-lipid with a cholesterol backbone

-percursor for sex hormone

-maintain fluidity of cell membrane

-polymers of amino acids

-20 biologically relevent amino acids

-Monomer -amino acid backbone(shared) -variable group 'R' 

4 categories of amino acids -non polar HC - polar uncharged OH- polar charged acid(-) base (+)

-amino acid polymers are formed during trandlation at ribosome

-covalently linked by peptide bond btw C end and N of next a.a.

Primary structure

-polymerization of amino acid-

-linear sequence of amino acids

-directionality

-primary structure dictaes the folding pattern

-folding dictates the function

-peptide bond

Secondard structure 

-primary determines if a protein can fold in either a alpha helix or beta pleated sheets

-driven by 'R' group interation

-held together by H-bonds btw amino acid backbone

-hydrophobic interactions ie) nonpolar 'R' group

Forces that maintain: 1)covalent bond-disulfide bridge btw 2 cyteines(a.a. with a SH group at end of 'R' group) 

2) ionic bonds- bond btw polar charged basic and polar charged amino acid

3)hydrophobic assiciation -btw nonpolar amino acids

4)H-bonds btw polar uncharged amino acids ie. OH group at end 

-> stabilized by interactions btw 'R' group

-formation of a multi protein complex to create functinoal unit

-stablized by some forces that are used in 3^o

-tetramer

ie. ribosomes, nucleosomes, ATP synthase, collogen, hemoglobin, not all need 4^o

-proteins that help others achieve final functional confirmation

-environment that provides correct folding

-targets miss folded proteins for degregation

-prevent miss folding

Human disease of protein folding

-alzheimers

-parkinsons

-mad cow

-sickle cell anemia 

Nucleic Acids

(DNA + RNA)

-store and transmit information

-DNA stores genetic info in the form of genes and transmits it to its offspring

-RNA transmits info from DNA to protein

Structure of

monomer 

+

polymers

1)Ribose 5C sugar

2)Nitrogenous base (A, T, C, G)

3)Phosphate 

-polarity-

directionality (5-3 or PO₄ - OH)

-hydrophobic aggregate away from water

-spontaneously form a bilayer

-phospholipids are amphipathic and cylindrical

-not held together by convalent bonds

-lateral movement is rapid and frequent(hydrophobic)

-flip flop movement is rare (hydrophilic) 

high- more movement, fluidity, more permeable, cholesterol holds phospholipids together becasue its highly hydrophobic and restricts movement, loss of function

solution-increase length of fatty acid tail, remove C=C bonds, cholesterol as pylon

low- phospholipid packing and decreased movement, cholesterol acts as a spacer, loss of function

solution- decrease length of fatty acid tails, add C=C bonds(creates kink or bend), add cholesterol

Membrane associated proteins

integral membrane protein-part is embedded in the bilayer, must be amphipathic

(must have hydrophobic amino acids(nonpolar) and hydrophilic amino acids(polar))

Peripheral membrane proteins- must associate with integral membrane proteins(intracellular)

permeability -permeable cancross by going btw bilayer, based on size and polarity, short dipole movement, small nonpolar

impermeable-ions because they are a hydration cell

Passive transport- down [ ] without energy, permeable molecules 

-turgid, swell(hypotonic) -isotonic(neutral) -hypertonic, shrink(plasmolysis)

Facilitated diffusion-Aquasporins(channel), used for impermeable substances, 

-channel(specific hole specific molecule) -carrier(changes shape in transport)

Transport

PART B

Active transport- up [ ] gradient, increase [ ] inside, to excrete solut, requires energy

Cotransport-source of energy for active transport, work together, same time, coupled transport one establishes other uses 

Bulk transport- exocytosis(secretion) golgi>vesicle>plasma>extra cellular fluid

endocytosis-cell eating, formation of vesicles

Cell size

-bacteria ~1-10um

-eukaryotic ~10-100um

-prokaryotes:

diffusion/dilution hard to get [ ] in large cytoplasm,

surface area² =volume ratio, increase volume faster than surface area

-plasma membrane, cytoplasm/cytosol, single circular chromosome located in nucleoid region(not membrane enclosed), often have flagellum and cell wall.

-0.1-100um    -prevents osmolysis

-rotation movement, powered by H gradient, flow of p⁺down gradient and releases energy

-cell wall for defense

-Gram positive uses structural polysaccharide called peptidoglycon

-Gram negative lipopolysaccharide associates with the outer membrane to neutralize (-) charge of LPS

Anitbiotics- specific for certain cell types, useful to target only prokaryotes

-bacteria attach to each other and surfaces

ie. biofilm consortion of bacteria that secretes slime-sugars

-internal membranes originated from infoldings of plasma membrane 

-evolution of mt and cp likely came from a primative eukaryote 

-GOOD ROOMMATE HYPOTHESIS- O₂ is toxic, primative bacteria need to aviod this [ ], prokaryote is engulfed by eukaryote...so... prok escapes toxic [ ] and euk gets a cook- mutually benificial

EVIDENCE- mt and cp have own DNA 

prok like DNA

mt and cp have prok like ribosomes

prok 70s and euk 80s

Eukaryotic cell

~endomembrane system~

-nucleus stores DNA and sight of RNA synthesis, DNA is a storage molecule and contains linear chromosomes, enclosed by nuclear envelope

-nucleous is sight of ribosomal RNA synthesis and ribosomal/subunit assemby

-nuclear envelope is made of 2 phospholipid bilayers and it seperates nucleoplasm from cytoplasm, it protects DNA

-DNA packing, DNA associates with (+) charged proteins called histomes, complex is called chromatin, nucleosome is the octomer that DNA wraps around, histone stacks nucleosomes to form 30mm fiber/soleniod, looped domains, mitotic chromosome mechanism 

-more permanent membrane bound compartment then the vesicles

-functions for storage and osmoregulation

RER- rtanslation of proteins destined for the endomembrane system, is a membranous network covered in ribosomes, function as protein translation, protein quality control, chapterons

SER- no association ribosomes, used for ion storage, phospholipid synthesis, lipid synthesis, detox

Golgi apparatus

-fedex

recieves cargo(vesicles with proteins, lipids, ect.) from the ER, sorts the cargo, ships it off, structure is a set of membrane sacs called cisternae, larger things can be trnasported via vesicle trafficng or cisternal maturation model

cis>medial>trans

Lysosomes

cell stomach

-cell support and motility -tubulin dimers, protein made of alpha and beta subunits, polymer of tubulin, forms a hollow tube

-compression resistant, chromosome movement in cell division, vesicle trafficing, eukaryote flagellum

-motor protein, changes shape with hydrolysis to walk along cytoskeleton

ie. kinesin positive end directed +

dynein negative end directed(force for flagellum) ATP hydrolysis

Microfilaments 

(actin filaments)

-rope like chain

-tension resistant cytokinesis

-muscle motor- myosin(hopping), myosin can walk along the actin filament and shorten the length of a muscle

Intermediate filaments 

-heterogenous 

-tension resistance 

-cell shape

-stable, non motile 

ie. keratin, nuclear lamina