Bio topics 1-4 (unit 1)

Systema Naturae

• the 5 kingdom taxonomic hierarchy became the standard in western science

• developed binomial nomenclature

• genus species

• hierarchy based off similarities and differences in morphological and nutritional characteristics

The 5-kingdom classification system

• final version of the old system

• everything is grouped

how molecular biology changed everything

all life stores genetic information within DNA molecules use ribosomes to translate the information into proteins

• ribosomes are essential components of life

• mutations occur randomly overtime

• nucleotide sequences of the ribosome gene among species can be compared

• some nucleotides are critical to the function of the ribosome and must be conserved but some can change

the 3-domain classification system

• bacteria, archaea and Eukarya

• based on similarities and differences in molecular information (rRNA)

Eukaryotes vs prokaryotes

E:

• multiple linear dsDNA

• Nuclei

• 80s ribosomes

• Endomembrane system

• 10-100um

P:

• single circular dsDNA

• nucleoid

• 70s ribosomes

• no membrane bound organelles

• 0.5-5um

both: cell membrane, ATP, DNA, ribosomes and cytosol

Domain Bacteria

• Prokaryotic

• Unicellular

• Cell walls of peptidoglycen

• small (0.5- 5um)

Domain Archaea

• Prokaryote

• Unicellular

• Cell walls of psuedopeptidoglycon

• small (0.5-5 um)

Domain Eukarya

• Eukaryotic

• uni- and multicellular

• cell walls (when present) of cellulose, pectin and chitin

• large (10-100um)

As cells get larger what happens to their surface area and volume?

both the surface area and volume increase but the ratio decreases

• everytime a cell doubles in size teh ratio decreases by 1/2

why are prokaryotic cells small?

• prokaryotic cells are small because of diffusion

• so nutrients can reach the middle (if they don’t the middle dies causing the cell to die)

• the rates of diffusion and ATP synthesis will be the same

• SA>V in order to reach teh middle

how can Eukaryotes be large?

• allows them to be more complex

• they have internal membranes therefore internal surface area so they can be large

All life on earth has a shared ancestry?

• LUCA- population of early cells that exchanged genes freely

• beginning of all life forms

Horizontal gene transfer

• occurs when a gene from one species becomes part of the genome of another species

  • this is what allowed bacteria to become organelles and explains why mitochondria and chloroplasts have their own DNA, bacterial ribosomes, double membranes and gene sequence similar to bacteria

Endosymbiotic theory

• Some Eukaryotic organelles were originally independent prokaryotic cells

• mitochondria and chloroplasts were likely formed when two organisms formed a relationship that was beneficial to both and now permanent because they lost the ability to live without each other

Endosymbiosis

• host cell was an anaerobic (lived without O2) archaea-like prokaryotic

• endosymbiont was a bacteria like prokaryote that was efficient at aerobic respiration

• Archaea received lots of ATP

• Bacteria received protection source of nutrients

• host cell used its excess energy to evolve endomembrane system and become a eukaryote

• overtime bacteria lost ability to swim on its own and host needed that ATP

Evidence for Endosymbiotic theory

• Mitochondria and Chloroplasts

• 1. are the same size as modern prokaryotes

• 2. have their own singular circular dsDNA molecule

• 3. Divide by binary fission

• 4. Have (use) 70s Ribosomess

A "polypeptide" is a polymer of amino acids that consist of _____ amino acids.

More than 10

It is often stated that the phosphate bonds in ATP are “high energy,” but in fact, they are not notably high in energy. Rather, they are easy to break, and the ∆G of hydrolysis is a “useful” quantity of energy. What makes the phosphate bonds easy to break?

Negative charges on phosphate groups repel each other

How are the membranes of animal cells in summer able to remain viscous when the weather becomes extremely hot?

The percentage of saturated phospholipids in the membrane increases

The percentage of cholesterol molecules in the membrane increases

Ribosome DNA sequence:

• mitochondria rRNA and prokaryote rRNA are more closely related compared to prokaryote rRNA and Eukaryote rRNA

what do animal cells and plant cells have in common?

• both have nucleus and mitochondria

• both have plasma membrane

• both have endomembrane systems

what do plant cells have that animal cells don’t?

• chloroplast

• central vacuole

• cell walls (cellulose)

how can organisms be classified?

• by nutrition

Organisms need a source of energy

• phototrophs - light/ chemical

• chemotrophs

  • chemoorganotroph- organic (2+ carbon)

  • chemolithotroph- inorganic (1 or 0 carbon)

organisms need a source of carbon

• autotrophs- make their own organic molecules (inorganic)

• heterotrophs- eat other organisms to get organic molecules (organic)

what is the name of an organism has an organic chemical energy and carbon source?

Chemoorganoheterotroph

what is the name of an organism has an inorganic chemical energy and carbon source?

chemolithoautotroph

what is the name of an organism has an organic chemical energy and inorganic carbon source?

chemoorganoautotroph

what is the name of an organism has an inorganic chemical energy and organic carbon source?

chemolithoheterotroph

organic carbon source and light energy source?

photoheterotroph

inorganic carbon source and light energy source?

photoautotroph

what is a biological system?

a system is anything of interest to a biologist

• each biochemical system interacts with its surroundings

whats an isolated system?

does not exchange energy or matter with surroundings

what is a closed system?

exchanges energy with its surroundings but does not exchange matter

what is an open system?

exchanges energy and matter with it’s surroundings

what kind of systems are biological systems?

biological systems are open systems

• both energy and matter enter and leave the system

• biological systems must acquire energy and matter from surroundings an allow for waste to leave the system

what types of work do cells/ organisms do?

• homeostasis

• growth

• DNA synthesis

• mitosis

what are the sources of cellular energy?

1. High energy electrons: the amount of PE within a molecule depends on the arrangement of electrons in its chemical bonds (molecules with many more non-polar covalent bonds which have more EP

2. Electrochemical gradients: Electrochemical gradients store potential energy by separating ions across membranes, and cells tap that stored charge difference to drive work like ATP synthesis and active transport.

Enthalpy (H)

• sum of EP and EK

• when work occurs teh system has a different enthalpy

• teh change of enthapy represented as delta H which si measures as teh amount of heat that is released or absorbed from teh surroundings

• if heat is released H is negative

• if heat is absorbed it is positive

spontaneous reactions

• can occur under current conditions the phosphorylation of glucose and the isomerization of G6P to F6P are spontaneous

• spontaneous reactions are not instantaneous

• if a reaction is spontaneous tehn under teh same conditions it is non-spontaneous in teh opposite direction

what are important current conditions for spontaneous reactions?

• temperature

• pH

• atmospheric pressure

• concentration of reactants and products (easily manipulated)

Enthalpy does not determine if a reaction is spontaneous or not

yea

Entropy (S)

• entropy is how dispersed the energy and matter in the universe is

• every time work occurs the new system/ surroundings have a different entropy

• if the energy has become more dispersed delta S is positive

• if energy has become less dispersed delta S is negative

Total entropy

• total entropy (delta Stotal)

• delta S total= delta Ssystem +delta Ssurroundings

• this means the entropy of the system can decrease if teh enthalpy of the surroundings increase at a greater number

Free energy (G)

• molecules have free energy

• free energy is a measure of the energy in a system that is free to do work

• for work to occur energy must be available to carry out the change

• the reactants have more free energy than the products

• the change of free energy is delta G

• measured as the AMOUNT OF ENERGY THAT WAS USED TO MAKE THE CHANGE

• if G is negative energy is available (has not been used yet)

• if energy is not available G is positive (has been used)

are spontaneous reactions exergonic or endergonic?

exergonic

how are delta G and delta S total related?

delta G= -T (delta Stotal)

• there is enough energy available to change the system and increase the total entropy of the universe

What is an exergonic rxn?

free energy is released products have less free energy than reactants and the rxn proceeds spontaneously

are non-spontaneous exergonic or endergonic?

they are endergonic

• there is not enough energy available to change the system and increase the total entropy of the universe

what are endergonic rxns?

• free energy is gained

• products have more free energy compared to products

• non- spontaneous

relationship between delta H anf Delta S is G

delta g can also equal -TDSsurroundings +-TDSsystem

at constant pressure in the cell enthalpy change can = TDSsurroundings

delta G= delta H-TdeltaSsystems

what is chemical equilibrium?

occurs when rate of forward rxn= backward rxn

what happens to free energy as the spontaneous reaction proceeds?

• as the system changes DG increases until it equals zero and chemical equilibrium is reached

• at this point there is not enough free energy in the system to allow further overall change

• so for the rxn to be able to proceed in the forward rxn more reactants have to be added or more products removed

what is standard free energy change?

measurements made under standard conditions lik 25 degrees, 1atm,

• but to use this to see what occurs in cells it must be converted to dG

how to adjust for cellular concentrations/ convert from G in standard to just same old

DG= G standard +RTln( [P]/[R])

what is metabolism?

• the sum of all rxns in a cell is called metabolism

• in cells metabolic rxns are linked to biochemical pathways

what is catabolism?

• the breaking down of complex molecules

• an overall exergonic prcoess

what is anabolism?

the build up of complex molecules

• overall endergonic

what is a connected rxn?

two rxns are considered to be connected if the product of teh first rxn is the substrate of teh second rxn

what is the product/ substrate that connects the two reactions of glycolysis?

glucose-6-P

the first rxn of glycolysis

• is a coupled rxn bc while glucose is being converted to glucose-6-p ATP is also being converted to ADP

seond rxn of glycolysis

• is not a couple rxn

• conversion from glucose-6-P to fructose-6-P

• is connected to a thrid rxn when fructose-6-p is phosphorylated (gains phosphate group)

what are proteins?

polymers of amino acids

how are amino acids linked together?

together into peptides

amino acid polymers fold into proteins

what is a peptide?

polymer of amino acids

what is a polypeptide?

a peptide with more than 10 amino acids

what is a protein?

a polypeptide folded into a specific 3D shape

what is teh primary structure (the polypeptide)

The primary structure of a protein is the exact linear sequence of amino acids linked by peptide bonds, which determines all higher levels of its structure.

• the sequence of amino acids in the polypeptide

what is secondary structure?

• helices and sheets

• when the backbone atoms hydrogen bond to each other

• backbone is everything but the R group

• local folding into helices and sheets

what is the tertiary structure?

• when the R groups interact

• the overall 3D shape of one polypeptide chain caused by interactions between R groups

how is hexokinase formed?

• because of the way the secondary structure has helices and sheets annd turns made by teh primary structure

• rthe tertiary structure is the overall resulting shape of teh polypeptide because fo theose turns

• teh shape of hexokinase is important because Hexokinase has a specific 3D shape that creates its active site, where glucose can bind.

what is quarternary structure?

• when multiple proteins each with tertiary structure come togethr

• basically multiple polypeptide chains assembled together

what is a homotrimer?

3 identical protein subunits together

what is a heterotrimer?

3 different protein subunits together

how many subunits does hemoglobin have?

has 4; each with tertiary structure (heterotetramer)

why does it take a longer time for a measurable product to be obtained from glucose and ATP mixing?

• bonds in both substrates are stable

• energy must be added to destabilize these bonds

  • the energy destabilizes the bonds in the reactants which allows for the formation of bonds that generate the product

  • activation energy is the energy required to start a reaction

what are ways to speed up a chemical rxn?

1. increase the concentration of reactants so they collide withe ach other more

2. increase the temperature so that reactants have more energy when they collide with each other

3. use a catalyst

   1. protein enzymes

      1. - will decrease Ea but will not change G

   2. RNA ribozymes

how do enzymes reduce activation energy?

by forming an enzyme-substrate complex

• this occurs when the active site of an enzyme interacts with a specific substrate

• when the substrate enters the active site the enzyme changes conformation which forms the enzyme-substrate complex

what is the induced fit model?

• when the substrate binds to the enzymes active site

• the enzyme changes shape slightly to fit substrate better

• this positions the substrate and stabilizes the transition state lowering the activation energy

• has 3 ways to do this

  • 1. bring reacting molecules close together

  • 2. charge interactions

  • 3.distort or strain substrate molecules

what influences how fast a cell can convert substrates (reactants) to products?

• the rate of enzyme reaction (enzyme kinetics) which deponds on teh concentration of enzymes and or concentration of substrates

how do cells control/ regulate enzyme kinetics?

concentration of inhibitors and or concentration of activators

how does pH alter enzyme function?

• alters Hbonds +ionic bonds

• proteins will change conformation \

• enzyme function decreases as the shape changes

how does temperature alter enzyme function?

• low temp reduces molecular motion

• high temp will break chemical interactions

what is reversible competitive behavior?

• inhibitor is chemically like the substrate

• inhibitor noncovalently binds to the enzyme at the active site in competition with substrate

• the molecule with the highest concentration will win the composition

what is reversible noncompetitive behavior?

• inhibitor is not chemically like the substrate

• inhibitor noncovalently binds the enzyme at some other site on the enzyme

  • not the active site

• high concentrations of the substrate

Enzymes at high affinity state

the enzyme binds an allosteric inhibitor

enzyme low affinity state

the binding inhibitor converts teh enzyme to a low affinity state and teh substarte is released

what are regulatory allosteric enzymes?

control the rate of the entire biochemical pathway

Allosteric activator

bind to the enzyme which can change shape to a more active form

• for noncompetitive activation when the allosteric activator binds to an enzyme in low affinity state it will make it high

allosteric inhibitor

bind to the enzyme which will change shape to a less active form

feedback inhibition

the final product of a pathway inhibits an enzyme early in the pathway

what are lipids?

water insoluble (hydrophobic) molecules composed mostly of carbon and hydrogen atoms (hydrocarbons)

what are the kinds of biological lipids are there?

• triglycerides- triacylglycerids

• phospholipids

• sterols

what are fatty acids?

hydrocarbons with a carboxyl group at one end

fatty acid molecules vary in the

• number of carbon atoms in the chain (C12, C20 and C32)

• presence/ number of C=C (double bonds)

saturated fatty acids vs unsaturated fatty acids

• saturated fatty acids have no carbon carbon double bonds

• unsaturated fatty acids have 1 or more carbon carbon double bonds

what are triglycerids?

• energy storage molecules

• 3 fatty acid tails bound to a glycerol anchor

what are phospholipids?

• are amphipathic bc head is hydrophillic an dtail is hydrophobic

• made up of a head and tail group,

  • head: charged organic molecule, phosphate group and glycerol anchor hydrophillic

  • tail: two fatty acid chains, hydrophobic, uncharged, non-polar hydrophobic

when do phosphlipids spontaneously form bilayers?

• in water

spill the beans abt biological membranes

• compartmentalize the cell

  • the plasma membrane separates out from in

  • internal membrane create additional cellular regions

• membranes are selectively permeable

• membranes are scaffolds for communication and chemcial rxns