BSCI 207 Exam 1 Prep

What are the two laws of physics

-Conservation of matter -conservation of energy- thermodynamics

What does thermodynamics specify?

it specifies the rules for converting energy in the environment into useful forms for sustaining life. -the first law deals with energy balance -the second law deals with reaction directions

what is the first law of thermodynamics

-the total energy in the niverse is neither created nor destroyed. it can be transformed or converted between forms.

• the energy of the reactants and the products are equal. -enthalpy can accuire enrgy from its surroundings

• the enthalpy in the uhniverse equals zer. delta H=0

What does it mean when we say that overall, initial energy= final energy

it means that organisms need to accuire energy from theri environment to enable theri metabolic and structural needs.

what does this equation mean -∆H = ∆G + T∆S

-it means that the change in total energy of a system equals the sum of chemical work that occurs (ΔG) plus heat in kelvin and disorder in the system (ΔS). -if we do no work (ΔG=0) and have no change in disorder (T∆S=0), then there is no change in energy

when we do work is all of it contributed to work

no, only some of it does work and the rest is lost as heat and or entropy (TΔS).

what is total energy comprised of

usable plus unsuable energy

what is the second law of thermodynamics

the entropy (s) of the universe can only increase. -any decrease in entropy of the system must be paid for by increased entropy of the universe

• energy transfer is never 100% efficient g<h -this law tells us that T∆S is positive for any spontaneous (= possible) reaction. ∆G must be < 0 for the above to be true.

what does it mean when a system has a positive delta g

they are not spontaneous, but could be in an expanded system in which delta g would be negative overall.

what are the characteristics of spontaneous reaction

delta S, disorder, is increasing and is greater than zero. Therefore -delta is less than zero and so delta , free energy, is less than zero

How can you get negative delta g in a reaction (negative free energy)

loss of enthalpy, any increase in entropy or disorder

loss of enthalpy that offsets a decrease in entropy or disorder

increase of enthalpy offset by a large increase in entropy

what is activation energy

energy input needed to initiate the reaction.

what is the role of catalysts

they help to lower the activation barrier -types of biocatalysts *inorganic(often metallic ions) *enzymes with metallic ion cofactors *enzymes lacking cofactors

what can lead to disorder

movement and mixing. the second law says that in any spontaneous process, the universe gets more disordered. this is also truw for a physical system where there is no chemical reaction ( disorder of the universe is greater than zero) -an increase in heat leads to more movement and so more entropy. mixing two kinds of chemicals lead to more entropy

what can organisms use their entropy increases for

they can use entropy increases in their surroundings to drive biologiscal order, specifically self assembly. -ex: Directed movement of a fish by muscle contraction releases heat and mixes the water around its body, both of which contribute to a positive value for T∆S.

describe membrane phospholipids

-hydrophillic head group and hydrophobic tailss -polar head group is charged phosphate -tails are fatty acids

why do lipid bilayers form spontaneously

lipid molecules in awueous solution are surrounded by ordered arrays of water molecules -when lipids assemble, the water is released, increasing its entropy. assembly is favored.

describe hydrophobic interactions

non poar molecules tend to neither attract or repel e/ o. polar molecules and charged ions attract or repel e/o and they tend to squeeze hydrophobic regions together. this is an example of self driven assembly

give examples of entropy driven order, self assembly

bacterial ribosomes and virus assembly

Fill in the blank: Spontaneou _____ order maximizes _______ order

Spontaneous local order maximizes universal disorder.

What are the characteristics of things that have a low disorder verses high one

things that move freely have a very high s (like freely moving water molecules) and things that more rigid have a low s (like ice like shells around exposed hydrophobic amino acids).

-Entropy-driven local order: ∆Suniverse > 0

what is the thermodynamic definition of an organism

Organisms are open systems that:

1. ...use thermodynamically favored processes to transform available energy and matter into life's forms, 2....use high quality free energy (△G) for carrying out life's processes, 3....release low quality energy (heat), and 4...maintain ordered structures at the cost of increased universal disorder.

organisms are open systems, what is an open system?

is the earth open or closed system

stuff can go in and out

for matter, earth is a closed system. for energy, earth is open earth.

Free energy differs from total energy because:

It is available to do work.

Life relies on two key reactions: the oxidation of glucose to produce CO2 and water and the reaction of CO2 and water to produce glucose. These reactions are:

Exergonic and endergonic, respectively

A reaction that is exergonic AND spontaneous

Only occurs if the reactants have enough energy to get over the activation barrier

Which of the following is NOT true about cleaning your room?

It requires energy you acquire from food It leads to a release of heat It leads to an increase in the order in your room It leads to an increase in the order in the universe Eating leads to an increase in disorder of the food you eat

It leads to an increase in the order in the universe

Gibbs came up with his famous equation to determine if a reaction is spontaneous or not: ΔG=ΔH−TΔSΔG=ΔH−TΔS. Which of the following reactions is/are likely to occur at room temperature?

-Reactions A and C -Reaction D where delta H =+100 J/mole and delta S is = -1 J/mole -Reaction B where delta H =-100 J/mole and delta S is = -1 J/mole -Reactions B and D -Reaction C where delta H =+100 J/mole and delta S is = +1 J/mole -Reaction A where delta H =-100 J/mole and delta S is = +1 J/mole

If a reaction is spontaneous, its entropy is increasing and greater than zero.

describe how autotrophs and heterotrops use energy from each other/ how that energy is cycled

The producers / autotrophs take in CO2 and H2O from the atmosphere and convert them to glucose and O2, which are then used by the consumers / heterotrophs. The consumers release CO2 and H2O back to the environment. In the process, both types of organisms produce ATP. Energy flows through the organisms. It comes in as light energy, gets converted to chemical energy, and is then released as heat.

what happens to the molecues that make up life? where do they come from and where do they go

Molecules move from the environment into living organisms in the form of CO2, H2O, and various minerals. These are converted to chemical energy by autotrophs and made available to other organisms. But ultimately, the molecules are recycled through organisms and returned to the surrounding environment.

how does energy flow in the system of earth? what are inputs and outputs

life takes in energy in the form of light from the sun. Some organisms use this energy directly and store it as sugars. Other organisms use the sugars produced by the autotrophs and so take in chemical energy to fuel their life processes. Both autotrophs and heterotrophs give off energy in the form of heat. So energy flows from the sun, through organisms, and back into the atmosphere (and the universe) in the form of heat. If we consider the Earth, light comes to Earth from the sun and this energy is then radiated back into space as heat

what happens to heat released by organisms and does it have any useful functions

The heat released by the system (or taken up by the system) comes from the surrounding environment. The release or removal of heat causes either more motion or less motion of molecules in the surrounding environment. This increases or decreases the entropy of the surroundings. Changes in the entropy of the surroundings can be important in determining whether a particular reaction is exergonic and so spontaneous

which source of energy do you think is most useful for breaking chemical bonds to enable life?

Photons are just about right in providing the energy to break one bond. It also takes only a few ATP molecules to provide the energy to break a bond.

• When glucose (C6H12O6), is oxidized, it releases 688 kcal/mole of energy. Some of this energy gets stored in the form of ATP. Each molecule of ATP can stores 7.3 kcal/mole of energy.a. If all the energy from glucose oxidation was converted to ATP, how many ATP molecules would be produced for each molecule of glucose?

-b. In actuality, only 36 molecules of ATP are produced. What fraction of the available energy ends up as ATP?

In that case, 688 kcal/mole of energy / 7.3 kcal/mol of ATP = 94.2 ATP molecules per molecule of glucose. So you'd produce 94 ATP

-Since 36 molecules of ATP are produced to store energy out of 94 that could be produced then: 36 / 94 = 38% of the energy is stored as ATP.

When you couple a reaction, how does that allow the reaction to occur spontaneuously.

The ATP gives the reactants more initial energy. This makes the reactants higher in free energy than the products such that the reaction is exergonic and therefore spontaneous. Likely this occurs by first using ATP to phosphorylate one of the reactants. This energized reactant is then more easily rearranged to produce the sucrose prod

in an endergonic reaction hwo is the energy in relation to the products

Endergonic reactions have products which have more energy than the reactants. In order for them to proceed, they need to get energy from somewhere. One place they can get that energy is from ATP.

what were some of the indicators of more complex life

Multicellular eukyaryotes by ~1 Bya

More complex life forms arose ~550 MYa

Animals and plants Aquatic origins Terrestrial invasion

what are lifes requirements

-metabolism- the ability to do biological work -the ability to pass down genetic information -cells- the ability to contain metabolism and information

What is the first hypothesis for how life evolved

-Hypothesis 1: metabolism first. 1920s: Oparin and Haldane suggested ordered set of chemical reactions was the beginning of life. in this theory, life is seeded by hydrothermal vents which releaser trolite that acts as a catalyst for various chemical reactions.

-Thermal vents are high temp and high pressure Mineral clusters drive generation of complex organic molecules Pyruvic acid

-evidence is speculative: Metal atoms form the core for key enzymes Fe, Cu, Mo

what is the importance of a proton gradient

Early "cells" can take advantage of proton gradients Evolution of ATP synthase to convert the energy of moving protons into ATP ATP synthase is shared by all of life and arose just once

What is the second hypothesis for how life evolved

-life began with inheritance and the passing of information (relating to central dogmas setup for info flow: dna>rna>protein. dna. DNA is stable way to store information. It is carried by RNA and converted into proteins. Proteins do the enzymatic work in the system.

*rna can be an enzyme- rna acted to splice itself, no protein needed. Finally cloned gene into a different cell and proved the RNA spliced itself.

-RNA carries genetic information RNA also catalyzes reactions (like proteins) Selection will favor variants with effective replication. it has higher evolvability

what happens after two species diverge from their common ancestor

sequence similarity falls

what is the role of purifying selection

-Sequences with weak purifying selection change more quickly

-Sequences experiencing strong purifying selection change more slowly:

what are the three domains of life

eukarya archea bacteria

what happened in the great oxygenation event

a rise in oxygen occured and anaerobic life was largely wiped out (anaerobic bacteria) . this was triggered by cyanobacteria (photosynthetic prokaryotes) producing it

why are prokaryotes still in charge

they are over 90% of earths biomass, live in many habitats , form symbioses, and are major cause of disease

prokaryotic gene structure

1. Regulator - encodes repressor

2. Promoter - binding site for RNA polymerase

3. Operator - binding site for repressor (blocks RNA polymerase)

4. Structural genes - open reading frames encoding proteins acting in the same process

• inducible operon (inducer binds to repressor making it unable to bind to the operator - turn operon on)

what us the difference between gram negative and gram positive bacteria

positive- when exposed to crystal violet with iodine, it will retain crystal violet. Has a thick cell wall, outer peptodiglycan layer. many metabolic strategies, areobic, faculatative aerobic or anaerobic chemoheterotrophs. produce acids, antibiotics, cause diseases, and release exotoxins

negative- the violet will wash out and stain to pink. produce acids, antibiotics, cause diseases, and release exotoxins. thinner cell wall, many metabolic stategies- aerobic, faculatative aerobic or anaerobic photoautotrophs, chemoautotrophs and chemoheterotrophs. planetary engineers, helps digestion, cause diseases, bioluminescence

name the gram negative and characteristics

• proteobacteria Gram-negative Many shapes and lifestyles Many tightly associated with eukaryotes mutually beneficial symbionts pathogens of animals and plants

-cyanobacteria similar to first life on Earth photosynthetic, sometimes called "algae" Gram-negative source of chloroplast endosymbiont

name gram positive bacteria and their characteristics

-actinobacteria Gram-positive often form filaments original source of many antibiotic medicines includes Mycobacterium tuberculosis (TB pathogen)

-firmicutes Gram-positive (mostly) major component of gut and skin surface microbes ("flora") some make tough endospores (e.g. Bacillus anthracis) Mycoplasma: tiny organism (0.2 mm) with tiny genome (1/5 size of E. coli)

describe the environment that archaea thrive in

Tolerate & thrive in: high temperatures high salt complete darkness *most have anaerobic metabolism

name the archaea and its characteristics

-euryarchaeota include most anaerobic methanogens, include hyperhalophiles (super salt lover) live in swamps, lkes, large intestine

-crenarchaeota thermophillic acidophillic can be both or one

-Asgard phyla of archaea anaerobic low abundance has eukaryotic specific genes

what is the importance of the tack phylum

the first groups discovered

What does life require?

• source of energy ... light and high energy molecules -production of atp .. direct phosphorylation of adp, chemiosmosis (proton gradient and atp synthase -source fo fixed carbon .. in house carbon fixation (autotrophy), predation, scavenging, or symbiosis (heterotrophy)

name the three sources of energy that lead to atp

light- phototrophic

inorganic- chemolithotrophc organic- chemoorganotrophic both high energy reduced molecules (we are this, we get energy from fixed carbon in food by oxidizing it)

what are the two ways to get fixed carbon

inorganicly- autotrophic preexisting organic- heterotrphic.

these both lead to organic building block molecules

what are the 6 metabolic strategies

photoautotrophs(cyanobacteria) photoheterotrophs( halophilic archaea) chemoorganic autotrophs (methantropic bacteria) chemolithoautotrophs(sulfur oxidizing bacteria) chemoorganicheterotrophs (parasites) chemolitoheterotrophs (lots of bacteria)

what do redox reactions do

Redox reactions transform physical & chemical energy entering organisms into useful biological energy carriers.

what is the difference between oxidation and reduction

OIL = Oxidation Is Loss (of electrons)

RIG = Reduction Is Gain (of electrons)

what si an example of a redox reaction

glycolysis

Glucose + 2NAD+ + 2ADP + 2Pi

→ 2 pyruvate + 2 NADH

• 2H+ + 2 ATP + 2 H2O

Pyruvate is a 3 carbon molecule with a -1 negative charge so glucose (which has 6 carbon atoms) is oxidized (losing 2 electrons) and being split in two and pyruvate is reduced (with each of 2 molecules gaining an electron). NAD+ is also reduced, picking up two electrons (and one proton).

What is a benefit of the electron transport chain

energy metabolism occurs in small steps, the et caqn capture energy into small packets of energy. energy is captured as atp and other electron carriers (nadh, fadh2)

define an electron carrier and the electron transport chain

Electron carrier - any molecule capable of a redox reaction Electron transport chain (ETC) - a sequence of electron carriers that perform redox reactions coupled to useful work.

define an eectrochemical gradient

a gradient (difference over distance) of charge ("electro-") and concentration ("-chemical") across the membrane

examples are atp synthesis in bacteria, mitochondria

Describe the etc in oxidative phosphorylation. as well as the inputs and outputs of this process

ETC uses 4 electron carrier proteins plus two electron shuttles. It's an elaborate proton pump. This is then coupled to ATP. NADH brings high energy electrons from food to start things going.

Inputs: electrons from NADH and FADH2 and oxygen Outputs: H+ gradient, reduced oxygen (H2O), oxidized NAD+

what is the role of atp synthase

Converts H+ gradient into ATP The flow of H+ through the Fo unit causes the stalk to spin at a rate of 50 revolutions per second. The energy in the spinning motion leads to conformational changes in the active site of the F1 complex to catalyze the reaction of ADP + P -> ATP

describe the etc for anaerobic respiration

the ETC uses H2O as the electron donor and O2 as the electron acceptor.

Anaerobic organisms use different donors & acceptors in ETC.

Both harness energy to produce the same end product - an H+ gradient for ATP synthesis.

describe Phototrophy in halophilic archaea

Create H+ gradient across membrane with bacteriorhodopsin, a light-driven proton pump

No ETC required to run ATP synthase

No O2 produced

Autotrophic, but carbon fixed differently than cyanobacteria or chloroplasts

describe the photosynthetic etc of purple s bacteria

1. H2S donates 2 e' ( 2H+ + S) to the photosystem

2. Photosystem absorbs light, boosts e- from cytochrome c shuttle to high energy state.

3a) some e- reduces NAD+ to form NADH (used in C fixation)

3b) some e- shuttled to cytochrome complex by Q, driving H+ across the membrane.

4. H+ gradient used for ATP synthesis (used for many jobs)

describe how both endosymbionts, mitochondrion and chloroplasts use the rtc

The ETC pump protons across a membrane and then run the H+ back through ATP synthase to generate ATP

describe the key components of the biological nitrogen cycle

Nitrification - oxidation of N compounds from NH3 to NO3- Denitrification - reduction of N compounds from NO3- to N2 Fixation - the conversion of N2 (inert) to NH3 (reactive) by nitrogenase

show the oxidation and reduction for the biological sulfur cycle

Oxidation: H2S ---> S° ---> SO4-2 Reduction: SO4-2 ---> HS-1 or S° ---> H2S

describe the importance of venttubeworms, the chemoheterotrophs that evolved into chemoautotrophs

theylivearoundhydrothermalventaandrelyonchemosynthesis.Hemoglobin brings oxygen AND H2S to gut.

Bacteria convert H2S and O2 into sulfuric acid: H2S + 2O2 SO42- + 2H+ ΔG = -190 kcal/mol (similar to oxidation of methane!) sulfur and oxygen is oxidized

Reaction is coupled to ATP synthesis by proton gradient (as in oxidative phosphorylation).

Fixation of carbon to make sugars occurs via the Calvin Cycle (like plants).

define diffusion

Diffusion = random molecular motion that redistributes molecules from high to low concentration

it is a spontaneous process driven by increase in entropy

What drives diffusion?

delta G= delta H- T delta S

define flux

Flux is number of molecules moving through a given area per unit time

Diffusion * Concentration coefficient gradient

J= -D (dc/dx)

flux, J= molecules/area*time=molecules/cm^2s

where d is the diffusion coefficient and dc/dx is the concentration gradient

why is there a negative sign in this equation

Movement is opposite to the direction along which concentration increases

how do you calculate the concentration gradient

dc/dx= (c outside-c inside)/dx

• Dx (delta x) is the with of the barrier, for ex membrane

when does D, diffsion, increase or decrease

it increases with temperature, and is smaller for a bigger molecular radius

how can you increase the diffusion rate

-Increase area, A Increase concentration gradient with ...

• larger concentration difference (larger DC) and/or

• thinner diffusion zone (smaller Dx) -Higher temperature (move to warmer spot) -Lower viscosity (drink water) -Smaller radius of diffusing solute (digest big molecules into smaller ones)

what equation tells you How long does it take to diffuse a given distance, x?

Fick's Second Law (1 dimension)

t= x^2/2D t = diffusion time (s) x = diffusion distance (cm) D = diffusion coefficient (cm2/s)

What does diffusion suffice for? what is it too long for?

Diffusion suffices for: Movement within cell Across cell membrane Between nearby cells

Diffusion takes too long for: Movement between distant cells Movement between organisms

why does diffusion complicate getting big?

Bigger cell has bigger surface area Diffusion rate goes as cell diameter2 BUT: Bigger cell of same shape has even bigger volume Consumption rate of nutrients goes as cell diameter3

for example: Diffusion within cell and between cells is straightforward. But getting into and out of the cell requires getting across the membrane. Membrane is hydrophobic.

what effect does size and charge have on membranes when talking about diffusion

Size and charge affect permeability and diffusive flux through cell membranes.

ions like na have lower permeability and hydrophobic molecules liek o2 have higher permeability

how have cells overcome diffusion limitations

Transport proteins - channels, carrier proteins and pumps

what are key eukaryotic features

*nuclear envelope ("eukaryote" means "true kernel") *endosymbiotic organelles: mitochondria (all eukaryotes) chloroplasts (photosynthetic protists, algae, and plants) spliceosomal introns (not self-splicing) *dynamic cytoskeleton asymmetrical growth, cell shape changes possible sexual reproduction involving whole genome (meiosis + syngamy) *linear chromosomes *sexual reproduction (meosis + cel fusion/fertilization) *splicosomal introns

why is the origin of the nucleus still somewhat a mystery

-The endoplasmic reticulum (ER) is topologically connected to outside of cell -ER is associated with nuclear envelope

what is the martin and koonin hypothesis of why a nucleat envelope developed at all

Primordial eukaryotes evolved the nucleus and the spliceosome simultaneously to defend the themselves against transposons (which eventually became introns).

what obervations led to the endosymbiotic theory, origin of mitochondria and chloroplasts

both are the size of typical bacteria bounded by two membranes (like engulfed cell) have their own, bacterial-like ribosomes retain vestigial circular DNA genomes with similarity to bacteria

what are the two major lineages of photosynthetic eukaryotes

once the cyanobacterium was engulfed by the heterotrophic eukaryote, primary endosymbiosis occured and lis led to the red alga and the green alga . there was also the secondary endosymbiosis of the red algae and green alga

Which of the following eukaryotic organelles is not thought to have an endosymbiotic origin?

the nucleus chloroplast mitochondrion

the nucleus

True or false? "Martin and Koonin proposed that nuclear envelope evolved to help eukaryotes keep their multiple chromosomes all in one place in the cell."

false

Which of the following are forms of evidence for an endosymbiotic origin of mitochondria and chloroplasts? These organelles have their own circular genomic DNA.

They are about the same size as free-living cyanobacteria and alpha proteobacteria.

Organelle genes are often more similar to bacterial genes than those of their eukaryotic host.

all three of these

all three of these

True or False? "All photosynthetic organisms acquired their chloroplasts via the primary endosymbiosis of a cyanobacterium."

false

how is diffusion rate related to membrane thickness?

the diffusion rate is inversely related. so for example . If the membrane became ¼ as thick, the diffusion rate would increase by a factor of 4

If the cell diameter triples, what happens to the CO2 diffusion rate?

The diffusion rate is proportional to radius^2 so it would increase x9

characterize this key eukaryotic trait: Flexible cell membrane & dynamic cytoskeleton

Cells can change shape rapidly and reversibly Cells can move in new ways (cilia, flagella, pseudopodia) Cells can ingest bits of surroundings by endocytosis Cells can get bigger Mitotic spindle: multiple chromosomes OK!

characterize this key eukaryotic trait: the nucleus

its origin still up for question: The endoplasmic reticulum (ER) is topologically connected to outside of cell ER is associated with nuclear envelope

characterize this key eukaryotic trait: symbiotic organelles

Endosymbiotic theory (Sagan, 1967) based on these observations: both are the size of typical bacteria bounded by two membranes (like engulfed cell) contain ribosomes and DNA eukaryotes owe oxygen tolerance to mitochondria: the engulfer was anaerobic?

characterize this key eukaryotic trait: sexual reproduction

constant cycle of fertilization to diploid stage to meosis to haploid stage, back to fertilization

why did sex evolve?

DNA damage increased after the endosymbiosis (and great oxygenation event) of the mitochondrion. Sex begins as an expanded form of DNA repair, acting on the entire genome at once to produce new genotypes that might have fewer mutations.