BIOM 2

what is aerobic respiration?

a combustion rxn where glucose is burned in oxygen to produce CO2 and H2O with the release of energy (C6H12O6 + 6O2—→ 6CO2 +6H2O +energy

• series of coupled redox rxn’s that release free energy of glucose and transfers some of the released energy to other molecules

what happens in coupled redox rxn’s?

• Non-polar covalent (c-c, c-h, o=o) bonds in the reactants are broken

• polar covalent bonds in the products are formed (C=O, O-H)

• bonding electrons shared equally between carbon atoms in glucose move farther away from the C nuclei in CO2 so glucose is oxidized

• bonding electrons shared equally between O atoms in O2 move closer to the O nuclei in water so oxygen is reduced

what are reduced electron carriers?

energy transport molecules that move from one rxn to another

what do redox rxn’s generate?

reduction potentials that is stored in electron carriers:

• NAD+ +2e- +2H+ —→ NADH + H+

• NADP+ +2e- +2H+ ——> NADPH + H+

• FAD +2e- +2H+ ——→ FADH2

Glycolysis overview/ summary

• partial glucose oxidation

• consists of 10 connected (some coupled) rxn’s

• each step requires a unique enzyme

• 2 coupled rxn’s energize glucose

• 3 coupled rxn’s that yield high energy products

summarize the process/ rxn of glycolysis

• starts with the 6 carbon molecule glucose

• requires 2 ATP to start which are put out as ADP and this is where glucose receives the phosphate group from

• 2 NAD put in coem out as 2NADH

• 4ADP in 4ATP out

• ends with 2 3 carbon pyruvate molecules

how is ATP generated?

• substrate level phosphorylation

how come glycolysis is partial glucose oxidation?

• Not much ATP has been made, a lot of energy is trapped in pyruvate (the most free energy is currently within pyruvate and NADH)

• The cell needs to remove pyruvate so our final product isn’t building in the cell (don’t want change in free energy = 0)

• The cell needs to restore NAD+: we need to oxidize the NADH. It is expensive to make lost of ATP so lots of pyruvate is needed so we need a way to oxidize the NADH made in glycolysis

What is the checkpoint step of glycolysis?

This is the point where the reaction can go one of two ways depending on whether there is oxygen or not

• if oxygen is limiting pyruvate is reduced (fermentation)

• if oxygen is present pyruvate is oxidized (Aerobic respiration)

what is fermenattion?

occurs when oxygen is not present. Pyruvate is reduced and one of two fermentatiosn occur

1. lactate fermentation

2. alcoholic fermentation

what is aerobic respiration?

• oxygen is present and therefore pyruvate is oxidized and this leads to the citric acid cycle and oxidative phosphorylation

what is the bridge rxn?

• where pyruvate is oxidized (oxygen present) to Acetyl- CoA in the matrix

• Pyruvate the 3 carbon molecule is decarboxylated (releases CO2) and NAD+ comes in and is reduced to NADH

• Coenzyme A comes in and it is now Acetyl-CoA which is a 2C molecule

Krebs cycle simplified

• starting with that Acetyl-CoA molecule (2C)

• which is converted to citrate.

• the process from citrate to oxaloacetate (4C) includes the release of 2CO2, 3NADH, FADH2, 2ATP

protein complexes 1 and 2:

• NADH in matrix donates electrons (reduces) to complex 1 only

• Protons are pumped from matrix to IMS by complex 1

• FADH2 in matrix donates electrons to (Reduces) complex 2 only

What is Ubiquinone?

• a hydrophobic electron taxi that taxis electrons from complex 1 to complex 3

• also taxis electrons from complex 2 to complex 3

• when reduced it takes protons from the matrix and releases it in IMS when oxidized

complex 3, cytochrome c and complex 4

• electrons flow from complex 3 to cytochrome c

• cytochrome c is a hydrophilic electron taxi that moves electrons from complex 3 and complex 4

• electrons flow through complex 4 and way more protons are pumped from the matrix to IMS

• complex 4 donates electrons to oxygen which is the final electron acceptor which is reduced to H2O

explain how the electron transport chain generates an electrochemical gradient

• proton concentration is lowered in the matrix when they are

  • Pumped across the membrane. 2. To reduce O2

The proton electrochemical gradient is called

Proton motive force

What is proton motive force used for?

Chemiosmosis

how does chemiosmosis use PMF?

• uses PE of PMF to power ATP synthase

• As protons move through the enzyme back into the matrix enough energy is released to allow ADP+ pi=ATP

• the concentration of protons would be higher outside the membrane

• the concentration of protons would be lower inside the membrane which creates a chemical gradient and charge gradient

What happens at the ATP synthase>

• protons flow down its gradient and the energy drives phosphorylation of ADP

• couples the rxn through the Fo channel part of the enzyme to the phosphorylation of ADP by the ADP by F1 catalytic part of the enzyme

why is there variation in ATP yields?

• some PMF is used for other things (12 active pumps)

• NADH and FADH2 are used for other things

If you don’t need ATP where is it stored?

• glucose can be stored as a polymer (glycogen in animals and starch in plants)

• triglycerides can be generated for more long term storage (Acetyl Co-A can form fatty acids)

How can organisms generate macromolecules without going through the Krebs cycle?

• using Acetyl-CoA

what happens in Aerobic respiration prokaryotes?

• all metabolism would occur in the cytosol

• and on the cell membrane

• but everything else is the same

What is Anaerobic respiration?

• occurs in prokaryotes

• evolved at a time when oxygen was not abundant

• uses final electron acceptors other than oxgen, sulfate and nitrate

• other than that its the same

what happens during the photosynthetic reaction? (6CO2+ 6H2O —→ C6H12O6 + 6O2)

• Polar covalent bonds in the reactants are broken

• Non polar covalent bonds in the products are formed

• BE between the carbon and oxygen in CO@ have moved closer to C atoms in glucose so CO2 is reduced

• BE between the oxygen and hydrogen in water have moved farther away from the O atoms in oxygen so H2O is oxidized

What is the chloroplast made up of?

• The chloroplast is surrounded by cytosol and has an outer membrane, intermembrane space and inner membrane.

• inside the inner membrane is the stroma which is the space around thylakoids which are stored in “groups” called granum

• within the thylakoid membrane is thylakoid lumen

what happens in the thylakoids?

• light is absorbed by the chlorophylls and carotenoids

• electron transport

• ATP synthesis by ATP synthase

what happens in the stroma of the chloroplasts?

the calvin cycle

what photosynthetic processes are there?

• light dependent reactions

• the Calvin cycle

What happens when a photon (light) strikes an object?

• it can be reflected and bounced off

• transmitted and pass through

• or absorbed by electrons in the object

what are pigments?

molecules efficient in absorbing photons because their chemical structure allows their electrons to absorb the energy of the photon

• pigments absorb photons of specific wavelengths

• the wavelength has to be exactly enough to raise the electrons in the pigment up by one level

where can photosynthetic pigments be found?

• embedded in the thylakoid membrane

what are the main pigment of photoautotrophs?

• chlorophylls

• capture energy for photosynthesis

• carotenoids act as accessory pigments by extending the range of energy absorption and prevent sunburn

What happens during the light-dependent rxn?

• uses 2 photosystems

how are pigments organized?

• they are organized into photosystems (light harvesting complexes)

• hundreds of antenna pigments are grouped around a rxn center (RC) a collection of proteins that interact with the pigments

• when excited the antenna pigments channel energy (not electrons) to the rxn centre

what is inductive resonance?

teh transefr of energy from one electron to anotehr

how do reaction centers reduce a primary electron acceptor?

• light is absorbed by the antenna pigments

• the energy is transferred to the reaction center

• an excited electron is passed to a primary electron acceptor

This is the first redox rxn

how does PSII produce PMF?

• energy is coming to P680 from photons

• 1. P680* reduces its primary electron acceptor which passes the electrons to PQ

• 2. PQ is a hydrophobic electron taxi that grabs protons from the stroma when reduced

• 3. PQ passes the electrons to the cytochrome b6f complex and releases the protons into the thylakoid lumen

• 4. Cytochrome passes the electrons to PC a hydrophilic electron taxi that gives electrons to P700+

(P680+ replaces its electrons from H2o hydrolysis)

what is PQ?

• a hydrophobic electron taxi that grabs protons from te stroma when reduced

hwo does photosystem I produce NADPH?

• Energy coming from photons to P700

1. P700* reduces its primary electron acceptor which passes the electron to ferredoxin

2. Ferredoxin is a hydrophilic electron taxi that passes the electrons to NADP+ reductase

3. NADP+ reductase passes the electrons to the final electron acceptor: NADP+ —→ NADPH

P700+ is reduced using electrons from PC aka plastocyanin

how is the strong proton electrochemical gradient produced?

• electrons flow through both photosystems which produces this gradient across the thylakoid membrane

1. protons released into the lumen when water is oxidized

2. protons are moved by PQ from stroma to the lumen

3. protons are removed from the stroma during teh reduction of NADP+

what is phosphorylation?

• using solar energy to generate PMF to power ATP synthase

• ATP is generated on the stroma side of the thylakoid

• linear electron transport

the calvin cycle simplified:

1. Carboxylation: starting with RuBP CO2 enters and its converted to 3PGA

2. Reduction: ATP reduced to ADP and NADPH reduced to NADP+ and is now G3P

3. Regeneration: ATP reduced to ADP and G3P is now RuBP

why do we use cyclic electron transport and how?

the calvin cycle needs more ATP than NADPH

• Ferredoxin can reduce PQ instead of NADP+ reductase

• and then the electrons can help generate the PMMF instead of NADPH

what is the product of photosynthesis?

G3P

• the G3P formed in the calvin cycle is converted to glucose: G3P +G3P —→ glucose

The glucose can then be used in

1. glycolysis and aerobic respiration

2. linked into polymers of starch or cellulose

3. used to synthesize amino acids, nucleic acids and lipids

What about oxygenic photosynthesis in prokaryotes?

• all metabolism occurs in the cytosol and on the cell membrane

• cyanobacteria have a photosynthetic mechanism very similar to that of chloroplasts

PS2 —> PS1 —→ calvin cycle

Anoxygenic photosynthesis

• only occurs in prokaryotes

• evolved at a time before oxygen was present in the atmosphere and organic molecules much less abundant

• the first metabolism utilizing ETC and only use cyclic electron flow

all life is connected

central dogma

what are genetics?

• study of heredity and variation in cells individuals and populations

• genetics is the study of genes

what is the gene?

the functional unit of heredity and variation

specific DNA sequence that codes for a specific RNA molecule

what is a genome?

teh collection of genetic information of a specific species

what are alleles?

variant forms of a gene caused by differences in DNA sequence

genotype?

the specific gene alleles inherited by an individual

phenotype?

the physical traits of an individual (results from the interaction between the individuals genotype and its environment)

what is gene expression?

• turning the genotype into the phenotype

• turning on a gene follows the central dogma

• DNA goes through transcription to become coding or noncoding RNA then translation to become a protein

What specifies phenotypes?

• Protein expression

  • which refers to the type and abundance of proteins in a cell

  • Even though DNA is the info molecule which directs protein expression proteins are what ultimately determine the phenotype of the cell because they control everything in the cell

what are enzymes?

catalyze the synthesis and transformation of all biomolecules

what are structural proteins?

maintenance of cell shape

what are signalling proteins?

hormones and receptors

what makes individuals different from one another?

• different alleles

• different expression of gene and protein expressions

what is heredity and inheritance?

Transmission of traits from one generation to the next

• a trait is any characteristic that is heritable

who is Gregor mendel?

• studied inheritance of garden peas

• worked out a mechanism to show how traits from one generation could be passed to the next

• heritable traist that come from mixing particulate factors

what is the chromosome theory of inheritance?

• it was noted that chromosomes fit Mendel’s hypothesis

  • individuals have two copies of each chromosome

  • similar homologous chromosomes separate independently during meiosis

  • gamates and zygotes

what are gamates?

have one copy of each chromosome

Zygote?

are a random combination of 2 gametes

what are chromosomes composed of?

made up of Proteins and DNA

• 50-60% proteins which are composed of 20 amino acids and millions of possible 3D structures. They are complex enough to store heritable info

• 40-50% DNa which are composed of 4 nucleic acids and simple/ limited 3D structures that are thought to play a structural role

what are the 3 classical experiments that established DNA as a heridiatry molecule?

1. Griffith: discovered genetic transformation that genetically altered S. Pnuemoniae

2. Avery MacLeod and McCarthy who identified DNA as the molecule that transforms cells

3. Hershey and Chase who found final evidence establishing DNA as teh hereditary molecule

explain Griffiths experiment

used mice to test 4 different things.

1. Virulent bacteria (Smooth) kills the mouse of pneumonia

2. Nonvirulent bacteria (rough) mouse remains healthy

3. heat killed virulent bacteria smooth and the mouse stays healthy

4. heat killed virulent (dead S) and non virulent (live R) bacteria and the mouse dies

his conclusion was that some molecules released when S cells died could transform living R cells into living S cells. (transforming principle) when this transformation happened it was permanent and heritable

what was Avery, MacLeod and McCarthy’s experiment about?

they were experimenting with the purpose of finding out the chemical nature of ten transforming principle to see whether it was the protein, DNA or RNA

• experimental approach was to eliminate each type of molecule and see whether transformation of R cells into Virulent S form still occurs

• the conclusion was that if transformation stops when one type fo molecule was absent tthat missing one would be teh transforming principle

• they found out it was DNA

what about hershey and chase experiemnt?

• provided more evidence that DNA was the genetic material

• used bacteriophage(viruses taht infect bacteria) and its E.coli hot to show that DNA is the transforming pricniple

what is the life cycle of bacteriophage used in hershey and chases experiemnt?

Lytic Cycle: massive reproduction of virus in host cell lysis

• after attachment the virus genetic material is injected into the host and the phage coat remains outside

• viral DNA takes over the host and hundreds of copies are made

• DNA uses phosphorus but not sulfur

• some amino acids use sulfur but not phosphorus

• in the experiment 2 populations of virus were made

  • one with radioactive 32P in teh DNA and one with radioactive 38S in the proteins

  • they founf that the 32P was in host cells and progeny virus particles

what are the components of DNA?

• consistent of equal parts of Pentose sugar, Nitrogenous base and phosphate

what is pentose sugar made up of?

• Ribose(C5H10O5) used in ribonucleic acids (RNA)

• Deoxyribose(C5H10O4)- used in deoxyribonucleic acids(DNA)

what are nitrogenous bases made up of?

• Purines (double ring)- guanine and adenine

• Pyrimidines (single ring)- cytosine, uracil and thymine

whats teh differnce between the pentose sugars of DNA and RNA

the chemical group attched to the 2’ carbonn

whats teh difference between teh nitrogenous bases of RNA and DNA?

RNA uses ACGU

DNA uses ACGT

What are nucleosides made up of?

• pentose sugar and nitrogenous bases that are bounded to 1’ carbon of the sugar

what are nucleotides made up of?

• nucleoside + phosphates

• the phosphates are bound to the 5’ carbon of the sugar

how is DNA a polymer of deoxyribonucleotides?

• nucleotide monomers polymerize through phosphodiester bonds

• the covalent bonds form between the 3’ carbon and 5’ carbon of adjacent sugars which is what forms the pentose phosphate backbone

• the polynucleotide has polarity with a 5’ end and a 3’ end

• type of nucleic acid depends on the sugar in pentose phosphate backbone

how is the DNA double helix together?

• base pairing is complementary and therefore base pair sequence on one strand can be used to specify the sequence of the other strand

• base pairs are stacked flat lying perpendicular to the axis and contribute to stability of double helix

• hydrogen bonding between bases keeps the strands together

what is nucleic acid hybridization?

• the double helix can be denatured

• annealing of single strands of DNA or RNA by forming H bonds

• highly specific temperature driven and concentration dependent

• DNA RNA hybrids are important in DNA replication transcription and reproduction of some RNA viruses

What allows for parental strands to act as templates for replication oof new strands?

• complementary base pairing

How can parental strands unwind?

by breaking the hydrogen bonds between bases

What is semiconservative replication?

where the double helix will contain a parental strand and a newly synthesized daughet strand

what are the potential models of DNA replication?

• semiconservative

• conservative

• dispersive

what’s conservative model of DNA replication?

after replication both daughter strands pair up

dispersive model of DNA replication

daughter strands will have a mixture of parental and newly synthesized DNA

what is evidence for semiconservative DNA replication?

What us the DNA polymerization rxn?

the enzyme- DNA polymerase that adds nucleotides to a grow