Bio Exam 2

Kinetic Energy

energy of motion

Potential Energy

stored energy

Oxidation reactions

atom or molecule loses an electron (energy is lost)

Reduction

atom or molecule gains electron (energy is gained)

Second law of thermodynamics

every energy transfer increase entropy (which is disorder-dispersal of energy in a system)

First law of thermodynamics

energy cannot be created or destroyed (it can only be converted from one form to another)

living cells convert “organized” forms of energy to heat

Endergonic

not spontaneous reaction (they require energy)

—> energy inside or within (energy in)

Examples: DNA synthesis, photosynthesis

Exergonic reactions

spontaneous reaction that releases energy as heat

negative free energy reaction

products have less energy than reactants

Entropy

total disorderedness of a molecule —> high entropy means energy and matter are widely spread out and disordered (like gas filling a room) low entropy means molecules are packed together (like a solid ice cube)

If you make a molecule does entropy increase or decrease?

causes entropy of a system to decrease because there are more molecules packed together (fewer ways to spread out thermal energy)

if you break down a molecule does entropy increase or decrease?

entropy increases because there are more independent molecules and more freedom of movement

What does positive ΔG (free energy) mean

the products of the reaction have more free energy than the reactants (endergonic reaction)

These reactions do not proceed spontaneously because they require input of energy

Termed endergonic reactions

What does negative ΔG mean?

The products have less free energy than the reactants

Reactions occur spontaneously and energy is released

Exergonic reactions

Do spontaneous reactions always occur at biologically relevant speeds?

No, sometimes activation energy is too high so spontaneous reactions need catalysts to reduce activation energy and speed up reactions

Reaction with an enzyme catalyst

Lowers activation energy of reaction (reaction occurs quickly and more easily)

Reaction without enzyme catalyst

reaction takes longer and activation energy is higher (energy required to perform reaction is higher)

What macromolecule makes an enzyme?

proteins

Factors that influence enzyme function

temperature, pH, Inhibitors, activators

Competitive inhibitors

block enzyme binding site (if there is more substrate, can often interfere with competitive inhibitors)

Non-competitive Inhibitors

binds to a n enzyme at a location that is not the binding site but causes the binding site to open to the substrate (doesn’t matter how much substrate there is)

Biochemical pathways

Glycolysis, krebs cycle, catabolic and anabolic reactions

Biochemical Pathways and Feedback Inhibition

Enzyme regulates the occurrence of these reactions and shuts down reaction pathways so energy isn’t wasted

ATP hydrolysis

releases energy to drive endergonic reactions (readily expendable energy currency for cells) and is synthesized with energy from exergonic reactions

ATP and regulation of protein activity

allosteric regulation- binds to a protein to change shape and function

Autotrophs

convert the sun’s energy into chemical energy in the form of ATP and as chemical bonds in organic molecules ( plants, algae, bacteria)

Heterotrophs

live on the chemical energy stored in the organic molecules produced by autotrophs and survive by converting that chemical energy into ATP (animals, fungi, protists)

Redox reactions

transfer electrons from a donor molecule to an acceptor molecule (also transfer much of the energy associated with those electrons)

Electron carriers

facilitate the transfer of the electrons harvested from covalent bonds of organic molecules (ex: NAD+ accepts electrons and is reduced to NADH)

Electron carriers in cellular respiration

NAD+/NADH (accepts electrons during glycolysis and krebs cycle and delivers them to complex 1 of electron transport chain

FAD/FADH2 ( accepts electrons during the krebs cycle and delivers them to complex II of ETC)

Electron carriers in photosynthesis

NADP+ is reduced (gains two electrons) to NADPH

Aerobic Respiration of Glucose step 1

Glycolysis (cytosol)

Aerobic Respiration step 2

Pyruvate Oxidation (mitochondrial matrix)

Aerobic Respiration step 3

Krebs cycle (mitochondrial matrix)

Aerobic Respiration step 4

Electron transport chain/ chemiosmosis (inner mitochondrial matrix)

Products of Glycolysis

Converts 1 glucose into 2 pyruvate (3 carbons), 2 ATPs, 2 NADH

Products of Pyruvate Oxidation

Each 3-carbon pyruvate is used to generate 1 CO2, 1 NADH, 1 Acetyl-CoA (this links glycolysis to the krebs cycle)

Products of Krebs Cycle

For each Acetyl-CoA entering (so x2)

• Releases 2 molecules of CO2

• Reduces 3 NAD+ to 3 NADH

• Reduces 1 FAD (electron carrier) to FADH2

• Produces 1 ATP

After Krebs cycle on glucose molecule has been oxidized to…

• 6 CO2

• 4 ATP

• 10 NADH

• 2 FADH2

Substrate-level phosphorylation

cells are able to make ATP via transferring a phosphate directly to ADP from a substrate-bearing intermediate or substrate (one at a time)

Oxidative Phosphorylation

Use of ATP synthase and energy derived from a proton (H+) gradient

• Gradient formed from the oxidation of glucose passing down an electron transport chain

NAD+ and FAD

oxidized state (empty bucket)

NADH and FADH2

reduced state (filled bucket)

Electron Transport Chain

electrons from NADH and FADH2 are transferred to complexes of the ETC and each complex creates a proton pump creating proton gradient (transgress electrons to next carrier)

Chemiosmosis

H+ moves back across the membrane, passing through channels in ATP synthase. Flow of H+ through this gradient allows ATP synthase to use this proton gradient to drive phosphorylation of ATP

Electron transfer flow

pumps H+ from the mitochondrial matrix to the intermembrane space

Flow of energy in cellular respiration

Glucose —→ NADH —→ Electron transport chain—→Chemiosmosis—→ATP

Anaerobic respiration

Use of inorganic molecules (not O2 and not organic molecules) as final electron acceptor

Many prokaryotes use sulfate, nitrate, CO2 or even inorganic metals

Fermentation

Glycolysis is the only source of ATP

Use of organic molecules as final electron acceptor

Examples: Ethanol fermentation (alchohol) and Lactic acid fermentation

Ethanol fermentation

Occurs in yeast (Co2, ethanol, and NAD+ are produced)

Lactic Acid Fermentation

occurs in animal cells (especially muscles), electrons are transferred from NADH to pyruvate to produce lactic acid

Beta Oxidation (fats)

Acetyl group combined with coenzyme A to form acetol-CoA (catabolism)

Protein Deamination

removal of each amino group side chain. Remainder of the amino acid is converted into a molecule that either enter glycolysis or Kreb cycle

How are photosynthesis and respiration connected

The products of photosynthesis provide the energy utilized by Glycolysis and cellular respiration

Products of Photosynthesis include

glucose and oxygen…direct inputs to cellular respiration

Do plants have cellular respiration?

yes, plants have mitochondria and perform cellular respiration. Plants use photosynthesis to make their own glucose and oxygen that them fuels cellular respiration.

Photosynthesis as a Redox process

Occurs chloroplasts. H2O is oxidized and CO2 is reduced (chloroplasts split water molecules to release oxygen and transfer electrons to generate NADPH and ATP)

Light-dependent reactions

Require light, occur in the thylakoid and capture energy from sunlight to make ATP and reduce NADP+ to NADPH (O2 is produced as a byproduct)

Light-independent reactions (carbon fixation)

Occurs in the stroma and uses ATP and NADPH to synthesize organic molecules from CO2 (calvin cycle)

Chlorophyll a

main pigment in plants, absorbs violet, blue, and red light (only pigment that can directly convert light energy to chemical energy)

Chlorophyll b

Accessory pigment that absorbs blue and red-orange light

Antenna Complex

• Hundred of accessory pigment molecules

• Gather photons and feed the captured light energy to the reaction center

Photosystem II (P680)

grabs electrons from the splitting of water (firs photosystem in the transfer of electrons from light energy)

H+ ions from water contribute to H+ gradient

O2 is byproduct

Photosystem I

two photons are absorbed to excites two electrons that are passed to NADP+, reducing it to NADPH

ATP production via chemiosmosis

Photons from light excite electrons and then electrons are transferred from molecule to molecule which allows H+ to be pumped from stroma to thylakoid space, creating a concentration gradient. As H+ travels back out of thylakoid membrane through ATP synthase, it turns the motor that creates ATP

Noncyclic photophosphorylation

generates NADPH and ATP however building organic molecules sometimes requires more ATP

Cyclic Photophosphorylation

allows cells to produce additional ATP by redirecting electrons from Photosystem I back through the electron transport chain (enhances the proton gradient that ultimately drives ATP synthesis)

The Calvin Cycle

occurs in the stroma and forms sugar from CO2 using ATP and NADPH

• ket step is attachment of CO2 to RuBP to form PGA

• Uses enzyme ribulose bisphosphate carboxylase/oxygenase or rubisco

Steps of the Calvin Cycle step 1

Carbon fixation:

RuBP +CO2—> 2PGA

• uses enzyme Rubisco

Calvin cycle step 2

Reduction: PGA is reduced to G3P

Calvin Cycle step 3

Regeneration of RuBP (CO2 acceptor)

• G3P used to regenerate RuBP

• Three (3) turns incorporate enough carbon to produce G3P

• Six (6) turns incorporate enough carbon for 1 glucose molecule

Photorespiration

rubisco adds O2 instead of CO2 in calvin cycle (consumes O2 and organic fuel and releases CO2 without producing ATP or sugar)

C4 Plants

minimize photorespiration by incorporating Co2 into 4-carbon compounds in mesophyll cells

• requiers enzyme PEP carboxylase (has a higher affinity for Co2 tha rubisco does)

• 4-carbon compounds are then exported to bundle-sheath cells where they release CO2 that is then used in calvin cycle

CAM Pathway (Calving Cycle at a different time)

• Stomata open during night (cool temps) and close during the day (hot temps)

• Fix CO2 using PEP carboxylase during the night and store CO2 in vacuole and release CO2 during the day

C3 plants (most plants)

initial fixation of CO2, vis rubisco, forms a three-carbon compound

Nucleotide subunits of DNA

Purines: Adenine Guanine

Pyrimidines: Cytosine, Uracil (RNA), Thymine (DNA)

DNA structural Bonds

Phosphodiester bond creates covalent bond between new phosphate and 3’ -OH of original nucleotide (chain is built from 5’ to 3’)

Five prime Carbon: Carbon 1’

nitrogenous base

Carbon 2’

Sugar base responsible for DNA type (RNA is ribose)

Carbon 3’

• -OH group

Carbon 5’:

Phosphate group

Chargaff’s rule

Amount of adenine= amount of thymine

Amount of cytosine= amount of guanine

Watson and Crick

did not perform a single experiment themselves but key insight of their model was each DNA molecule was made of two intertwined chains of nucleotides (double helix structure)

DNA Gyrase

Relieves tension

DNA Helicase

Opens double helix

Primase

Makes RNA primer

DNA Polymerase

reads the strand from 3’-5’ and synthesizes 5’ to 3’

Leading strand:

goes from 5’-3’ so DNA polymerase can add in that direction (continuous replication with only the use of one RNA primer)

Lagging strand

opposite direction synthesized in fragments that are joined together by ligase and have multiple RNA primers (fragments are called okazaki fragments) syntheized discontinuously

DNA Replication steps

1. Initiation: process of replication starts

2. Elongation: new DNA strands are synthesized

3. Termination: process of replication ends

Elongation (DNA Replication step 2)

DNA Polymerase III: Elongates new DNA strand and synthesizes new strand from 5’ to 3’

DNA replication step 3

RNA primers added to start lagging strand by primase

• DNA Polymerase I: replaces RNA primer with DNA

DNA replication step 4

DNA Ligase: seals backbone nick after DNA polymerase I removes the RNA primers

Telomerase

Contains RNA template as part of enzyme and extends what was the parental strand so lagging strand can be synthesized as usual

Transcription

converts information in DNA to iformation in the RNA form

Translation

Converts RNA into protein

Transcription: Initiation

Occurs at promoter region—> RNA polymerase recognizes where to bind and sigma subunit recognizes the promoter elements and binds to DNA then disassociates from promotor

Transcription: Elongation

Transcription bubble (contains RNA polymerase, DNA template, and growing RNA transcript)

• After the transcription bubble passes, the now-transcribed DNA is rewound as it leaves the bubble

• RNA polymerase adds ribonucleotides in the 5’ to 3’ direction

RNA polymerase

• untwists the double helix, exposing about 10-20 DNA bases at a time for pairing with RNA nucleotides

• Nucleotides are added to the 3’ end

Coding stand

looks just like new RNA (same direction, similar bases) but with T’s instead of U’s

Template strand

base for new RNA (complimentary bases, anti-parallel direction)