Bio 111 Exam 2 Study Guide

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Potential Energy

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100 Terms

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Potential Energy

energy associated with position

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Kinetic Energy

energy associated with motion; molecularly - thermal energy

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Change in G = Change in H - T Change in S

Change in G - free energy change

Change in H - change in enthalpy (heat content)

T - temperature

Change in S - change in entropy (level of disorder - disorder in being in a state of lower energy)

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Exergonic Reaction

- releases energy

- heat out

- spontaneous

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Endergonic Reaction

- requires energy for the reaction to occur

- heat in

- non-spontaneous

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Energetic Coupling

exergonic reactions drive endergonic reactions

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Oxidation Reaction

a molecule loses electrons (exergonic) and has the potential to pick electrons

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Reduction Reaction

a molecule gains electrons (endergonic) and has the potential to donate electrons

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Transfer of High Electrons (Redox Electrons)

involve the lose or gain of electrons

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Transfer of a Phosphate Group (ATP Hydrolysis)

- ATP stores a large amount of potential energy of potential energy which is released when ATP is hydrolyzed

- the phosphate group that is released during hydrolysis covalently bonds to another molecule activating it

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Enzymes

they catalyze reactions

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Active Site

a region of the enzyme that has a high affinity to bind to substances

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Induced Fit

reorientates the substrates and binds them tighter to them tighter to the active site

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Stages of Enzymes Catalyzing Reactions

Initiation - reactants bind to the active site in a specific orientation forming the enzyme substrate complex

Transition State Facilitation - interactions between the enzyme and the substrate lower the activation energy needed for the reaction to occur

Termination - products have lower affinity for the active site and are released; the enzyme is unchanged after the reaction

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Competitive Inhibition

another molecule binds to the active site that the substrates bind too making it so that the substrates cannot bind

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Allosteric Activation

active site becomes available when a regulatory molecule binds to another site on the enzyme

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Allosteric Inhibition

active site becomes unavailable when a regulatory molecule binds to a different site on the enzyme

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Regulation through Phosphorylation

- phosphorylation changes the shape and activity of proteins

- unphosphorylated - inactive

- phosphorylated - active

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Cascade

proteins are phosphorylated and then go and phosphorylate other proteins

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Feedback Inhibition

can regulate metabolic pathways when an enzyme in a pathway is inhibited by the product of the reaction sequence

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Cellular Respiration

C6H12O6 (glucose) + 602 (oxygen) → 6CO2 (carbon dioxide) + 6H20 (water) + energy (ATP)

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Glycolsis

- occurs in the cytosol

- yields 2 pyruvate

- ATP yield

  • gross - 4 ATP

  • net - 2 ATP

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Fermentation

- occurs in cytosol

- occurs when no oxygen in present

- produces lactic acid in animals

- produces ethanol in plants

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Processing Pyruvate

- occurs in the mitochondria matrix

- turns pyruvate into 2acetyl CoA

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The Citric Acid Cycle

- occurs in the mitochondria matrix

- produces 6 NADH

- produces 2 FADH2

- produces 2 ATP

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Oxidative Phosphorylation (The Electron Transport Chain)

- occurs in the innermembrane system

- Typical

  • 10 NADH

  • 2 FADH2

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Proton Motive Force

the gradient created along the electron transport chain

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Photosynthesis

light energy (photons) + 6H20 (water) + 6CO2 (carbon dioxide) = C6H12O6 (glucose) + 6O2 (oxygen)

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Photosynthetic Pigments Absorb Light

the correlation between the Pigment Absorption Spectra and Photosynthetic Action Spectrum

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Chlorophyl A

if functional group is methyl

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Chlorophyl B

if functional group is carbonyl

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Pigment

absorbs different wave lengths

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“Excited” electrons

- electrons are in excited states meaning they have moved further away from the protons

- can cause them release energy when they return back to a lower state of energy or the electron can get picked up by an electron carrier

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Light Capturing Reactions

Photosystem II - occurs in the thylakoid interior

Photosystem I - occurs in the stroma

Produces ATP and NADPH

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The Calvin Cycle

- occurs in stroma

- takes 6 turns to produce glucose

- rubisco protein

- three phases

  • fixation - fixes CO2 (incorporates CO2)

  • reduction -

    • ATP → ADP + P

    • NADPH → NADP+

  • regeneration - 5×3 C → 3×5 C

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Rubisco Protein

- 16 subunits

- 8 active sites

- photosynthesis - reaction with CO2

- photorespiration - reaction with O2 (used to produce CO2 to drive photosynthesis)

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Stomata

- made up of multiple stroma

- O2 and CO2 pass through the stomata

  • closes off at night

  • open during the day

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Guard Cells

- form pores

- stiffen when greater H2O - open pore

- go limp when less H20 - close pore

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C4 Plants

- make a 4 carbon sugar

- Can briefly open during the day and use PEP carboxylase to quickly bind to CO2 and then close to prevent losing water

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PEP carboxylase

- fixes CO2

- higher affinity for CO2 than rubisco

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C4 Compound

stores CO2 that can be later used in the Calvin Cycle, even when they stomata is closed

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CAM plants

stomata are closed on hot days and are only open at night (only occurs in the most extreme environments)

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Unreplicated Chromosome

single strand of DNA wound around a histone (protein)

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Gene

small length of DNA that makes up chromosomes

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Replicated Chromosome

- makes a copy of the unreplicated chromosome

- single thread of DNA is now loose, not wrapped around a histone

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Condensed Replicated Chromosome

- wound tight around the histone protein

- now known as sister chromatids

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Four Phases of the Cell Cycle

- G1 phase - cell is bringing in materials to sustain itself (cells is growing)

- S phase - DNA replicates

- G2 phase - cell prepares to divide

- M phase - cell divides

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Interphase

- includes G1, S, and G2 phases

- chromosomes start to condense and the cell prepares to divide

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Mitosis

m phase

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Centrioles

microtubule organizing center (MTOC)

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Prophase

- centrioles move toward the poles of cells and chromosomes continue to condense

- early spindle apparatus - microtubules start to form

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Prometaphase

- nuclear membrane begins to break down and chromosomes become really condensed

- formation of kinetochore microtubules - attach to the kinetochore

- formation of polar microtubules - do not attach to a chromosome; opposed to one another which causes them to overlap

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Metaphase

- chromosomes line single file in the middle of the cell

- formation of astral microtubules - connect to the membrane of cell

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Anaphase

- cell begins to extend out at the poles caused by the microtubules pushing the cell outward

- sister chromatids are being pulled apart; cohesions split caused by kinetochore breaking the bonds between the two sister chromatids (tubulin)

- astral microtubules keep MTOC in place at the poles

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Telophase

- nuclear membrane reforms around the chromosomes

- actin and myosin cross each other which causes the cell to begin to pinch and split

- mitosis is complete

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Cytokinesis

- Parent cell divides into two daughter cells

  • cleavage furrow (animals)

  • cell plate (plants) - made up of callose (carbohydrate)

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Binary Fussion

- bacteria replication

  • DNA is copied

  • Protein structure that extends across the cell guides the new copy of DNA to migrate across the cell at the pole

  • Cytokinesis - cleavage furrow is formed

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G0

- possible path for cell

- cell will be stuck in G1

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G1 Checkpoint

- cells passes through if

  • it is the right size

  • has enough nutrients

  • the social signals are appropriate

  • DNA is undamaged

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P53

- tumor supressor

- can tell cell to go through apoptosis (programmed cell death)

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G2 Checkpoint

- cell passes through if

  • chromosomes have replicated properly

  • DNA is undamaged

  • activated MPF is present

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MPF

- metaphase promoting factor

- hetero dimer

- regulatory phosphate group - protein is not activated when this is attached

- activating phosphate group - must be attached for protein to be active

- ubiquitin tag - transports MPF to be deconstructed

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M Phase Checkpoint

- cell passes through if

  • chromosomes have attached spindle apparatus

  • chromosomes have properly segregated

  • MPF is absent

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Cancer

cancer is uncontrolled cell growth

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Benign Tumor

tumor cells continue to divide but do not spread from the tumor

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Malignant Tumor

- adhesion proteins of the cell are being compromised and the cells can no longer be together

- cancer spreads from tumor

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Hershey Chase Experiment

- which molecule carries DNA - proteins or nucleic acids

- did an experiment where they tagged the proteins and DNA of viruses to see which they left behind while infected bacteria host cell

- discovered nucleic acids hold DNA

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DNA

- synthesized from 5’ to 3’

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Meselton -Stahl Experiment

- three hypotheses for what happens after DNA is replicated - semiconservative, conservation, dispersive

- tagged the parent and daughter strands with 15n and 14n then used density gradient centrifugation to separate the parent and daughter strands

- determined that replication is through semiconservative replication

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Semiconservative

parent strand stays with the daughter strand after replication

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Conservative

parent strand leaves the daughter strand and goes back to the other parent strand

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Dispersive

the parent and daughter strand mix together and form hybrid strands

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DNA Synthesis Proceeds in Two Directions

- bidirectional synthesis - at the same time

  • leading strand - synthesizes into the fork

  • lagging strand - synthesizes away from the fork

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Helicase

opens the double helix (breaks hydrogen bonds)

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Single Stand DNA Binding Proteins (SSBP)

stabilizes the single strands by binding with them and preventing the hydrogen bonds from reforming

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Topoisomerase

relieves twisting forces by cutting the DNA and the allowing it to rejoin (prevents supercoiling)

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Primase

- synthesizes RNA primer

- RNA primer gives us a little fragment of double stranded nucleic acid

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DNA Polymerase III

binds to the RNA primer and starts moving along the single strand of DNA creating a complementary daughter strand

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Sliding Clamp

holds DNA polymerase in place

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DNA polymerase I

removes the RNA primer and replaces the RNA nucleotides and replaces them with DNA nucleotides

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Okazaki Fragments

fragments that occur during the synthesis of the lagging stand

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DNA Ligase

closes the gaps between the Okazaki fragments of the lagging strand to connect the fragmented strands

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Telomere

non coding segment of DNA the repeats

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Telomerase

- occurs in sex cells and cancer cells

- adds more nucleotides to the parent lagging strand

- can extend parent strand to be longer than before

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One Gene, One Enzyme Hypothesis; Later One Gene, One Polypeptide Hypothesis

- first believed one gene coded for one enzyme

- worked with red mold and used mutations to make certain proteins non-functional

- determined one gene could code for a polypeptide

- one gene can actually code for multiple proteins

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Central Dogma

DNA → mRNA → Protein

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Allele

different forms of the same gene

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Codon

triplets (sequence of three bases)

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The Genetic Code

- is

  • redundant - amino acids are coded by more than one codon

  • unambiguous - each codon creates a specific amino acid

  • non-overlapping

  • universal (nearly)

  • conservative - first two bases are the same for the amino acid

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Wobble

the third base variable

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Start Codon

- starts translation

  • AUG

- codes for amino acid

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Stop Codon

- stops translation

  • UAA

  • UAG

  • UGA

- does not code for amino acid

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Coding Strand

- sense strand

- non-template strand

- top strand

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Non-Coding Strand

- anti-sense strand

- template strand

- bottom strand

- gets transcribed because the RNA transcribed from it reflects the coded strand

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Mutations

permanent changes in DNA

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Point Mutations

caused by errors in the replication process of DNA

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Silent Point Mutations

- point mutation where the error occurs at the wobble and doesn’t change the amino acid that is coded for

- no effect on phenotype

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Missense Point Mutations

- point mutation that causes a different animo acid to be coded which changes the primary structure of the protein

- could be beneficial, deleterious, or neutral

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Nonsense Point Mutations

- point mutation where there is an early stop codon which shortens the polypeptide

- typically deleterious

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Frameshift Point Mutations

- point mutation where there is an addition or deletion of a nucleotide into the sequence which shifts the reading frame altering the meaning of all codons

- almost always deleterious

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