Bio 111 Exam 2 Study Guide

Potential Energy

Potential Energy

energy associated with position

Kinetic Energy

energy associated with motion; molecularly - thermal energy

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)

Exergonic Reaction

- releases energy

- heat out

- spontaneous

Endergonic Reaction

- requires energy for the reaction to occur

- heat in

- non-spontaneous

Energetic Coupling

exergonic reactions drive endergonic reactions

Oxidation Reaction

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

Reduction Reaction

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

Transfer of High Electrons (Redox Electrons)

involve the lose or gain of electrons

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

Enzymes

they catalyze reactions

Active Site

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

Induced Fit

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

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

Competitive Inhibition

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

Allosteric Activation

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

Allosteric Inhibition

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

Regulation through Phosphorylation

- phosphorylation changes the shape and activity of proteins

- unphosphorylated - inactive

- phosphorylated - active

Cascade

proteins are phosphorylated and then go and phosphorylate other proteins

Feedback Inhibition

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

Cellular Respiration

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

Glycolsis

- occurs in the cytosol

- yields 2 pyruvate

- ATP yield

• gross - 4 ATP

• net - 2 ATP

Fermentation

- occurs in cytosol

- occurs when no oxygen in present

- produces lactic acid in animals

- produces ethanol in plants

Processing Pyruvate

- occurs in the mitochondria matrix

- turns pyruvate into 2acetyl CoA

The Citric Acid Cycle

- occurs in the mitochondria matrix

- produces 6 NADH

- produces 2 FADH2

- produces 2 ATP

Oxidative Phosphorylation (The Electron Transport Chain)

- occurs in the innermembrane system

- Typical

• 10 NADH

• 2 FADH2

Proton Motive Force

the gradient created along the electron transport chain

Photosynthesis

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

Photosynthetic Pigments Absorb Light

the correlation between the Pigment Absorption Spectra and Photosynthetic Action Spectrum

Chlorophyl A

if functional group is methyl

Chlorophyl B

if functional group is carbonyl

Pigment

absorbs different wave lengths

“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

Light Capturing Reactions

Photosystem II - occurs in the thylakoid interior

Photosystem I - occurs in the stroma

Produces ATP and NADPH

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

Rubisco Protein

- 16 subunits

- 8 active sites

- photosynthesis - reaction with CO2

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

Stomata

- made up of multiple stroma

- O2 and CO2 pass through the stomata

• closes off at night

• open during the day

Guard Cells

- form pores

- stiffen when greater H2O - open pore

- go limp when less H20 - close pore

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

PEP carboxylase

- fixes CO2

- higher affinity for CO2 than rubisco

C4 Compound

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

CAM plants

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

Unreplicated Chromosome

single strand of DNA wound around a histone (protein)

Gene

small length of DNA that makes up chromosomes

Replicated Chromosome

- makes a copy of the unreplicated chromosome

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

Condensed Replicated Chromosome

- wound tight around the histone protein

- now known as sister chromatids

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

Interphase

- includes G1, S, and G2 phases

- chromosomes start to condense and the cell prepares to divide

Mitosis

m phase

Centrioles

microtubule organizing center (MTOC)

Prophase

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

- early spindle apparatus - microtubules start to form

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

Metaphase

- chromosomes line single file in the middle of the cell

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

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

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

Cytokinesis

- Parent cell divides into two daughter cells

• cleavage furrow (animals)

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

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

G0

- possible path for cell

- cell will be stuck in G1

G1 Checkpoint

- cells passes through if

• it is the right size

• has enough nutrients

• the social signals are appropriate

• DNA is undamaged

P53

- tumor supressor

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

G2 Checkpoint

- cell passes through if

• chromosomes have replicated properly

• DNA is undamaged

• activated MPF is present

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

M Phase Checkpoint

- cell passes through if

• chromosomes have attached spindle apparatus

• chromosomes have properly segregated

• MPF is absent

Cancer

cancer is uncontrolled cell growth

Benign Tumor

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

Malignant Tumor

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

- cancer spreads from tumor

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

DNA

- synthesized from 5’ to 3’

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

Semiconservative

parent strand stays with the daughter strand after replication

Conservative

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

Dispersive

the parent and daughter strand mix together and form hybrid strands

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

Helicase

opens the double helix (breaks hydrogen bonds)

Single Stand DNA Binding Proteins (SSBP)

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

Topoisomerase

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

Primase

- synthesizes RNA primer

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

DNA Polymerase III

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

Sliding Clamp

holds DNA polymerase in place

DNA polymerase I

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

Okazaki Fragments

fragments that occur during the synthesis of the lagging stand

DNA Ligase

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

Telomere

non coding segment of DNA the repeats

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

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

Central Dogma

DNA → mRNA → Protein

Allele

different forms of the same gene

Codon

triplets (sequence of three bases)

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

Wobble

the third base variable

Start Codon

- starts translation

• AUG

- codes for amino acid

Stop Codon

- stops translation

• UAA

• UAG

• UGA

- does not code for amino acid

Coding Strand

- sense strand

- non-template strand

- top strand

Non-Coding Strand

- anti-sense strand

- template strand

- bottom strand

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

Mutations

permanent changes in DNA

Point Mutations

caused by errors in the replication process of DNA

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

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

Nonsense Point Mutations

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

- typically deleterious

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