Biology Exam 2 Habersham BIOL 203

BIOL 203

Where are ribosomes assembled/made?

Nucleolus

What leaves through the NPCs?

mRNA (carries genetic info for protein synthesis), ribosomal subunits (made in nucleolus and sent to cytoplasm), other RNA types (ex: tRNA, snRNA)

What goes in through the NPCs?

Nucleotides (building blocks of DNA/RNA), enzymes (DNA replication and RNA synthesis), proteins (for chromatin assembly, ribosome construction)

Chromatin

Chromatin is used to make chromosomes; chromosomes made up of chromatin fibers

NPC diffusion (small molecs, large molecs)

Small (ex: nucleotides): passive diffusion

Large (ex: proteins, RNA): active transport

Nucleoplasmin

A protein that facilitates nucleosome assembly and chromatin remodeling

NLS vs NES

Made of specific AA sequence, brings molecules in to the nucleus via NPCs.

NLS = nuclear localization signal, signaling a MM into the nucleus

NES = nuclear export signal, signaling that a MM needs to leave the nucleus

Importin (nuclear import receptor) vs. exportin

Importin binds to the macromolecule once it has an NLS and carries it into the nucleus (through the NPC).

Exportin binds to the macromolecule in the nucleus and leaves through the NPC.

Process for importing macromolecules into the nucleus

Cargo has an NLS, binds to an importin in the cytoplasm, transported through the NPC. Once inside, ran-GTP bonds the importin and changes the structure of the importin, releasing the cargo. The importin is released into the cytoplasm through the NPC, and ran-GTP is hydrolyzed to GDP (ran acts as a GTPase). The GDP disassociates from the importin and the free importin can now be reused.

Process for exporting macromolecules into the nucleus

Exportin binds to nucleoporins and is transported to the nuclear lumen, binds to ran-GTP, binds to NES bearing cargo, binds to nucleoporins, exported to cytosol through NPC, GTP → GDP. Ran binding protein detaches ran form receptor and cargo and exportin are free. Exportin returns to nucleus.

ATPase

A group of enzymes that either hydrolyze ATP to release energy (ATP → ADP and in organic phosphate Pi) or synthesize ATP using that energy (ADP + Pi → ATP)

Protein synthesis + packing process (proteins made on ER ribosomes)

Ribosome (protein synthesis begins, if protein has ER signal sequence then to ER) → rough ER (signal recognition particle (SRP) binds and pauses synthesis, docks at SRP receptor on ER, protein inserted to ER via translocon, protein enters lumen and folds, glycosylation (carbohydrate tags added))  → Vesicle transport to Golgi (packaged in vesicles to cis face golgi)→ Golgi (cis → medial → trans cisternae; more packaging, tagged with molecular zip codes) → transport vesicles + motor proteins (motor proteins like kinesin walk vesicles along cytoskeletal tracks (microtubules), destination by tag) → final destination (ex: exocytosis (vesicle fuses with plasma membrane, protein secreted from cell), lysosome (M6P mannose-6 phosphate tag needed to go to lysosome for digestion (ex: enzyme), organelle membrane (becomes part of membrane structure))

What would happen if the ER signal sequence was disrupted in protein synthesis? 

Proteins stay in cytosol and don’t enter ER

What would happen if the SRP/SRP receptor was disrupted in protein synthesis?

Translation pauses, no ER targeting

What would happen if vesicle budding was disrupted in protein synthesis?

Proteins accumulate in ER, golgi starved

What would happen if golgi enzymes were disrupted?

Proteins not properly modified or tagged, misdelivery

What would happen if molecular zip codes were disrupted?

Proteins sent to wrong destination or degraded

What would happen if motor proteins were disrputed?

Vesicles can’t move, traffic jam in cytosol

What would happen if lysosomal enzyme tagging was disrupted/if lysosomes fail?

Enzymes not sent to lysosome → can’t digest cell waste (ex: Tay-Sachs disease)

Autophagy

Damaged organelles enclosed and digested

Phagocytosis

Cell engulfs large particles/cells → forms phagosome → fuses with lysosome

Receptor mediated endocytosis

Cell imports specific molecules via vesicles → early endosome → lysosome

Digestion

Contains acid hydrolases (enzymes that break down macromolecules like proteins and nucleic acids in acidic environments, most notably within the lysosome)

Enzyme function: amylase, lipase, protease

Breaks down:

amylase: carbs

lipase: lipids

protease: protein

Proteins made on free ribosomes:

Go to the nucleus first if NLS

Membrane proteins

ex: GLUT-1, Na+/K+ ion channels, ATPase

Proteins bound for the endomembrane system need a __.

molecular zip code.

ER signal sequence is 20 AA long. Protein folds in the ER with the help of molecular chaperones.

Glycosylation

The process of adding carbohydrates to proteins and lipids. Important for protein folding.

Actin

Actin filaments, microfilaments. Two coiled strands (+ end and - end). Diameter of 7 nm. Actin filaments made of actin subunits. Actin maintains cell shape by resisting tension and pull. Moves cells via muscle contraction. Divides animal cells in two. Works with myosin for movement like muscle contraction.

Intermediate filaments (IFs)

Fibers wound into thicker cables. 10 nm diameter. Ex: keratins, lamins. Maintain cell shape by resisting tension and pull. Anchors nucleus and some other organelles. Ex: nuclear lamins shape and stabilize the nuclear envelope.

Microtubules

Hollow tube composed of alternating alpha and beta tubulin dimers (has a + and a - end). The minus end is in the centrosome (MTOC - microtubule organizing center) in animal cells and the plus end extends outwards from it. 25 nm diameter. Maintains cell shape by resisting compression and pushing. Tracks for intracellular transport. Ex: moves chromosomes during mitosis and powers cilia/flagella.

Myosin

Moves on actin filaments toward + end to cause muscle contraction, cell crawling, cytoplasmic streaming

Kinesin

Moves on microtubules toward + end to move vesicles from center to edge (ex: golgi → membrane)

Dynein

Moves on microtubules toward - end (think dog coming back home to negative nucleus) to move vesicles inward, power cilia and flagella beating.

What do the motor proteins use for movement?

ATP hydrolysis with each “step”

When are lysosomal enzymes optimally active?

In acidic conditions maintained within the lysosomes

How is the lumen of the lysosome maintained?

It is maintained at an acidic pH by an ATP driven H+ pump in the membrane that hydrolyzes ATP to pump H+ into the lumen.

Required processes for lysosomal hydrolases to be properly targeted to the lysosome?

Synthesis on rough ER ribosomes, addition of core oligosaccharide modification in the RER lumen, addition of M6P tag in Golgi lumen, binding of modified lysosomal protein to the M6P receptor in trans-Golgi membrane via a vesicle, transport to the endosome (matures into lysosome) from the trans-Golgi via a vesicle.

Where do proteins without a tag go?

Cytosol

First law of thermodynamics

Energy not created nor destroyed

Covalent bonds hold potential energy. Weaker longer bonds (ex: C-H) and shorter stronger bonds (ex: O-H) have what levels of potential energy, respectively?

Weaker longer: higher potential energy

Shorter stronger: lower potential energy

Exergonic

Higher starting energy level in reactants, ΔG < 0, spontaneous, products have lower free energy than reactants, releases energy. 

Endergonic

Reactants have less starting energy, ΔG > 0, nonspontaneous, products have higher free energy, requires energy input

Gibbs free energy

ΔG: used to determine whether a reaction is spontaneous or not. 

ΔG = ΔH - TΔS

• ΔH = change in enthalpy (heat energy)

• ΔS = change in entropy (disorder)

• T = temperature in Kelvin

At high temps, entropy (ΔS) becomes important

Endothermic reactions (ΔH > 0) can be spontaneous if ΔS is large and positive. Exothermic reactions (ΔH < 0) can be nonspontaneous if ΔS is highly negative (decrease in disorder)

Enthalpy (ΔH)

Total energy of a molecule (bond energy + effects on pressure/volume)

ATP energy storage

Energy stored in the unstable high energy bonds between its phosphate groups (especially in the bond between the 2nd and 3rd phosphate)

ATP hydrolysis

Breaking off of a phosphate group. Exergonic reaction.

The energy from ATP hydrolysis is used to…

drive endergonic reactions in cells such as building molecules or performing work.

Coupling

When an exergonic reaction like ATP hydrolysis is directly linked to an endergonic reaction, the total reaction is exergonic. Cells use ATP to couple energy releasing and energy requiring actions. 

Coupling examples

Phosphorylation (transfer of a phosphate group), transfer of elections (redox reactions).

Redox reactions

Energy transferred via electrons (often with protons H+), oxidation: loss of elections, reduction: gain of electrons

Oxidation (exer or endergonic?)

Typically exergonic

Reduction (exer or endergonic?)

Typically endergonic

Electron donors are __ and electron acceptors are __.

oxidized, reduced.

Phosphorylation changes the thermodynamics of a reaction making an otherwise __ reaction __.

nonspontaneous, spontaneous

Phosphorylation

Adding a phosphate group (usually from ATP)

Enzymes lower activation energy. Explain this.

Enzymes bring substrates together in the right orientation, enzyme changes shape to fit substrate more, stabilizes unstable transition state (r groups in active site interact with substrate to stabilize the transition state), active sites provide a unique chemical environment (ex: pH, polarity) to make reactions easier, weak bonds form between substrate and enzyme, helping to stretch or stress specific bonds in substrates.

Adding lots of substrates effect

All active sites are occupied (enzyme saturated) so adding more substrate does not increase reaction rate

Uncatalyzed reactions trend

No enzyme, slow linear increase

Cofactors

Inorganic ions (ex: Zn2+, Mg2+, Fe2+) that help stabilize the transition state

Coenzymes

Organic molecules (non-proteins) (ex: NAD+, FAD, vitamins) that temporarily bind to enzymes and assist in reactions.

Prosthetic groups

Tightly bound helpers to a protein, often permanent (ex: retinal). Often involved in enzyme catalysis, acting as cofactors.

Coupled reaction

ATP hydrolysis + reaction = net exergonic. Linking exergonic and endergonic reactions to make the overall process exergonic.

Enzyme regulation

Enzymes regulated by noncovalent interactions (reversible binding of other molecules) and covalent modifications (chemical changes to the enzyme’s structure). Competitive and allosteric inhibition.

Competitive inhibition

Molecule mimics substrate binds to active site, blocking real substrate. No reaction, enzyme temp off.

Allosteric inhibition

Regulatory molecule binds in an allosteric site and changes the enzyme shape. Either inhibition or activation.

What type of enzyme mechanism is this: Fast and reversible

Likely competitive or allosteric

What type of enzyme mechanism is this: Part of a signal cascade or longer term control?

Likely phosphorylation

What type of enzyme mechanism is this: Part of a metabolic pathway.

May be regulated by its products or intermediates

Intermediates

Molecules produced between steps in a pathway (ex: B and C in pathway from A - B - C - D)

Concentration of molecules in a pathway (A,B,C,D) depends on…

Relative reactant/product concentrations at each step, and ΔG (change in free energy) of each reaction

In a metabolic pathway, which products typically accumulate in the highest concentration at equilibrium?

Final products (like D)

Pathway disruption impact

If one enzyme is inactive or missing, intermediates before that step build up and those after it are depleted. (ex: if enzyme 2 is removed in (A,B,C,D), A and B increase, C and D decrease)

Catabolic pathway

Break down molecules to generate ATP (ex: cell resp: glucose, fats, proteins broken down)

Anabolic pathways

Build molecules using energy (ex: photosynthesis)

Cellular Respiration

ATP is unstable and not stored, cells must produce ATP mostly from glucose. Glucose obtained from photosynthetic organisms (photosynthesis), indirectly from animals, fungi and other organisms by consuming photosynthetic organisms.

Cellular Respiration Equation

C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP

Photosynthesis equation

6CO₂ + 6H₂O + sunlight → glucose + 6O2 + ATP

Glycolysis

1st step of cellular resp; occurs in the cytosol, glucose is split into 2 3-carbon pyruvates, ATP and NADH are generated (glycolysis is a 10 step process with 2 main phases, energy investment phase, energy payoff phase)

Glycolysis inputs and outputs

Inputs: glucose, 4 ADP, 4 Pi, NAD+, 2 ATP

Outputs: 2 pyruvate, 4 ATP, 2 NADH

Pyruvate processing

2nd step of cellular respiration, occurs in the mitochondrial matrix (or cytosol in prokaryotes), pyruvate is oxidized to form acetyl CoA. Releases one carbon as CO2, the remaining 2 carbon fragment is oxidized, NAD+ is reduced to NADH, two carbon acetyl group is now part of multi enzyme complex, molecule of CoA attaches to acetyl group forming Acetyl CoA.

Pyruvate processing inputs and outputs

Inputs: 2 pyruvate, NAD+, CoA

Outputs: 2 Acetyl CoA, 2 CO2, 2 NADH

Citric acid cycle (Krebs Cycle)

Occurs in mitochondrial matrix (cytosol for prokaryotes), Acetyl CoA is fully oxidized to CO2; NADH and FADH2 store high energy electrons

Krebs Cycle inputs and outputs

Inputs: 2 Acetyl CoA, NAD+, FAD, ADP (or GDP), Pi

Outputs (per glucose): 4 CO2, 6 NADH, 2 FADH2, 2 ATP (or GTP)

Electron transport chain and oxidative phosphorylation

ETC: series of protein complexes that moves electrons to make a proton gradient.

Oxidative phosphorylation: larger process that uses this pump to make ATP

Occurs in the mitochondrial membrane (or plasma membrane in prokaryotes), electrons flow through ETC, proton gradient forms, ATP synthesized via chemiosmosis

ETC and oxidative phosphorylation inputs and outputs

Inputs: NADH, FADH2, O2, ADP, Pi

Outputs: 29 ATP, H2O

NADH

NADH carries and donates high energy electrons to produce ATP. Reduced to NAD+ (coenzyme).

Acetyl CoA

Provides fuel for Krebs cycle to make energy. Delivers a two-carbon acetyl group to the Krebs cycle for further oxidation. It is produced from pyruvate (from glycolysis) and then enters the cycle to be broken down. This broken down energy is captured by NADH and FADH2.

FAD

A coenzyme that acts as an electron carrier that gets reduced to FADH2 in the Krebs cycle and then donates its electrons to the ETC.

Where do carbs go in cellular respiration? (what are they broken down to?)

Broken down to glucose → glycolysis

What are fats broken down to and where do they go in cellular respiration?

Glycerol → glycolysis

Fatty acids → acetyl CoA

What are proteins broken down to and where do they go in cellular respiration?

Amino acids → intermediates (ex: pyruvates, Acetyl CoA, Krebs cycle)

Where does carbon from glucose end up in?

CO2 → completely oxidized

Anabolic functions

Metabolic processes that build complex molecules from simpler ones.

Glycolysis intermediates serve an anabolic function, what is it?

Glycolysis intermediates → nucleotides

What anabolic function does Acetyl CoA serve?

Acetyl CoA → fatty acids/lipids

What anabolic function does this citric acid cycle serve?

Citric acid cycle → amino acids

Anaerobic fermentation

No oxygen available (no final electron acceptor in the ETC), glucose partially oxidized (→ less ATP), inefficient compared to cellular respiration, but fast and sustains ATP production temporarily. Fermentation has glycolysis (produces ATP and NADH) and redox reactions (that convert pyruvate into a waste product, regenerating NAD+)

Products of fermentation

ATP + small organic molecules (like lactate or ethanol)