BIOL 416 Exam 3

Endocytosis

Away from plasma membrane

Exocytosis

To plasma membrane

Key step for vesicular transport

Fusion or budding of vesicles to or from membrane

Endosome

Receives vesicles from the cell surface(Early), golgi, or phagocytes; sends vesicles back to the golgi or to lysosomes(late)

Lysosome

Heavily glycosylated with protective coating, breaks down things via enzymes, ph sensitive, receives from Endosome or autophagosomes

Lysosome functions

1. Break down molecules 2. Recycle parts via metabolite transporter 3. Maintain acidity via proton pump

Cholesterol uptake by endocytosis

Result of Endosome and lysosome fusion

Endolysosome

Endosome + lysosome

Phagocytosis

Break down of whole cells, only in specialized cells

Autophagy

Self eating, degradation of Intracellular components

Phagophores engulf cell components and create

Autophagosomes

Phagolysosome

Phagosome and lysosome

Autolysosome

Lysosome + autophagosomes

Endolysosome

Lysosome + Endosome

3 Major autophagy forms

Macroautophagy, microautophagy, chaperone mediated autophagy

Macroautophagy

Degradation of organelles other than proteins, formation of autophagosome, selective or bulk transfer

Microautophagy

No autophagosome, non selective, lysosomal degradation of vesicles contained macromolecules

Chaperone-mediated autophagy

No autophagosome, individual cytosol if proteins targeted to lysosome and translocated across membrane, highly selective

Peroxisome

Metabolic processes, make H2O2, beta oxidation and systhtesis of bile acids intermediates, breakdown of d amino acids

Beta oxidation

Long chain fatty acids broken down into medium chain, shuttled to mito, used for ATP generation

Synthesis of bile acid intermediates

Used in lipid digestion and cell signaling

Detoxification

Breakdown of d amino acids

Proteasome

Critical for protein degradation, 26S: 18 cap and 20S core

Ubiquitin system

Uses sequential specificity, E1, E2 and E3 ligases, E3 more diverse, facilitated degradation by proteasome

Metabolism first Hypothesis

Hypothesis that explains the origin of life was the evolution of metabolism

Oxidizing glucose releases

-2850 kJ/mol all at once

Glycolysis

The process of splitting glucose into 2 Pyruvate

Negative delta G is

Highly favorable

Number of Glycolysis steps

10

Glucose to Glucose 6 phosphate

Irreversible, -16 kJ/mol, 1 step

Isomerize glucose 6 phosphate to fructose 6 phosphate

2nd step, -1.4 kJ/mol, reversible

Fructose 6 phosphate to fructose 1,6 phosphate

3rd step, regulatory, phosphfrucrokinase burns one ATP, irreversible, -16.2 kJ/mol

6 carbon chain into two 3 carbon chains

4th stem, glucose split in half, halves not the same

Convert to glyceraldehyde 3 phosphate

5th step, halves are same

Oxidation + phosphate

6th step, unfavorable, also produces NADH

Removal high energy phosphate to make ATP

7th step, - delta G, drags previous rxn forward

3 phosphoglycerate to 2 phosphoglycerate

8th step, dehydration

2 phosphoglycerate to phosphoenolpyruate

9th step, dehydration

Creation of Pyruvate

10th step, 1 ATP per Pyruvate, highly favorable

How much ATP and NADAH do we make per glucose molecule in Glycolysis

2 NADH and 4 ARP

Why is fructose an issue?

It enters after the regulatory step and is stored for lipogenesis as fat

Glucogenesis

Uses 6 ATP equivalents to make Glucose

Lack of O2 or NAD+ results in

Fermentation

Three types of fermentation

Lactic acids, ethyl alcohol, an acetic acid

Lactic acid fermentation

Pyruvate is turned into lactate and NAD+ is recycled

Does ATP get created during fermentation?

No despite the fact that it is favorable

Ethyl alcohol fermentation

Pyruvate → acetaldehyde → ethanol

Cancer cells consume Glucose up to ___ times faster than normal cells

20

Detecting cancer via Warburg effect

Radio labeled molecule is injected into patient, cancer cells pick up molecules and are shown by PET scan

Warburg effect

Aerobic glycolysis, emphasis of Pyruvate to lactate pathway, production of intermediates for proliferation, acidic micro environment, aids immune system evasion

Location of Krebs cycle in Eukaryotes

Mitochondrial matrix

Location of OXPHOS In Eukaryotes

Electron Transport System

Location of Krebs cycle and OXPHOS in prokaryotes

Cytoplasm, aided by bacterial membrane invaginations

Names of the TCA cycle

Tricarboxylic Acid Cycle, The Citric Acid Cycle, Krebs Cycle

Krebs cycle functions

Central hub for making and breaking things, regulation of inflammatory response, production of NADH & FADH2, 2 passes: 1st pass = oxaloacetate 2nd pass = oxolacetate to CO2

Backward Krebs cycle

Occurred during early earth conditions and in some anaerobic microbes

Acetic Acid fermentation

Pyruvate → Acetaldehyde → acetate → acetyl-CoA

Acetyl CoA is created by the break down of fats which is a process called

Beta-oxidation

OXPHOS major pieces

Electron transport system and ATP synthase

Electron transport system

Use electrons from TCA to create a proton gradient using complex I, III and IV

ATP synthase

Uses proton gradine to generate ATP

Proton gradient

High concentration in the inter membrane space and low concentration in the matrix

Complexes that pump protons

I, III & IV

2 entry points to the ETS

NADH enters in complex I & FADH enters in complex II, converge at Q to make QH2

CI road to QH2

NADH enters, hydrogens added to Q via NADH dehydrogenase, Q2 is made, 4 protons pumped into inter-membrane space

CII road to QH2

FADH2 enters complex II, Removed two hydrogens, add two hydrogens to Q to make QH2 via succcinate dehydrogenase

What makes CII special

It does not pump protons, it works simultaneously in the TCA cycle and OXPOS

Creation of CI, CIII, CIV super complex

When CII is skipped

1st Q cycle

QH2 enters, electron moves to CytC which moves to CIV, 2 H+ pumped across membrane, 1 electron move to another Q. Result is Q*

2nd Q cycle

QH2 enters, 1 electron moves to CytC which moves to CIV, 2 H+ pumped across membrane, Q* receives second electron, making QH2

The Q cycle

The recycling of QH2 by CIII

CIII

Performs two steps, each step pumps two protons across membrane, each step adds electrons to cytochrome C, uses Cytochrome C reductase

CIV

Removes electrons from Cytochrome C and pumps 2 protons to gradient via Cytochrome C oxidase

ARP generation by ATP synthase

Protons flow through F0 and convert potential energy to mechanical rotation, rotation alternated conformations of F1, driving enzyme through enzymatic cycle to make ATP

ATP yield per NADH

3 ATP per 10 protons, 10 protons for 1 NADH

Why does FADH give less energy?

It has less protons

What makes the most energy?

Aerobic Bacteria

Why are Eukaryotes better at making ATP?

Endosymbiosis

Inverse Warburg effect

Emphasis on OXPHOS instead of fermentation, increasing neurotransmitter intake of GABA

Totipotent

Plants feels can differentiate into any cell type via dedifferentiation

Telomerase

Reverse transcriptase that rebuilds telomeres, allowing plants to be “immortal”

Tolerance to Ploidy changes affects

Efficacy of cross reading and gene transfer

Cell wall

Contains cellulose and pectin

Plasmodesmata

Channels between cell walls, provides structure and transport

Chloroplast

Originated from Cyanobacteria, utilized for photosynthesis

Chromoplasts

Chlorophyll pigment is degraded and carotenoids accumulate, internal membrane are modified

Leucoplasts

Used for storage, lack photosynthetic pigments, found in roots

Amyloplast

Stores starch

Elaioplast

Stores lipid

Proteinoplast

Stores proteins

Oil bodies

Provide energy source for germination and growth of seedlings

Glyoxysomes

Breakdown fatty acids in oil bodies into acetyl-coa via beat oxidation, type of peroxisome

Gerontoplasts

Breakdown thylakoid membrane & dismantles photosynthetic machinery

Chloroplast genomes

Lost or moved to the nucleus over time, can not dedifferentiate

Tannosomes

Synthesize tannins for defense

Cytotoxic chemicals

Chemicals that provide plants defense, an example is taxol

Another target for cancer drugs

Glycolysis

Vacuole

90% of cells, made of tonoplast on the outside and cell sap inside. Contains water, ions, nutrients, enzymes and waste. Acts as a storage for water and handles waste

Mitochondrial movement in plants

Cluster and guide root growth using ROS

Phycobillisome

Antennae like structure that captures light energy to transfer to photosynthetic systems