Cell Function Final

The total of all chemical reactions that process molecules from the environment to survive, grow, and reproduce.

Metabolism

The break down of foodstuffs into smaller molecules, generating energy and precursors for cellular processes

Catabolism

The use of energy from catabolism to drive synthesis of complex molecules from smaller precursors to support cell growth, maintenance, and function

Anabolism

Light is captured and stored as chemical-bond energy in activated carrier: What stage of photosynthesis is this? 

Stage 1 

Activated carriers used to drive sugar formation using carbon dioxide: What stage of photosynthesis is this?

Stage 2

Stores energy in an easily exchangeable form either as readily transferable chemical groups or high energy electrons for the cell to drive chemical reactions in the cell (most common types are ATP and NADH/NADPH)

Activated carriers

Energetically favorable reaction is used to drive an energetically ufavorable reaction, facilitated by enzymes 

Coupled reactions 

The most widely used activated carrier in cells; couples to unfavorable reactions which often involves a transfer of a phosphate group to a molecules (phosphorylation).

ATP as an active carrier

Group carried in high energy linkage in ATP

Phosphate

Used to activate substrates for chemical reactions, drives active transport, powers muscle contractions,a nd facilitates intracellular signaling pathways.

ATP

Two different activated carriers that carry energy in the form of hydride ions. When they pass their hydrogen to a donor molecule, they are oxidized and differ from one phosphate group, changing conformation to make them interact with different enzymes.

NADH/NADPH

Used in catabolic reactions, generated ATP through oxidation of food molecules by accepting high energy electrons, kept mostly in its oxidized form and is ready to accept electrons

NAD+/NADH

Used in anabolic reactions, synthesizing energy-rich macromolecules by donating high energy electrons, kept mostly in reduced form and is ready to give electrons

NADP+/NADPH

Carries two hydrogens and high energy electrons produced in the citric acid cycle

FADH2

Acetyl forms a high-energy thioester bond with CoA, input into the citric acid cycle

Acetyl CoA

The process where a variety of enzymes catalyze the breakdown of macromolecules (glucose) into stored energy (ATP) to provide fuel to build larger molecules needed for cellular functions through a series of tightly controlled series of reactions, releasing energy in small bits to give to activated carriers.

Cellular Respiration 

Three stages of cellular respiration

1. Digestion

2. Glycolysis and Pyruvate Oxidation

3. Citric Acid and Oxidative Phosphorylation

Where does glycolysis and pyruvate oxidation take place?

• Glycolysis happens inside the cell

• Pyruvate oxidation happens in mitochondrial matrix

Where does the citric acid and oxidative phosphorylation take place? 

• Citric acid cycle occurs in mitochondrial matrix 

• Oxidative phosphorylation occurs in the inner mitochondrial membrane 

Three stages of glycolysis

1. Energy investment

2. Cleavage of glucose

3. Energy harvesting

Reactants and products of glycolysis

6-carbon glucose and 2, 3-carbon pyruvates → 2 ATP and 2 NAD+

When cell perform respiration using oxygen to fully oxidize glucose, generates large amounts of ATP

Aerobic conditions 

When cells switch to fermentation, allowing glycolysis to continue by regenerating NAD+ and produced much less ATP

Anaerobic conditions

When low oxygen causes pyruvate to be converrted to lactate, NADH restored to NAD+ to be used during glycolysis, low ATP yield

Lactate fermentation

Low oxygen environments cause pyruvate to be converted to ethanol and CO2, NADH restored to NAD+ to be used during glycolysis, low ATP yield

Alcohol fermentation

Reactant and products of pyruvate oxidation 

Uses the pyruvate after glycolysis → acetyl CoA, NADH, and Co2

Where else can acetyl CoA be found?

Fatty acids in the long hydrocarbon chains, amino acids

8 reaction process that uses acetyl CoA to harvest high energy electrons, these electrons power ATP production in oxidative phosphorylation

Citric Acid Cycle 

Final stage of cellular respiration that uses chemical energy that uses chemical energy from activated carriers (from glycolysis and citric acid cycle) to generate ATP (30 ATP molecules)

Oxidative Phosphorylation

NADH and FADH2 donate their high energy electrons to the ETC, creating a proton gradient. A series of electron carriers embedded in the inner mitochodrial membrane in eukaryotic cells

Electron Transport chain

Making glucose from pyruvate; energy intensive process

Gluconeogenesis 

Branched polysaccharide of glucose stored in mammalian liver and muscle cells

Glycogen 

Enzyme that breaks glycogen down one glucose at a time

Glycogen phosphorylase

When ATP: ADP/AMP ratio is HIGH

• Phosphofructokinase is inhibited to shut down glycolysis

• Fructose 1,6-bisphosphate is activated to induce gluconeogensis

When ATP: ADP/AMP ratio is LOW

• Phosphofructokinase is activated to induce glycolysis

• Fructose 1,6-bisphosphate is inhibitaed to shut down gluconeogensis

• Organelle that produces the bulk of the cell’s ATP

• Can adjust their location, shape, and number depending on cell needs

• Has an inner membrane where oxidative phosphorylation takes place and outer membrane responsible for transport of protein porin

Mitochondria

When the mitochondria is more negatively charged in the matrix, H+ ions will move towards negative charge into matrix.

Membrane Potential

When the mitochondria is more acidic in the inter membrane space (more H+ ions) where H+ ions will move from higher to lower concentration into the matrix

pH gradient 

A large, multiunit protein embedded in the mitochondrial membrane that generates the synthesis of ATP from ADP and organic phosphphate (Pi).

ATP synthase

Structure of ATP synthase enzyme

F0 Rotor, F1 ATPase Head, Peripheral Stalk

Membrane-embedded, rotation motor driven by protons

F0 Rotor 

Stationary, catalytic head that makes ATP

F1 ATPase Head

Holds the F1 head stationary

Peripheral Stalk

The tendency for a redox pair to donate or accept electrons; a measure of electron affinities

Redox potential

Types of mobile carriers in the ETC

Ubiquinone and cytochrome

• A smaller molecule that ferries from NADH dehydrogenase complex to cytochrome c reductase complex.

• Accepts high energy electrons from FADH2 

Ubiquinone

Found in NADH dehydrogenase complex; has weak electron affinity compared to ubiquinone, allowing for transfer of electrons to ubiquinione

Iron sulfur centers in ubiquinione

• A protein that ferries from cytochrome c reductase complex to cytochrome c oxidase complex.

• Redox potential is between that of cytochrome c reductase complex and cytochrome c oxidase complex

Cytochrome C

• Found in cytochrome c, cytochrome c reductase, and cytochrome c oxdiase used as electron carriers.

• Heme groups of difference cytochromes have difference electrons affinities because of differences in heme structures and protein environment

Iron atoms held in heme groups

Removes electrons from cytochrome c so they can bind to the heme carrier

Cytochrome C Oxidase Complex

Relaying of one signal converted into another which involves a receptor and ligand, cells will respond if it has the specific receptor for that ligand

Signal transduction 

Types of signaling

Endocrine, paracrine, neuronal, and contact-dependent

Cells release hormones into bloodstream to signal through whole body

Endocrine cells

Cells release signaling molecules into extracellular fluid around to affect nearby cells (local mediator)

Paracrine cells

Cells are electrical signals that travel along a neuron’s axon where the signal arrives at nerve terminals to trigger neurotransmitter release, which act on target cells

Neuronal cells 

Signal molecules are bound to surface of signaling cell where it requires direct contact with a receptor protein on an adjacent cell

Contact-dependent

Embedded into the surface of cell membrane where ligands may be too large or hydrophilic to cross cell membrane

Cell Surface Receptors

Bind to the intracellular receptors where ligands are small or hydrophobic enough to cross the cell membrane

Intracellular receptors 

Responses that alters a protein function

Fast

Response that changes gene expression and synthesis of new proteins 

Slow responses 

Activated by ligand binding to receptor protein, facilitated by intracellular signaling molecules, alter affector protiens to produce specific cellular responces

Intracellular signaling pathways

Types of signaling responses

Relaying, amplification, integration, distribution, and feedback modulation

Intracellular signaling proteins that use a signal to toggle between an active and inactive state

Molecular swiches 

add a phosphate group to phosphorylate a target protein

Kinases

remove a phosphate group to dephosphorylate a target protein

Phosphotases

use GTP binding as their molecular switch
• on when bound to GTP
• off when bound to GDP

GTP binding proteins 

activated by G-protein coupled receptors (GPCRs)

Trimeric GTPase

activated by GEF proteins and inactivated by GAP proteins

Monomeric GTPase

• extracellular ligand binding opens channels to allow ion flow across membrane

• often seen in neuronal synapses

ion-channel coupled (ionotropic) receptors

extracellular ligand binding causes receptor to activate the associated G-protein through exchange of GDP for GTP

G-protein coupled receptors (GPCRs)

extracellular ligand binding causes activation of an associated enzyme that
induces intracellular signaling pathway

enzyme-coupled receptors

Describe GCPR activation

1. Ligand binds to GPCR, causing a conformation change in receptor

2. This change in the G protein will allow for the a subunit to exchange GDP for GTP (activation)

3. By subunit will dissociate from a subunit and will activate individually

Describe GCPR inactivation

1. a subunit will hydrolyze its own GTP to GDP

2. each subunit will reassocciate, which inactivated the G protein

Adenylyl cyclase and phospholipase c are what kind of molecules and from where are they produced?

messenger molecules produced by G proteins

enzyme that converts ATP to cAMP when the a subunit is activated in Gs protein

adenyl cyclase

enzyme that turns off cAMP signaling by converting cAMP to AMP

cAMP phosphodiesterase

how is protein kinase A is activated (PKA)

cAMP activates PKA

Describe cAMP signaling in epinephrine

1. epinephrine binds to GCPR and activates the a subunit of Gs protein to produce cAMP

2. cAMP activates PKA by phosphorylation

3. PKA phosphorylated and activates kinase

4. kinase activates the break down of glycogen into glucose for energy

cAMP signaling in neurons

1. cAMP activates PKA which phosphorylates specific transcription regulator

2. Stimulates transcription of a set of target genes

3. Target genes help with learning and synapse connection

enzyme that cleave inositol phospholipid anchored on cytosolic side of the plasma membrane, a subunit activated Gq protein, that produces inositol triphosphate and diaglycerol

phospholipase c (PLC)

Binds to Ca2+ channels on the ER to trigger a release of Ca2+ into the cytosol

inositol triphosphate

remains in plasma membrane, works with Ca2+ to activated PKC enabling it to phosphorylate target proteins

diacyglycerol

Fundamental units of life that have a wide variety of sizes, shapes, and functions that perform specialized functions

Cells

Describe the central dogma

1. DNA encodes our genes using nucleotides

2. DNA transcribes into RNA

3. RNA translates into a protein

Complete set of genetic information of an organism, only expresses a specific set of genes depending on their internal state and cues which define the cell type

Genome

Type of microscope used to visualize cells around 5-20 micro meters

Light microscope

Type of microscope to visualize the subcellular structures - like organelles

Electron microscope

Type of electron microscopy to look at the surface of the cell

Scanning

Type of electron microscopy to look at slices of the cell

Transmission

Dense material outside of cell membrane that provides structure, made of proteins and polysaccharides

Extracellular matrix

Stores genetic material

Nucleus

Transparent substance enclosed in the lipid membrane, houses organelles for function

Cytoplasm

• Possess membrane-bound nucleus and organelles

• Much larger than prokaryotes

Eurkaryotes

• No membrane bound nucleus or organelles

• Much smaller than eukaryotic cells

• Most diverse and numerous cells on Earth due to their wide range of habitats and functionally diverse energy production

Prokaryotes

Two domains of prokaryotes

Archea and bacteria

The most common type of prokaryotic cell on Earth

Bacteria

Other type of prokaryotic cell, most diverse habitats

Archea

• Double layer membrane surrounding nucleus

• Provides structural support

• Controls transport between the nucleus and cytoplasm via the nuclear pore complex

Nuclear envelope

• Production of ATP through cellular respiration

• Double membrane structure

• Contains their own DNA (which is separate from nucleus)

• Hypothesized to have been engulfed from bacteria (symbiotic relationship)

Mitochondria - cellular respiration

• Helps plant cells produce energy through photosynthesis

• Double membrane structure containing thylakoids and own DNA

• Hypothesized to have been engulfed from bacteria (symbiotic relationship)

Chloroplasts