Molecular Biology exam 4

Cytosol

Fluid portion enclosed by plasma membrane, contains many metabolic pathways

1 per cell

Mitochindria

Conducts ATP synthesis (metabolism) via oxidative phosphorylation

1700 per cell

Endoplasmic reticulum

A network of membranes involved in protein and lipid synthesis, serving as a transportation system within the cell.

1 per cell

Nucleous

Contains the main genomes and conducts both RNA and DNA synthesis

Golgi apparatus

Modification, sorting, and packaging of lipids and proteins for secretion or distribution to other organelles

1 per cell

Peroxisomes

Oxidation of toxic molecules

400 per cell

Lysosomes

Small digestive enzymes responsible for intracellular degradation

300 per cell

Endosomes

Series of compartments responsible for sorting of endocytosed material

200 per cell

Three mechanism of protein transfer

1.Transfer through nuclear pores to the nucleolus

2.Transfer across membrane from the cytosol to other organelles

3.Transfer via vesicles from the endoplasmic reticulum outward

Why do we have membrane-enclosed organelles?

To allow cells to compartmentalize. Each organelle can become specialized and carry out a specific function.`

How did we get membrane-enclosed organelles?

Endosymbiosis lead to development of chloroplast and mitochondria

Invagination llead to development of other organelles

Signal seqeunces

Strings of amino acids, usually at the ends of a protein that direct the protein to the correct location

Nuclear envelope

Encloses nuclear DNA and forms the nuclear compartment, perforated with nuclear pores

Outer nuclear membrane

Is continuous with the endoplasmic reticulum membrane

How are proteins moved into the nucleus?

Nuclear proteins must display the proper nuclear localization signal to be recognized by the nuclear import receptor, which opens the pathway in the nuclear pores embedded in the outer nuclear membrane.

Nuclear pores

Form gates through the nuclear envelope to allow the passage of molecules. Made up of a meshwork of proteins that prevent the passage of large molecules, but allow small molecules to pass.

Nuclear localization signal

Displayed by nuclear proteins to enter the nucleNus. Positively charged.

Nuclear import receptors

Recognize nuclear localization signals and open nuclear pore pathways into the nucleus.

What process drives protein nuclear transport?

Hydrolysis of GTP to provide energy

Hydrolysis of GTP?

Two forms of GTPase: Ran-GTP is converted to Ran-GDP

Signal recognition particle (SRP)

Binds the ribosome and signal sequence, brings the complex to SRP receptor on endoplasmic reticulum membrane

Signal recognition particle receptor

Embedded in the endoplasmic reticulum membrane, recognizes the signal recognition particle

What are the two molecules matchmakers that guide proteins to the endoplasmic reticulum?

Signal recognition particles (SRP) and signal recognition particle receptors

How are proteins released into the endoplasmic reticulum? (pt1)

Signal recognition particle (SRP) binds to a ribosome, synthesizing a protein displaying the endoplasmic reticulum signal sequence. SRP binds the SRP receptor embedded in the ER membrane, and the signal sequence binds to a protein translator also in the membrane. SRP is released, and protein synthesis continues.

Endoplasmic reticulum signal sequence

Amino acid sequence at the N-terminus of polypeptides synthesized by ribosomes directs the protein to the ER, and opens the channel in the protein translocator

How are proteins released into the endoplasmic reticulum? (pt2)

Protein translocator in the ER membrane binds the ER signal sequences and remains bound as the polypeptide is threaded through in a loop. Signal peptidase cleaves the signal sequence, and the polypeptide is released into the ER lumen as a soluble protein.

Cathrin

Protein used to form a coat around vesicles budding from the Golgi or the plasma membrane. Helps to shape the vesicle by driving formation.

How are proteins moved via vesicular transport?

As vesicles begin to form, adaptin binds cargo receptors that are bound to their cargo and cathrin molecules to the cytosolic surface. Cathrin drives the formation of the vesicle, and dynamin wraps around the neck of the budding vesicle to pinch the vesicle off. The protein coat is then shed so the vesicle can fuse with the target organelle.

Adaptin

A protein that binds cargo receptors and cathrin in the formation of vesicles

Dynamin

A binding protein that wraps around the neck of a budding vesicle. It hydrolyzes its GTP to pinch off the vesicle once completed.

Rab proteins

Located on the surface of each vesicle and serves as a molecular marker to be recognized by tethering proteins

Tethering proteins

Located on the surface of target membranes and recognize specific Rab proteins on vesicles to ensure vesicles bind to the proper membrane (initial recognition)

V-snare

Transmembrane protein located on the vesicle

T-snare

Transmembrane protein located on the target membrane

SNARE proteins

Complementary proteins that function to dock the vesicle in place on the target membrane and catalyze membrane fusion

How are proteins modified in the ER?

Proteins are covalently modified in the ER, usually by glycosylation

Glycosylation

Conversion of proteins to glycoproteins via the covalent attachment of carbohydrate ‘oligiosaccaride’

Why glycosylation?

Glycosylation hels to ensure proper protein folding and stability, and affects how proteins interact with other cellular components

Unfolded protein complex

Response triggered when there is an accumulation of misfolded proteins in the ER, triggering the cell to produce more chaperones to increase folding capacity and quality

Chaperone proteins

Fold proteins once they enter the endoplasmic reticulum

How do cells resolve misfolded proteins in the ER?

The buildup of misfolded proteins is recognized by ER sensor proteins in the membrane, activating the unfolded protein response. Sensors stimulate the production of chaperone proteins to help fold proteins in the ER. If the accumulation is prolonged, apoptosis may be triggered. 

What happens in the golgi?

Proteins are modified and sorted to be sent back to ER or to the cell surface via lysosomes

Exocytosis

Process by which cells expel molecules out of the cell via vesicle fusion with the membrane (EX. release of insulin in response to high blood glucose levels).

Endocytosis

Process by which a cell engulfs a substance from outside to bring into the cell

(Phagocytosis, pinocytosis, receptor mediated)

Phagocytosis

The ingestion of large molecules or whole cells (cell eating)

Pinocytosis

The ingestion of fluid and molecules (cell drinking)

Receptor mediated endocytosis

Ingestion of specific molecules via complementary receptors on the cell surface. The selective mechanism allows for efficient macromolecule internalization.

LDLs

Low-density lipoproteins: A form of proteins, ‘bad cholesterol’, used to transport cholesterol in the bloodstream

Secreted by the liver

LDL recepters

Located on the cell surface for recognition and binding by LDLs carrying cholesterol. Make one round trip every 10 minutes during 20 20-hour life span.

How do cells uptake cholesterol via receptor mediated endocytosis?

LDL molecules carrying cholesterol bind to LDL receptors on the cell membrane and are internalized via the formation of clathrin-coated vesicles. The vesicle carries the LDL complex to endosomes, where LDL dissociates from LDL receptors and is delivered to endosomes. Here, LDL is degraded and free cholesterol is released into the cytosol. LDL receptors are transported back to the cell surface until they are ‘retired’ and degraded. 

What are the components of lysosomes?

Lysosomes carry out intracellular digestion of materials and worn-out organelles. They contain enzymes known as Acid Hydrolases that are optimally active at an acidic pH of 5

Acid Hydrolases

Enzymes within lysosomes that break down macromolecules. They are optimally active at pH 5 and are only present in acidic conditions

How is the acidic environment maintained within lysosomes?

Via ATP-driven H+ (proton) pump constantly pumping H+ into the lumen via the hydrolysis of ATP to ADP (loss of phosphate)

Examples of signal molecules

Epinephrine

Cortisol (STEROID)

Estradiol (STERIOD)

Insulin

Testosterone (STEROID)

Thyroid hormone

Ethylene

How does nitric acid play a role in cell signaling?

Cells within the walls of blood vessels (endothelial cells) release nitric acid in response of neurotransmitters, triggering the relaxation of blood vessels to allow an influx of blood

What is the importance of cell signaling?

Cell signals are required for cells to survive, grow/divide, and to differentiate. Cell signals work in combinations to regulate cell behavior.

Cells deprived of signals may trigger apoptosis.

Fast response

Happens in seconds to minutes 

Affects proteins already present in the cell, causing changes in cell movement, secretion, or metabolism

ALTERED PROTEIN FUNCTION

Slow response

Happens in minutes to hours

Requires a change in gene expression and the production of new proteins.

ALTERED PROTEIN SYNTHESIS

Positive feedback

Downstream component in a signal pathway acts on an earlier component to ENHANCE the signal

Negative feedback

Downstream compound in signal pathway acts on an earlier component to INHIBIT the signal

EX. An increase in prey may cause an increase in predators that kill more prey

Kinase

Phosphorylating enzyme that covalently attaches a phosphate group

Phosphorylation

The addition of a phosphate group, may turn molecular switches on OR off

Three main classes of cell receptors

Ion channel coupled receptors

Protein coupled receptors

Enzyme coupled receptors

Substances that act of cell receptors

Barbiturates/Benzodiazepines - anxiety relief/sedation

Morphine and Heroin - pain relief, euphoria

Capsaicin - painful, burning

What are the steps the G-protein couples receptor of K+ channels

The binding of acetylcholine to G-protein-coupled receptors on the outside of heart cells activates the G-protein on the other side of the membrane. The activated BY complex opens the K+ channel, causing an influx of potassium into the cell, making the membrane harder to activate and slowing the heart rate. 

G-protein

Molecular switches in signal transduction. Made up of a(alpha), B(beta), and Y(gamma) subunits.

G-protein coupled receptors

Bind extracellular signals and activate G-proteins on the other side. Involved in taste, smell, behavior, mood, and immune system regulation.

What molecules bind to GPCR in the brain?

Dopamine, Serotonin, GABA

Pathophysiology

The study of physiological process associated with disease/injury

How does epinephrine decrease glycogen levels in skeletal muscle cells?

Epinephrine (adrenaline) stimulates its corresponding G-protein-coupled receptor, activating a G-protein on the other side of the membrane within the cell. This triggers the activation of adenylyl cyclase to produce cyclic AMP. cAMP molecules activated PKA, which inactivated glycogen synthase and activated glycogen phosphorylase (breaks down glycogen).

Receptor tyrosine kinases

A phosphorylation molecule. Transmembrane proteins that display ligand-binding domains on the outer surface of the plasma membrane. Activation of RTKs causes of chain of events in intracellular signaling pathways.

How do RTKs work?

The binding of a signal molecule in the form of a dimer to two of the extracellular receptor tyrosine kinases activates them by bringing them together. This stimulates the RTKs to phosphorylate the tails of tyrosines, relaying a signal down intracellular pathways.

Ethylene

A critical hormone present in plants that turns genes on by relieving inhibition.

What is the ethylene signaling response in plants?

Ethylene turns genes on by relieving the inhibition of their transcription regulator.

In the absence of ethylene, empty receptors are active without ethylene bound, allowing for the activity of protein kinase as well. Protein kinase contributes to the degradation of transcription regulators, causing the gene to be off.

In the presence of ethylene, receptors are bound and inhibited by ethylene, causing the inhibition of protein kinase. The inactivation of protein kinase allows for the activation of transcription regulations, allowing ethylene-responsive genes to be transcribed.

Cytoskeleton

A network of protein filaments extending throughout the cytoplasm.

Gives the cell its shape, organizes internal compartments, and allows the cell to move.

Made up of intermediate filaments, actin filaments, and microtubules.

Microtubules

Hollow cylinders made of TUBULIN protein

Long and straight with one end attached to centrosome

Critical for organization

Actin filaments

Helical polymers of ACTIN protein

Dispersed throughout the cell but are highly concentrated in the cortex of the cytoplasm

Intermediate filaments  (structure)

Made up of fibrous intermediate filament proteins

Strong and ropelike (many strands twisted together), consisting of 8 tetramers associated via lateral non-covalent bonds

Intermediate fibers (function)

Strength cells against mechanical stress

Create a meshwrok of filaments to support the nuclear envelope

Nuclear lamina

A meshwork of intermediate fibers that lies beneath the inner nuclear membrane, providing support for the nuclear envelope and attachment sites for chromosomes (chromatin).

Plectin

A giant protein that acts as a link between the 3 components of the cytoskeleton to each other, and links the cytoskeleton to junctions in the plasma membrane

How are microtubules and motor proteins similar?

They function to position organelles in the cytoplasm

Function of microtubules

Organization - grow outward from the organizing center (mitotic spindle and basal bodies)

Guide the transport of organelles, vesicles, and macromolecules in both directions along the nerve cell axon

Cellulose

A structural polysaccharide found in the cell wall of plant cells. Absolutely necessary for plant structure but indigestible by humans

Why can mammals such as cows digest cellulose but humans can’t?

Mammals contain bacteria in their gut that produce enzymes that break down high cellulose content foods. Humans do not possess those enzymes. The molecular structure of strings of glucose in cellulose makes it hard to digest.

What is the structure of cellulose?

It is a straight, unbranched chain of glucose monomers that exhibits hydrogen bonding

How do microtubules function on the nerve cell axon?

Materials are synthesized in the cell body but are needed at the axon terminals. Microtubules line the axon and serve as a tract for the directional transport of those materials via motor proteins. The backwards traffic consists of materials ingested by the axon terminals.

Motor proteins

Molecular machines that convert chemical energy from the hydrolysis of ATP into mechanical work to move materials

How do motor proteins walk?

They use their two globular heads to walk along the microtubules lining the axon. The hydrolysis of ATP loosens one of the heads from the microtubule. The release of ADP and attachment of ATP changes the conformation of the other head, shifting it forward and pulling the loose head in front of it.

Two kinds of motor proteins

Kinesis and dyenis. Both are dimers with two globular heads for walking and a single tail to carry cargo.

Kinesis

Type of motor protein that moves towards the plus end of the microtubule

Dyenis

Type of motor protein that moves toward the minus end of the microtubule

What are three drugs that affect micortubules?

Taxol (prevents depolymerization)

Colchicine, colcemid (prevents polymerization)

Nocodazole (prevents polymerization)

What are the functions of actin filaments?

Allow animal cells to adopt different shapes and functions and are essential for cell movement

Structure of actin filaments

Made up of actin protein

Thin and flexible

Each actin subunit is made up of actin monomers containing clefts for ATP/ADP binding

Myosin-1

Actin-binding motor protein always walks towards the plus end of the actin filament

Consists of a head domain and a tail that may bind to various cargoes (Ex. a vesicle to propell it through the cell, or the plasma membrane to pull it into shape)

How do cells crawl?

The polymerization of cytoplasmic actin monomers at the leading (plus) end of the cell pushes the plasma membrane forward. A new attachment is made between the cell and the surface. The rear end of the cell contracts and draws the cell body forward. The cycle is repeated.

Myosin-2

Muscle myosin (thick filaments) that make up the sarcomere

Myofibrils

The contractile unit of the muscle cell made up of a chain of sarcomeres

Sarcomeres

Assemblies of actin filaments (thin) and myosin-II filaments (thick) that slide past each other during muscle contraction

Consists of a Z-disk that attaches thin filaments at this plus end, and large central regions of thick filaments

The minus ends of actin filaments overlap with the ends of thick myosin filaments.