BIOL 1090

What does it take to make a cell

information, chemistry, compartments

What is the Information of a cell

all cells possess DNA, which provides the information necessary to build various proteins

The central Dogma of Biology

DNA —> RNA —> Proteins through transcription and translation

What did the Miller Urey Experiment prove?

Simulated early earth conditions, which shows that amino acids can be made from inorganic compounds

What does compartments mean when it comes to what it take sit make a cell

Single or double lipid layer where cells can preform important functions (communication, protection etc.)

What is cell theory

1. All living organisms are composed of one or more cells

2. Cells=basic unit of life

3. All cells arise from preexisting cells

Evidence of endosymbiotic theory

1. Have their own DNA

2. Replicate independently

3. Double Membrane

4. Similar size to bacteria

What are the 9 basic properties of cells

1. Highly complex and organized

2. Controlled by genetics

3. Can reproduce

4. Assimilate and utilize energy

5. Carry out chemical reactions

6. Mechanical activities

7. Respond to stimuli

8. Self-regulate

9. Evolve

What are the 5 basic properties of viruses

1. Highly complexed and organized

2. Activity controlled by genes

3. Can reproduce only with a host

4. Carry out chemical reactions if in host

5. Evolve

What is a viron

Exist as an inanimate particle

What is baltimore classification

categorizes viruses based on type of genome and their method of replication

What is CRISPR-Cas

Immune-like system that bacteria have to battle bacteriophages

Narrow host range vs Wide Host Range

Narrow host range: Human cold

Wide host range: Rabies which can infect humans, dogs, foxes, bats, raccoons

Which type of virus infection ruptures and kills cells

Lytic cells

What is lytic infection and what are some examples

Production of virus particles ruptures (and kills) cells

• Influenza

• Rabies

What is non-lytic infection

Viral DNA is inserted into host genome, and these infected cells can survive and reproduce the virus cells

• HIV

• Chicken Pox

What is the life cycle of a Rabies Virus

1. Absorptions

2. Endocytosis

3. Fusion

4. Release

5. Replication

6. Transcription

7. Glycoprotein synthesis

8. Transport

9. Fusion

10. Matrix and nucleocapsid synthesis

11. Progeny capsid

12. Association at membrane

13. Budding

What 5 genes does the RNA genome encode for in Rabies Virus

1. Nucleoprotein

2. Phosphoprotein

3. Matrix protein

4. Glycoprotein

5. Viral RNA polymerase

How do RNA Vaccines work

Trick the body’s cell to produce a fragment of a virus.

• Instructions to assemble a replicase, which can make a lot of copies of the DNA template for producing antigens

What are the functions of biological membranes

1. Define cell boundary

2. Define enclose compartments

3. Control movement of material into and out of the cell

4. Allow response to external stimuli

5. Enable interactions between cells

6. Provide scaffold for biochemical activities

What is the Sarcoplasmic Reticulum

A specialized type of smooth ER that is found within muscle cells. Its main function is to store and regulate calcium ions, which is used for muscle contraction

What do amino acids make and with what bond

Amino acids make proteins which are linked with peptide bonds

What do nucleotides make and with what bond

Nucleotides make nucleic acids via phosphodiester bonds

What do sugars make and with what bond

Sugars make carbohydrates via glycosidic bonds.

What are the building blocks of life

Polymers

• Amino acids

• Nucleotide

• Sugar

Not a polymer

• Phospholipid

What are the steps for phospholipid synthesis

1. In cytosol, fatty acids are activated by the attachment of CoA

2. They bond to glycerol-phosphate and are inserted into the cytosolic leaflet of the ER via acyl transferase

3. The phosphate is removed by an enzyme (phosphatase)

4. Choline (already linked) is attached via choline phosphotransferase

5. Flippases transfer some of the phospholipid

6. Moves to the golgi by vesicles and then to the cytoplasmic cellular membrane through exocytosis

Where does phospholipid synthesis occur

Cytosol and outer ER membrane

What is exocytosis

molecules moved out of cell “exit”

What is endocytosis

Molecules brought inside

What are the 3 types of endocytosis

Phagocytosis

Pinocytosis

Receptor-mediated

What are carbohydrates attached to lipids or proteins on the membrane important for

Cell-cell recognition and adhesion

What do fatty acids do to the phospholipids

They make the phospholipids both flexible and fluid, making a rapid lateral movement of molecules

What is the meaning of Fluid Mosaic

Fluid = individual lipid molecules move

Mosaic- Diverse particles like proteins, carbohydrates and cholesterol

Who proposed the fluid mosaic model

Seymour Jonathan Singer and Garth Nicolson in 1972

How can membrane fluidity vary

• lipid composition, short unsaturated chains increase fluidity, as they create more spaces, cholesterol alters interactions, fills up the spaces

• Temperature, decreases in cold conditions

How do phospholipids vary

• fatty acid chain length

• Degree of saturation

• Polar groups

The Frye-Edidin experiment

Greater intermixing at higher temperatures

Mouse cells x human cell

1. The cells are fused together at 37 degrees Celsius to create a hybrid cell

2. Initital the proteins are separate

3. After 40 minutes the proteins of the mouse and human cells are fully intermixed

What are structural characteristics of biological membranes

• 6nm thick

• Stable

• Flexible

• Capable of self assembly

Three classes of membrane proteins

1. Integral membrane proteins

2. Peripheral

3. Lipid anchored

What are the functions of integral membrane proteins

• Transport of nutrients and ions

• Cell-cell communication

• attachement

How does the biological membranes change with temperature

Warming increases fluidity → Liquid crystal

Cooling decreases fluidity → crystalline gel

What does Cholesterol do for the membrane

Modulates membrane fluidity, as it acts a bidirectional regulator of membrane fluidity

• High temperatures, stabilizes, raises melting point

• At low temperature, intercalates between the phospholipids and prevents them from clustering together

Types of transmembrane proteins

• Transporter

• Receptor

• Enzyme

• Anchor

What is the most common protein structure element crossing biological membrane

Alpha helice

What are tetraspanins

A family of membrane proteins found in all multicellular eukaryotes

Functions:

• Adhesion

• Motility

• Proliferation

Movement of substances across membranes

Small uncharged molecules move easily

Large, polar, charged compounds cannot easily cross the membranes because of hydrophobic traits of the tails

Types of controlled transport for large, polar, charged molecules

1. Simple diffusion

2. Channel

3. Facilitated Diffusion

4. Active Transport

What is Simple Diffusion

The movement of molecules down their concentration gradient does not require any energy, small uncharged molecules

What is facilitated diffusion

need a receptor, open and close, only carry one molecules at a time, high → low concentration, no energy required

Uniporter

Goes in one direction

What do channels do

• protein channels provide another way for passive transport

• Effective for small charged molecules

• Ions move down concentration gradient (do not require any energy)

• Selective, only allow specific molecules to pass

What are ion channels

• Often gated, can be open or closed

• Provides the channel the ability to respond to different stimuli

What are the different stimuli that ion channels react to

1. Voltage

2. Ligand

What are voltage-gate channels

Some channels can respond to changes to charge across membrane, different in voltage creates membrane potential, depolarization leads to opening of the gate, action potential

What are ligand-gate channels

The channel responds to the binding of a specific molecules, a ligand (hormone, enzyme, neurotransmitter), which causes a conformational change of the receptor

What is conformational change

Changes the shape of the channel

What are the steps of a Glucose Transporter

1. Transporter ready to accept glucose molecule

2. Glucose is accepted by transporter

3. Intracellular side of transporter opens

4. Glucose is released and cycle repeats

Symporter

Molecules can go in and out, movement back and forth

What are carrier: symporters

Cells need to move substances from a lower to higher concentration, rely on teh chemical gradient of another molecule.

Steps of a Na+ - glucose symporter

1. Simultaneous binding of 2 Na+ and 1 glucose to the transporter with outward-facing binding site

2. This causes a conformational change in the transporter

3. Eventually the transporter adopts and inward-facing conformation that allows

4. the dissociation of the two Na+ molecules in the cytosol. As a result, glucose gets pushed-in

5. Return to the outward-facing conformation to repeat the cycle

What is an antiporter

Two things go through together, the concentration gradient of one molecule is used to transfer a second molecule in the opposite direction

What is an example of an antiporter

Sodium-proton exchange

Transports Na+ into the cell and protons out of the cell to maintain pH

What is active transport

Change in the conformation of the transporter caused by the hydrolysis of an ATP molecule allows molecules to be released on the other side of the membrane.

• Move against the concentration gradient

What does Active transport use to move molecules

Proton pump

Two types of active transport

Primary: direct hydrolysis of ATP

Secondary: energy comes from an ion concentration gradient that is established by primary active transport

What is an example of primary active transport

Na+ - K+ pump

How does the Na+ and K+ pump work

• Pumps Na+ out of the cell against gradient

• Pumps K+ into cell against gradient

• Use ATP for energy

What are the steps of the sodium potassium pump

1. 3 Na+ and 1 ATP bind to the protein pump

2. Hydrolysis of ATP releases ADP and phosphorylates an amino acid in the pump

3. The shape changes causes Na+ ions to be released outside the cell and 2 K+ ions to enter the pump

4. Two K+ ions bind to the pump

5. Dephosphorylation of the pump release P causing the two K+ ions to be released into the interior of the cell

6. Repeat

How many Na+ and K+ move in the pump

3 Na+

2 K+

What is an example of secondary active transport

The glucose-Na+ transporter

How does the glucose Na+ transporter work

Glucose needs to be transported across the membrane against its concentration gradient

Movement of Na+ provides the energy to move glucose molecules (which comes from the primary active transport, Na+ and K+ pump)

What do carbohydrates attach to in the plasma membrane

Lipids - glycolipids

Proteins - glycoproteins

Where are peripheral proteins attached

To either membrane surface or even actin/cytoskeleton

What is signal transduction

telephone game, a signal is passed on form one molecule to another, but the signal must remain the same

What do receptors do in signal transduction

changes the morphology of the protein

What are the chemical and physical stimulus

Chemical: nutrient, waste, ion, hormone

Physical: light, sound, temperature

Where can signals come from

Inside the cell or outside, they can travel a short or great distance

How does signal transduction work

Transmitted → cells on the outside of the cell can communicate inside the cell → ligand binds to the receptor → morphology changes → cascae effect

What are the common themes in signal transduction pathways

• Specificity

• Ligand binding causes receptor protein to change change

• Activate receptor alters function (amplification)

• Response is executed

What does specificity mean

Receptor proteins have a very specific binding sites for chemical signal molecules

What are ligands

are chemical messengers, released by a cell, which can be sent to a different cell or stay at the same cell, cancer cells send the signals to themselves, to divide again

Components of a signal transduction pathway

• The signal

• A receptor

• Response (long or short term)

• Amplification by other cellular molecules (cascade)

What is long and short term response in signal transduction

Long term, change in DNA, causes long term changes

Short term, specific movement, enzyme activation, cell movemtn

Steps of signal transduction

1. signal arrive at a target cell (hormone or enzyme)

2. The signal molecule binds to a receptor protein on the cell surface or inside the cell

3. Signal binding changes the three-dimensional shape of the receptor and exposes its active site

4. The inactive signal transduction then becomes activated

5. The activated receptor activates a signal transduction pathway

6. Signal transduction pathway activates the cell’s response

What are allosteric changes and what are they caused by

molecules binding to a protein (like an enzyme or receptor) at a site distinct from the active site and it is caused by phosphorylation.

Signal transduction cascade of mitogen using Kinase

1. Mitogen binds to receptor

2. Phosphorylates itself

3. The activated receptor initiates a series of events that allow RAS to bind GTP and become activated

4. Activated RAS binds and activates MAP3K

5. Activated MAP3K is a protein kinase that phosphorylates many MAP2K molecules

6. Activated MAP2K is protein kinase that phosphorylates many molecules of MAP kinase

7. MAP kinase, when activated by phosphorylation can enter the nucleus

8. Cellular Response, cell division

What is the strutcure of the mitogen receptor

two dimers and two receptors which come together to activate

Signal transduction allows for cell to

• Grow

• Divide

• Survive (or not, apoptosis)

• Move

• Differentiate

What side of the receptor protein is effected by the conformation change

Cytosolic

What are the three stages of signal transduction

1. Reception: ligand binds to receptor

2. Signal Transduction: cascade of message

3. Response (cellular growth, division, movement

What are the steps of Insulin receptor

1. The alpha subunits of the receptor binds insulin (signal)

2. The conformational change in the beta subunits transmit a signal to the cytosol that insulin is present

3. Insulin binding causes autophosphorylation or tyrosines in the cytosolic region of the receptor, activating its protein kinase

4. Phosphorylates insulin-response substrates, triggering a cascade of chemical responses inside the cell

What subunit does insulin bind to

Alpha subunit

What are G-proteins

are mobile membrane proteins with three subunits (alpha, gamma, beta)

How does the g protein-linked receptor work

1. Signal binds to the G protein-linked receptor and inactive G protein has a GDP bound to it

2. Causes G protein to activate, by causing the GDP to become GTP

3. The GTP-subunit alpha separates from G protein and moves through plasma membrane until it encounter an effector protein

4. The activated G protein alphas subunit activates an effector protein which catalyzes a reaction of a cytoplasmic reactant

5. Amplification

6. GTP (hydrolyzed)

7. GDP

8. Finds gamma and beta subunit

What is glycogenolysis

How epinephrine (adrenaline) activate conversion of glycogen stored in the liver to glucose

(signal transduction)

What is glycogenin

an enzyme that acts as a primer to polymerize the first glucose molecules

Where is epinephrine made

the adrenal glands on the kidney

How is glycogen turned into glucose via Epinephrine

Epinephrine binds to a receptor on the liver, which turns a G-protein on, which will bind to GTP, the G-protein will then turn on an enzyme called adenyl cyclase, which will cause the accumulation of cAMP inside the cell (secondary messenger), which then causes a molecular cascade

What do anchor membrane proteins do

play an important role by interacting with components of the extracellular matrix

What are the Extracellular matrix (ECM) functions

1. Cell adherence

2. Cell communication

3. Cell shape

4. Filteration

5. Barrier