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208 Cards in this Set

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What is a pseudo-first order reaction?

What does the rate of reaction look like?
There are two substrates but only one of them is rate limiting.

V = k * [A]
Name the classes of enzymes and their function.
LIL HOT

Ligase: join two molecules together

Isomerase: cause intramolecular rearrangement

Lyase: remove a group from or add a group to a double bond

Hydrolase: cause hyrdolytic cleavage

Oxidoreductase: cause oxidation-reduction reactions

Transferase: transfer functional group from one molecule to another
Write the standard and actual free energy change.
G = G' + RT Ln ([Prod]/[React])

G' = -2.303 RT Log Keq
What is the difference between an apoenzyme, holoenzyme, cofactor, and coenzyme?
Apoenzyme: protein portion of a conjugated enzyme

Holoenzyme: the native, complete, enzyme

Cofactor: the non-protein portion of a conjugated enzyme

Coenzyme: an organic cofactor
What are the functions of coenzymes?
* Accomplish goals that a.a side chains cannot

* Most notable use of coenzymes are in REDUCTIONS/OXIDATIONS
Why does ATP (and ADP) have large negative free energy?
* Electrostatic repulsion

* Stabilization of products by ionization and resonance
What are the two models of binding at an enzyme's active site?
* Lock and key model

* Fit-induced model
What is the equation for describing the reaction velocity of an enzyme reaction?

Please state in terms of Vmax, Km, [S], and v.
v = (Vmax * [S]) / (Km + [S])
What is Kcat?

Write the formula.
The turnover number - the max number of substrate molecules converted to product per enzyme molecule per unit of time.

Kcat = Vmax / Et
What is Et in a reaction order equation?
Et = [ES] + [E]free
What is catalytic perfection?
Kcat = k1 * Km
Kcat / Km = k1
What is Kcat/Km?
It measures how the enzyme performs when S is low -- it describes an enzymes preference for different substrates.
Describe the following forms of inhibition.

Competitive
Non-competitive
Uncompetitive
Irreversible
Competitive: the inhibitor competes with the substrate for binding to the enzyme, that is, inhibitor and substrate can not bind to the enzyme at the same time.
Note that contrary to what is stated in many textbooks, this does not necessarily mean that binding is to the active site. If binding of the inhibitor changes the conformation of
the enzyme so that no substrate binding is possible and vice versa, typical competitive inhibition will be observed.

Increases the apparent Km while leaving the Vmax unchanged


Non-competitive: inhibitor and substrate can be bound to the enzyme at
the same time, thus the inhibitor must bind to a site distinct from the substrate binding
site. If the inhibitor binds equally well to the free enzyme and the enzyme-substrate
complex, Km remains unchanged but Vmax is reduced.


Uncompetitive: the inhibitor binds only to the enzyme-substrate complex
but not the free enzyme.

This type of inhibition reduces both Km and Vmax .


Irreversible: the inactivator forms a stable bond (often but not necessar-
ily covalent) with the enzyme protein, frequently in the active site. In the body,
inactivation can be overcome only by the synthesis of new enzyme.
Name a compound that inactivates enzymes.
Organosphosphate compounds are used as pesticides and nerve gases. They react con-
valently with a serine residue in the active site of acetylcholinesterase, the enzyme that
destroys the neurotransmitter acetylcholine at cholinergic synapses.
Allosteric enzymes follow this type of kinetics.
Sigmoidal
Do allosteric enzymes follow MM kinetcis?
No.
Describe covalent modification as it relates to allosteric regulation.
* Covalent modification is slower than allosteric regulation

* It is reversible

* Requires one enzyme for activation and one for deactivation

* Freezes enzyme in Tense or Relaxed conformation
Name the most common form of covalent modification.
Phosphotylation / dephosphorylation
Which enzyme attacks the bacterial cell walls and where can it be found in the human body?
Lysozyme is found in tears, saliva, and nasal secretions.

Bacterial cell wall has NAM-NAG repeats which these enzyme breaks.
Which enzyme is found in the digestive system?

What is unique about it?
Chymotrypsin

It is a serine protease
Describe serine proteases.
By definition they have a catalytic center of SERINE, HISTIDINE, and ASPARTIC ACID.

The only a.a. to accept and donate protons in a serine protease is HISTIDINE.

The SERINE forms a transient covalent bond with carboxyl, metallo, or thiol groups.
Describe both Km and Ki separately and in relation to one another.
Km is the concentration at which half of the substrate is bound to an enzyme.

Ki is the concentration at which half of the inhibitor is bound to an enzyme.

If Ki >> Km, then you will require more Km to overcome the inhibitor.
Describe achirality and chirality.

Which is associated with molecular symmetry and superimposability and which isn't?
Chirality: non-superimposable mirror images (e.g. socks) or have four different groups attached to the tetrahedral carbon atom

Achirality: superimposable mirror images (e.g. gloves, golf club) or if any of the groups attached to the tetrahedral carbon atom are the same.
True or False.

Enantiomers only differ in the way they rotate polarized light.
True
The chirality of stereospecific biomolecules is important because _________________
Chiral molecules have different functions, different specificities when dealing with other molecules/receptors
What is a stereogenic center?
A stereogenic center is also known as a chiral center. It is characterized by an atom which has different groups bound to it in such a manner that its mirror image is non-superimposable.
The bicarbonate blood buffer in a normal adult maintains the blood pH at what value?
7.4
Acidity is usually expressed in terms of what?

What is the formula for expressing acidity when given Ka?
pKa

pKa = - log Ka
Write the formula for Ka.
Ka = [A-] * [H30+] / [HA]
Write the formula for Kb (dissociation constant for base).
Kb = [B+] * [OH-] / [BOH]
Write the henderson-hasselbach equation.
pH = pKa + log ([A-]/[HA])
What are buffers?
Aqueous systems that resist changes in pH when small amounts of strong acid or base are added.
A buffered system consists of what?
a weak acid and its conjugate base
Buffers are effective at pHs that are within what pH unit of the pKa?
+/- 1
Primordial germ cells are found in which structure?
Wall of the yolk sac
Germs cells undergo 2 meiotic divisions. Give their names and what is actually being separated at each step.
Reduction division: separation of homologous chromosomes

Equitational divsion: separation of sister chromatids
Name the 5 phases of prophase I.
MNEMOMIC: (The) Product of Led ZePellin's Disjunctional and Disappearing (Tour)

Leptotene: condensation of chromatin, sister chromatids become connected

Zygotene: Synapsis of homologous chromosomes

Pachytene: Crossing-over of chromatids

Diplotene: Disjunction between homologous chromosomes occurs, chiasmata appear

Diakinesis: Nucleolus disappears and nuclear membrane disappears
Why is meiosis significant for genetic viability?
1. Constancy for chromosome number

2. Independent assortment of maternal and paternal chromosomes

3. Crossing over of genes
What disturbance can occur during meiosis I?

What prominent disease do this disturbance create?
Non-disjunction at either meiosis I or II

Non-disjunction creates Down's syndrome among other diseases
Name the steps for the formation of spermatozoa.
MNEMONIC: Sperm GOATZ

SpermatoGONIA (G)
SpermatOCYTE (O)
SpermATIDS (AT)
SpermatoZOA (Z)
The process of transformation from spermatoGONIA to spermatoZOA takes how long?
64 days
Before birth all primary occytes in primordial follicles are arrested at this stage.

What inhibitor causes this to occur and what cells secrete this inhibitor?
Diplotene stage of Prophase I.

Caused by OMI released by the follicular cells in primordial follicles.
What is atresia?
Atresia is the death of oocytes between the 5th month of fetal development until puberty.
Name the two layers of the endometrium.
Basal and functional layer
Which layer of the endometrium is removed during menstruation?
Functional layer
In order of first to last, name the arteries and branches of the endometrium as they emerge from the basal layer.
* Uterine artery
+ Arcuate artery
+ Radial branch
- Straight artery
- Spiral artery
Which artery and gland will re-grow after each menstruation period?
Spiral artery and uterine gland
How long are the sperm and egg viable?
Sperm: 48 hours
Egg: 24 hours
One a separate piece of paper draw the female reproductive cycle starting with hormone release to follicle growth to LH/FSH release and ending with fertilization of the egg
See diagram
How large is the primordial follicle, multilaminar primary follicle, and graafian follicle?
primordial: 25 microns
primary: 150 microns
graafian: 2.5 cm
If the egg is fertilized, it becomes a blastocyst. During this period, this layer of cells releases a hormone that keeps the corpus luteum from degrading.
Syncytiotrophoblast releases HcG
Which cells of the secondary follicle release androstenedione?

What happens to this hormone once it is secreted?
Theca interna cells release androstenedione and as it diffuses past the basal membrane the granulosa cells convert it to estrogen
Steroid secreting cells have three types of features. Name them.
1. Lots of SER
2. Mitochondria with tubular cristae
3. Lots of lipid vesicles
In order for the sperm to pass through the zona radiata, this must first occur.
Capacitation of the sperm
The acrosomal reaction of sperm allows it to penetrate the zona pellucida. What enzymes are released?
Acrosin, neuro amidase, enterase
Polyspermy is prevented through the action of these two block.
Fast block: depolarization of PM

Slow block: cortical reaction cause Ca++ release from stores in the egg and thus triggering cortical granules to migrate to the PM
In order to get through the zona radiata, this enzyme is used to break down the radiata cells. Name it.
Hyaluronidase of sperm cleaves hyaluronic acid between radiata cells
What is the general formula for carbohydrates?
Cx(H20)y
What is van't Hoff's rule?
# of stereoisomers = 2^n

For example, if we have 4 stereogenic centers then we have 16 stereoisomers
What is an epimer?
One of two optical isomers that differ from each other only in the configuration about one asymmetric carbon atom
Do carbohydrates have D or L configuration?
D configuration
Benedict's and Tollens' reagents reduce sugars. Which specific feature of a sugar allows for this to happen?
The hemiacetal linkage
Do carbohydrates with acetal groups react with benedict's and tollen's reagents?
No
Carbohydrates with hemiactel groups are called ____________
Reducing sugars
What is mutarotation?
The term is given to the change in the specific rotation of plane polarized light, when it is passed through an aldohexose.

Mutarotation refers to the conversion of a pure anomer of a hemiacetal carbohydrate to an equilibrium mixture of two anomers (alpha and beta).
What is an anomer?
Two stereoisomers (alpha and beta) of a given sugar that differ only in the configuration about the carbonyl carbon atom.

alpha if the hydroxyl group is below the sugar

beta if the hydroxyl group is above the sugar
Describe sucrose in terms of

* Disaccharides
* Linkage
* Reducing/non-reducing
* Glucose and fructose
* Alpha 1, beta 2
* Non-reducing
Describe maltose in terms of

* Disaccharides
* Linkage
* Reducing/non-reducing
* Glucose only
* alpha 1,4
* Reducing due to hemiacetal moiety on second glucose
Describe cellobiose in terms of

* Disaccharides
* Linkage
* Reducing/non-reducing
* Glucose only
* beta 1,4
* Reducing due to hemiacetal moiety on second glucose
A glucan is made of only ____________
Glucose units
What are three types of glucans?
* Glycogen
* Starch (Amylose/Amylopectin)
* Cellulose
Describe starch in terms of

* Different forms of starch
* Linkage
* Branching
* Amylose and Amylopectin
* Alpha 1,4 for both
* Only amylopectin has branching and it occurs at alpha 1,6 (crosslink)
What is important about branching in starch?
* The more branches, the more sites for phosphorylase attack

* Branches provide a mechanism for quickly releasing glucose units
Describe glucose in terms of

* Linkage
* Branching
* Storage
* Alpha 1,4
* Alpha 1,6 branching
* Stored in liver and muscles
Describe cellulose in terms of

* Linkage
* Branching
* Can humans digest cellulose?
* Beta 1,4
* No branching, just rigid and insoluble fibers
* Humans cannot digest cellulose as we lack the enzymes to digest beta linkages
Biological systems only synthesize and use this type of amino acid. L or D?
L
What is the isoelectric point?

What does the formula look like if the side chain is neutral, acidic, or basic?
The isoelectric point (pI) is the pH at which a molecule or surface carries no net electrical charge. In order to have a sharp isoelectric point, a molecule (or surface) must be amphoteric, meaning it must have both acidic and basic functional groups.

pI = pKa (C) + pKa (N) / 2 [neutral]

pI = pKa (C) + pKa (C side chain) / 2 [acidic]

pI = pKa (C) + pKa (N side chain) / 2 [basic]
What is a zwitterion?
It is a chemical compound that is electrically neutral but carries formal positive and negative charges on different atoms
When a peptide bond forms between two amino acids, what is lost?
H2O
When reading a peptide chain, where do we start to read from?
N terminal end
What determines the overall charge of a peptide?
The side chain
What is the primary structure?
The sequence of amino acids in a peptide or polypeptide starting at the N-terminal end and going to the C-terminal end
What are some common post-translational modifications of the primary structure of a.a.?
* Hydroxylation (proline, lysine)
* Addition of Pi onto ser, thr
* Addition of sugars to give glycoproteins
Describe the peptide bond.
It has partial double bond character, is planar, and shorter than a regular C-C bond

As a result, it cannot rotate freely in space
What is the secondary structure of an a.a.?
The three dimensional shape of a protein chain that result from hydrogen bonding between peptide bonds on the polypeptide chain

Can take the form of either alpha-helix (keratin) or beta-pleated sheet (silk)
In a right handed alpha helix, how many residues are there per turn, what is the rise per residue, and what is the rise per turn?
3.6 residues per turn
1.5 angstroms rise per residue
5.4 angstroms rise per turn
IMPORTANT!

Which amino acids are disrupters in the polypeptide chain?
MNEMONIC: SAGA VIP

* Proline (No H on N for H-bonding)

* Glycine (too much free rotation)

* Ser, Asp, Asn (interfering H-bonds)

* Ile, Val (steric effect)
In a beta pleated sheet, which is more stable: anti-parallel or parallel arrangement of chains?
Anti-parallel
What is the tertiary structure of an a.a.?
The folding of the total chain, the combination of the elements of secondary structure linked by turns and loops.

IMPORTANT: The primary structure determines its tertiary structure
What are five types of tertiary interactions/bond?
* Hydrophobic forces
* Van der waals interactions
* H-bonding
* Ionic bonds (salt linkages)
* Disulfide linkages
What is the quartenary structure of a.a.?
Organization of multiple chain associations.

Can be with self (homo) or different (hetero) oligmers
What are the three types of quarternary interactions?
* Electrostatic charges
* Hydrogen bonds
* Hydrophobic interactions
What are two ways of binding sugars to proteins?
1. O-glycosidic bonds using hydroxyl groups of serine and threonine. (GOLGI)

2. N-glycosidic bonds using side chain amide nitrogen of asparagine. (RER)
Contrast fibrous and globular proteins.
Fibrous:

1. long strands
2. water insoluble
3. strong but flexible
4. structural (keratin, collagen)


Globular:

1. spherical / globular form
2. water soluble
3. several types of secondary structure
4. diverse function (enzymes, regulatory proteins)
What is the definition of a Prion?
Proteinaceous Infectious Particles

PrPc (normal) vs. PrPsc (scrapie)
What are the two major types of protein folding problems?

Name a few examples of each.
Prions and Amyloid formation

Prions: MAD cow, CJD, nvCJD, KURU

Amyloid: Alzeihmers, Parkinsons
What is common to both Prions and Amyloids in terms of symptoms and progression?
1. Self replicating
2. Long latency period between exposure to disease agent and clinical disease
3. Rapid progression of neurological dysfunction
4. Spongy degeneration of brain tissue
What is a major difference in the polypeptide structure of PrPsc when compared to PrPc?
PrPsc's secondary structure is dominated by beta conformations where as PrPc was dominated by alpha helices
As a protein, PrPsc is different from PrPc in that:
1. Insoluble in all but strongest solvents

2. Highly resistant to digestion by proteases

3. Extremely resistant to heat, sunlight, and normal sterilization processes

4. No detectable immune response
How is a Prion replicated in a laboratory setting?
See http://w3.aces.uiuc.edu/AnSci/BSE/Figures/PMCA_Assay_3D_100_8bit.gif


Steps:

1. Incubate PrPc with PrPsc (100:1 ratio)

2. Sonicate and thus disrupt the aggregate

3. Re-incubate (repeat steps 2 and 3)

[ NOW CONTAINS MOSTLY PrPsc PROTEINS ]

4. Digest with PKK and analyze with gel electrophoresis

5. Banding pattern is suggestive of presence and possibly the strain of TSE in the test sample.
Antibiotics kill bacteria by targeting _________
1. Bacterial enzymes that have no eukaryotic counterpart or are dissimilar enough from their eukaryotic counterparts
With regards to ribosomes, why might you feel a little sick or lacking energy when taking certain antibiotics?
Mitochondrial ribosomes are similar to bacterial ribosomes and as such small concentrations of antibiotics diffuse through the plasma membrane and inhibit ATP production
Name the components of a phospholipid.
* Glycerol backbone
* Two long, non-polar fatty acid chains
* Phosphate containing polar group
Which types of phospholipids will you find on the extracellular surface of the plasma membrane?

Which will you find in the cystosolic side of the plasma membrane?
Extracellular: choline containing phospholipids

Cystosolic: non-choline containing phospholipids
What are two choline containing phospholipids?

What are three non-choline containing phospholipids?
Choline: phosphotidylcholine, shpingomyelin

Non-choline: phopshpotidyl-
serine/ethanolamine/inositol
Due to phosphotidylserine being located on the cystosolic side of the plasma membrane, it contributes this to the charge?
Negative charge
Embedded membrane proteins can be visualized by this technique.

Describe the results in detail.
Freeze fracture allows the proteins to be viewed because the interface between the fatty acid tails is the weakest point in the membrane.

- The P face is closer to the protopolasm, the E face is closer to the extracellular space
Which increases membrane fluidity of the plasma membrane, saturated or unsaturated fatty acyl tails?

Why?
Unsaturated tails do because the cis double bond causes a bend in the tail

- Allows phospholipids to stay further apart and be more fluid
Does cholesterol increase or decrease fluidity?
Decrease
Why does detergent disrupt the phospholipid bilayer?
1. Contains charged head group and hydrophobic tail that penetrate the bilayer and disrupting protein attachment
Where are carbohydrates (and by relation glycoproteins and glycolipids) found?
On the outer leaflet of the plasma membrane
Which of the following is NOT an organelle?

Mitochondrion
Lysosome
Peroxisome
Proteosome
Golgi appartus
Proteosome
Name four ways of restricting the lateral mobility of membrane proteins.
1. Protein self-assemble into large aggregates

2. Tethered by interactions with macromolecules on outside

3. And inside of cell

4. Interact with proteins on the surface of another cell
True or False.

The smaller the molecule and the less strongly it associates with water, the more rapidly the molecule diffuses across the bilayer.
True
Name the six major types of intermediate filaments and the cell type each is found in.
* Keratins - Epithelium
* Vimentin - Mesenchymal cells
* Desmin - Muscle
* Glial fibrillary acidic proteins - Glial cells
* Neurofilaments - Neurons
* Nuclear Lamina - Found in all cells
What is the function of the nuclear lamins?
They line the nuclear envelope and as such are intimately involved in its assembly
Describe the organization of a microtubule in terms of:

* Alpha, beta, gamma tubulin
* Which tubulin is closest to the negative (-) end and which to the positive (+) end?
* How are GDP and GTP involved?
* Which end is growing and shrinking dynamically?
Gamma tubulin initiates MT growth at the negative end towards the positive.

Alpha and beta tubulin form a heterodimer before attaching to the microtubule. The alpha tubulin points in the negative direction while the beta tubulin points in the positive.
What is the process by which microtubules grow and shrink rapidly from the center of the MTOC?
Dynamic instabiliy
The basal body of cilium and flagellum has this configuration in contrast to the body?
Basal: nine triplets of MT

Body: nine doublets of MT
True or False.

The nine double MTs of a cilium or flagellum grow out of the nine triplet MTs of the basal body.
True
Microtubule sliding of the cilium or flagellum is made possible by this motor.
Dynein motor
Describe actin filament formation in terms of:

* + and - ends
* G-actin and F-actin
* GDP and GTP
Actin cycles between an unassembled state (G-actin bound with GDP) and assembled state (G-actin bound with GTP bind to actin filament)

Actin subunits add on the + end and fall off (or add more slowly) on the - end.
What is treadmilling?
* Actin bound to ATP associates with the plus end of the filament.

* ATP bound to actin is hydrolyzed to ADP.

* Actin bound to ADP dissociates from the minus end of the filament.

These steps repeat, causing the plus end of the filament to grow and the minus end to shrink.
Why is spectrin important in forming actin networks?
Spectrin is an actin-binding protein that helps to form the supporting network of the plasma membrane of RBC
Which drugs affect the actin network?
Phalloidin, Cytochalasin
Which drugs affect the MT network?
Taxol, Vinblastine, Colchicine
Which intermediate filaments provides (1) support for the nuclear membrane, (2) helps attach chromatin to the nuclear envelope, and (3) controls disassembly of nuclear envelope during mitosis?
Nuclear Lamina
The nucleolus is where ________ are synthesized.
rRNA subunits
What is heterochromatin?
What is euchromatin?
Heterochromatin is highly condensed DNA that is transcriptionally inactive

Euchromatin is less condensed DNA that is transcriptionally active
What is the basic unit of DNA packaging?

What does it consist of?
Nucleosome

Core histones (H2A, H2B, H3, H4) and DNA make up the nucleosome
What charge is attributed to histones?
Positive
The movement of macromolecules including ribosomal subunits, RNA strands, and proteins between the nucleus and cytoplasm occurs through _________________
Nuclear Pore Complexes (NPC)
What is a targeting signal?
It is a signal that allows the cargo to pass through the Nuclear Pore Complex and enter the nucleus
What are two ways in which a sorting signal can be built into a protein?
1. The signal resides in a single discrete stretch of amino acid sequence

2. The signal can be formed by the juxtaposition of amino acids from regions that are physically separated before the protein folds
What are the two types of nuclear targeting signals?

What types of amino acid do each of the signals contain?
1. NLS (nuclear localizing signal)
- Basic amino acids

2. NES (nuclear export signal)
- Hydrophobic amino acids
What are two types of nuclear carriers?
* Importins

* Exportins
If nuclear proteins contain more than 1 NLS, what advantage does it confer?
* Increases affinity for NLS receptor

* Increases rate of nuclear entry
Having delivered their cargo, do exportins and importins recycle back?
Yes
Unlike importins, exports have this small GTPase macromolecule that aids in regulating cargo binding and release
That GTPase is called Ran
Do viruses (like HIV and SV40) contain NLSs and NESs on their proteins and viral mRNAs?
Yes
For each glucose that enters the mitchondrion, how many ATP molecules are produced?
36 ATP
Most of the encoded mitochondriol proteins are encoded by the nuclear genome, they are then imported into the mitochondria:

* Pre-transcriptionally
* Post-transcriptionally
* Pre-translationally
* Post-translationally
Post-translationally
Transmembrane proteins called porins are open channels that allow the contents of the cytosol to resemble that of the

* Outer membrane
* Inner membrane
* Matrix
* Intermembrane
* Cristae
Intermembrane
Where is the mitochondrial DNA located?
In the matrix
Is the matrix of the mitochondrial membrane basic or acidic? Why?
It is basic when compared to the intermembrane space because the electron transport chain exports most, if not all, of the H+ ions.
What are the three main steps for producing ATP?
1. Oxidation of pyruvate and fatty acids in the matrix creates Acetyl CoA

- Transfer of protons to electron carriers (NAD+, FAD2+)

2. Electrons from electron carriers transferred via four electron transport complexes to oxygen

- Concomitantly, H+ ions are transported from the matrix to intermembrane space == creation of PROTON MOTIVE FORCE

3. Protons flow back into the matrix space through ATP synthase

- Energy is used from proton flow to couple Pi to ADP and create ATP

- ATP transported outside mitochondria
What is cardiolipin?

Where is it found?

What is its function?
Cardiolipin is a "double" phospholipid that contains 1 polar head group, 2 phosphate groups, and 4 tails

It is mainly found in the mitochondrial inner membrane

It serves as an insulator and stabilizes the activity of protein complexes important to the electron transport chain
What are peroxisomes?

What is catalase?
Peroxisomes are membrane bound organelles that contain enzymes that use molecular oxygen

Oxygen is used to remove hydrogen atoms from specific organic substrates in an oxidate reaction that produces HYDROGEN PEROXIDE

Catalase is a peroxisomal enzyme that utilizes hydrogen peroxide to oxidize other substrates
What are two functions of peroxisomes?
1. Rid body of toxic substances like hydrogen peroxide, phenols, formic acid, alcohol

2. Breakdown fatty acid molecules in a process called BETA OXIDATION

- Convert fatty acids to Acetyl CoA (remove two carbon atoms)
Where are peroxisomes most numerous?
Liver
What are two ways in which new peroxisomes can be created?
1. Division of pre-existing peroxisomes

2. De Novo formation

- pre-peroxisome membrane vesicles bud off from ER

- new synthesized peroxisomal proteins are imported from the cytoplasm into the pre-peroxisome

- peroxisome is created
What is Zellweger's syndrome?
It is an inherited genetic disease where the peroxisome have a defect in importing peroxisomal proteins.

This leads to "empty" peroxisomes and eventually quick death
Ubiquin and ubiquination occur in this component.
Proteosome
Where in a protein can one find the signal for ubiquination?
In a properly folded protein, this signal is hidden

In a old or degraded protein, this signal is exposed to the cytoplasm
These types of molecules aid in protein folding and prevent aggregation of unfolded proteins.

Name two.
Chaperones

HSP70 and GroEL family
The smooth ER synthesizes these major class of macromolecules.
* Phospholipids
* Cholesterol
* Steroids
In what ways are the lipids synthesized on the smooth ER able to reach other membranes?
1. By vesicles that bud off and fuse with other membranes

2. Diffuse to the rough ER

3. By transfer proteins that take lipids to organelles that don't receive vesicle traffic from the ER
The ER in general has an important function in sequestering ______________
Intracellular Ca++
This particle binds to the growing polypeptide chain because it recognizes the ER signal.
Signal recognition particle (SRP)
These signal sequences aid in threading an integral protein within the lipid bilayer.
Stop tranfer and start transfer sequences
As a protein enters the ER lumen, it can be modified in the following ways:
1. N-terminal signal peptides are cleaved by signal peptidase

2. Proteins receive N-linked glycosylation

3. Formation of disulfide bonds

4. (Some) proteins lose transmembrane domain and gain a GPI anchor

5. Chaperones aid in folding which is necessary for exit from ER
Name a HSP70 homolog that is abundant in the ER lumen.
BIP
If a protein is not correctly folded in the ER, what happens to it?
It is exported out of the ER where ubiquitin attaches to the ubiquitin signal region of the misfolded protein.

The protein then enters the proteosome where it is degraded
Why does Cystic Fibrosis occur?
CF occurs because the mutant form of the CFTR protein misfolds and as a result does not reach the plasma membrane. Instead, the protein is degraded by the proteosomes.
What are the three types of coat proteins used in vesicular traffic?

What are their functions?
1. COP I
- Mediates retrograde transport from the trans to medial to cis Golgi

2. COP II
- Mediates transfer of vesicles from rough ER to cis Golgi
- In some cases, COP II coates vesicles fuse to form larger intermediate compartments that are transported along MT and eventually fuse with cis Golgi

3. Clathrin
- Mediates transfer of vesicles that bud from the trans Golgi and the plasma membrane and then fuse with late endosomes
What four types of machinery proteins are used in vesicle docking and fusion?
* SNARES (T and V form)

* SNAPS

* Rabs

* NSF
Where are glycolipids formed?
Golgi appartus
As proteins move through the secretory pathway, what happens to it?
1. N-linked carbohydrate is added to the protein (ER)

2. N-linked carbohydrate is removed from the protein (GOLGI)

3. O-linked carbohydrate is added to the serine or threonine amino acid (GOLGI)
What is the carbohydrate group is added to glycolipids or glycoproteins?
Sialic acid (otherwise known as NANA)

- It is the only carbohydrate that has a negative charge
What are the three pathways that a protein or enzyme or lipid will take to get to its destination? (From ER to Golgo to ...)
* To plasma membrane

* Signal mediated diversion to lysosomes

* Signal mediated diversion to secretory vesicles
What will cause the release of secretory vesicles stored in the cytoskeleton to the plasma membrane?
Ca++
What is the signal for targeting a protein to lysosomes?
Mannose-6-phosphate (M6P)
Where is the lysosome targeting signal added?
On the cis Golgi
Name two types of "eat me" signals for phagocytosis?
1. Soluble chemoattractants released by bacteria that the phagocytosing cells have receptors for

2. Antibody activated phagocytosis (IgG antibody coat surface)
Which antibody coats the surface of bacteria and damaged cells?
IgG
What are clathrin coated pits?
The assembly of the clathrin molecules on the pit appears to drive the pit to invaginate. This cage-like molecule may help stabilize the vesicle as it buds from the membrane.

Clathrin coated pits may move in the plane of the membrane.
How many different types of receptors can be internalized in the same coated pit?
Many (> 30)
Describe the process of receptor mediated endocytosis.
* Certain membrane receptors cluster in the clathrin-coated pits

* Ligands are bound to the receptors

* Together they are internalized by the cell when the vesicle pinches off

* The vesicle fuses with early endosome and is later passed onto the lysosome for processing

* The clathrin cycles back up to the plasma membrane
What is one important molecule internalized by receptor mediated endocytosis?
LDL receptor and cholesterol ligand
If the LDL receptor is not internalized by receptor mediated endocytosis, what occurs?
High serum cholesterol because LDL provides a critical mechanism for reducing cholesterol levels and getting it into cells
What specific proteins aids in the binding of both clathrin and the cytoplasmic tail of the LDL receptors?
Adaptins
What occurs if the adaptins proteins are defective in LDL receptor mediated endocytosis?
High serum cholesterol
The endosomal compartments act as a _____________ similar to the Golgi network.
Main sorting station
What causes the receptors in the endosome to release their ligands?

At which stage of the endosome does this occur?
Low pH (< 6) allows the receptors to be recycled back to the plasma membrane

Early endosome stage
Describe the transferrin cycle.
* Apotransferrin and tranferrin receptor associate together at the extracellular surface

* Create a ferrotransferrin complex

* The complex bind iron atoms

* The iron is released at the late endosome stage due to low pH

* The complex recycles back to the extracellular surface where the high pH causes apotransferrin and transferrin receptor to dissociate
What is the difference between primary and secondary lysosomes?
Primary lysosome is the cytoplasmic cell organelle that buds off from the golgi complex

Secondary lysosome stage is achieved when it fuses with vesicles that contain matter to be ingested
What are the three pathways to degradation in lysosomes?
* Phagocytosis

* Endocytosis

* Autophagy
Hydrolytic breakdown of vesicle contents in lysosomes produce these debris filled vacuoles.

What are they called in neurons?

What is their significance?
Residual bodies

Lipofuscin granules

They are an important barometer of cell aging
The creation and maintenance of caveolae requires this protein.
Caveolin
What are caveolae?
Caveolae are one source of clathrin-independent endocytosis involved in turnover of adhesive complexes
What are the three functions of caveolae?
1. Concentrate substances from the EC space and move them into the cytosol

2. Transport material across cells by transcytosis (caveolae abundant in endothelial cells)

3. Concentration of signalling molecules
What are the two major cell cylce checkpoints (mitosis)?
* G1 checkpoint

* G2 checkpoint
How long does each of the following phases of mitosis take?

G1
S
G2 + M
G1: 25 hours
S: 8 hours
G2: 2.5 - 3 hours
What role do cohesin and condensin play in mitosis?
Cohesin: cross-links two adjacent sister chromatids - gluing them together

Condensin: cross-link coiled DNA in the process of chromosome condensation
What is taxol?

What does it target?
Taxol is an ant-mitotic drug that targets MT

* Taxol bind to MTs and stabilizes them

* Spindle cannot form, this arrests the cell at mitosis

* Cells undergo apoptosis
Of the two types of cell death, which one causes damage?
Necrosis
What are some of the features of necrosis?
* Cell swells and bursts

* Loss of plasma membrane integrity

* Spilling of cellular contents
True or false.

Necrosis can be due to ischemia
True
Ischemia results in:

(think in terms of mitochondria)
* Decreased ATP
- Increased cytosolic Ca++
- Increased anaerobic glycolysis, increased lactic acid, decreased pH
- Decreased action of Na+/K+ pump == increased intracellular Na+
What distinguishes apoptosis from necrosis?
In apoptosis, phagocytosis occurs on the targeted cell where:

* No leakage of cellular contents occurs

* No inflammation

* Cell death is imperceptible to the organism
In what ways can apoptosis be triggered?
1. Withdrawal of positive ("live") signals

2. Receipt of negative ("death") signals

3. Interplay of both positive and negative signals
Which signals can cause a cell to enter apoptosis?
BLC2 family of proteins [REGULATORS]

Caspases [EFFECTORS]
What is the BCL2 family of regulators?
It contains both pro and anti apoptotic members that regulate one another' activities through heterodimerization

Depending on the ratio of the pro and anti members, the cell can either live or die
What are the caspases family of EXECUTORS?
These are the executionary arm of the apoptotic machinery.

These proteases cleave critical proteins leading to apoptosis
How is activation of apoptosis achieved from inside the cell?
Release of cytochrome c from the intermembrane of the mitochondria
What mitigates the release of cytochrome c from the mitochondria?
BCL2 family of regulators
What is the "eat me" signal on apoptotic cells that attracts phagocytic cells?
Phosphotidylserine

Through the efforts of "scramblase", phosphotidylserine is flipped from the cytolsolic to EC space. Phagocytic cells have a receptor for it
What is Tay-Sachs disease?
It results from the absence of hexoaminidase A which breaks down glycolipids in the lysosomes

Histologic examination shows that neurons are ballooned with cytoplasmic vacuoles
-> distended lysosome
-> progressive destruction of neurons