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2CB3 Cell Bio Exam Review

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Intermolecular forces (forces between 2 separate molecules) between hydrophobic molecules and water. The hydrophobic molecules will form in a way that will limit their interaction with water. Is not a true bond. Significant within larger biological molecules (away from water). Due to dipoles. Sensitive to the distance between 2 atoms/molecules.

Alpha helices:
- right hand coil, rod like
- hydrogen bonds parallel to polypeptide backbone
- hydrogen bonds between NH group and C=O of amino acids
- only one type and exists in a single chain
- R groups of amino acids are outside of helix
- Ex. DNA, hemoglobin

Beta Sheets:
- sheet like
- hydrogen bonds are perpendicular to polypeptide backbone
hydrogen bonds between neighbouring NH and C=O of adjacent peptide chains
- can be parallel, antiparallel or both
- R groups of amino acids are both inside and outside of sheet
- Ex. Silk

Is a neurodegenerative disorder that results in dementia, disorientation, confusion, etc. Due to mis-folding of proteins.
Amyloid hypothesis: effect in gene plaque (beta-amyloid) formed which causes signal conduction to stop
Taupathies: Tau protein enters neuron and causes plaque buildup (beta-amyloid) which sops signal conduction

Loss of heat is exothermic. Gain of heat is endothermic.

Both act as a "key" to start the reaction, will bind and activate an enzyme (inactive enzyme, no cofactor/coenzyme, is a apoenzyme). Cofactors are inorganic (metals), coenzymes are organic. Enzyme with cofactor is a holoenzyme

Compete with substate for active site. Can be overcome if there is more substrate than inhibitor.
- Increases Km without affecting Vmax
Ex. ACE inhibitor that stops angiotensin II from binding to ACE and thus will lower blood pressure

Does not bind to active site but instead binds to the allosteric site and will change the shape of the enzymes active site. Cannot be overcome with higher substrate to inhibitor ratio

Decreases Vmax without affecting Km
Ex. Tipranavir with inhibit the anti-retroviral protease inhibitor and is used for prevention and treatment of HIV

A) glycolysis since it is a BREAK down of glucose
- gluconeogenesis is the making of glucose from non carbohydrate sources

They are based on the glycolipids since they have an enzyme that adds N-acetylgalactosamine to the ends of RBC membrane glycolipids. A lack of these proteins results in the O-blood group

RBCs were treated with phospholipase. Since different lipids have different properties so each leaflet will have different properties. Responsible for the asymmetry of a membrane

can identify transmembrane segments of known amino acid sequences from integral proteins

Higher temperatures make the membrane more fluid, lower temperatures does the opposite. The more unsaturated (shorter chain) the more fluid.

The lipid is more rigid as it it is converted into a frozen crystalline gel.

The lipid content of the sample taken in the summer will be higher than the lipid content of the sample taken in the winter. In the winter the membrane will be more unsaturated, making the membrane more fluid but due to the lipids crystallizing the membrane will be more rigid. In the winter the membrane will have more double bonds to make it fluid to counteract the effects of the cooler temperature. This would be the opposite in the summer.

- Increasing the number of double bonds by desaturating single bonds, catalyzed by desaturases
- reshuffling of chains between different phospholipid molecules that to make them have 2 unsaturated fatty acids

Relies on molecular size and polarity. Smaller molecules penetrates the lipid bi-layer faster than larger ones, polar molecules (sugars and amino acids) poorly penetrate membranes, greater the lipid solubility the greater the penetration

ATP is needed for this transport to occur.
Ex. the sodium-potassium pump (ATPase) needs ATP to function and let in 2 potassium and let out 3 sodium. The ATP is phosphorylated/hydrolyzed for the diffusion to occur

Their action is terminated by re-uptake or enzymatic breakdown

Neurotransmitters can be eliminated through enzymes that will destroy the neurotransmitters in synaptic cleft and the neurotransmitter re-uptake process.
Ex. cocaine inhibits the re-uptake of dopamine in the synaptic cleft which causes a short feeling of euphoria and makes one want to repeate the activity

First step occurs in the cytoplasm and doesnt use oxygen (anaerobic). Glycolysis will produce 2 pyruvate, 2 NADH and net 2 ATP per glucose. Most of the energy is in pyruvate. ATP is produced by substrate-level phosphorylation

Holoenzyme has a cofactor while an apoenzyme does not

Are polypeptides bound to FAD and FMN which can donate 2p+ and 2e-. Major flavoproteins are NADH dehydrogenase of the ETC and succinate dehydrogenase of the TCA. They are found in the mitochondria

Contain heme prosthetic groups having Fe or Cu ions. Found in the cristae of mitochondria. Cytochrome c is a soluble protein found in the inter-membrane space and is apart of the ETC.

Also known coenzyme Q which is lipid soluble. Able to accept 2e- and 2p+

Complex I: NADH dehydrogenase, is a catalyst for the transfer of e- from NADH to ubiquinone and transports 4H+ per pair of e-

Complex II: succinate dehydrogenase, catalyst for transfer of e- from succinate to FAD to ubiquinone without H+, used in both TCA and ETC

Complex III: cytochrome bc1, catalyst for the transfer of e- from ubiquinone to cytochrome c and transports 4H+ per pair of e-

Complex IV: cytochrome c oxidase, catalyst for transfer of e- to O2 and transports 2H+ per pair of e- across inner membranes

Carries out electron transfer and proton translocation

NADH --> FMN --> 7Fe-S complexes --> UQ

Dysfunction is linked to neurological diseases

2 parts; F1 and F0
F1 is the catalytic subunit and has three catalytic sites (3 alpha, 3 beta and 1 gamma) for ATP synthase, has 5 subunits ~ 3 alpha, 2 beta, 1 delta, 1 epsilon and 1 gamma
F0 attaches to F1 and contains a channel that allows p+ to be conduced from inter-membrane space to matrix, has 3 subunits ~ 1a, 2b and 10-14c

The coupling of H+ translocation to ATP synthase

Are oxidative organelles which breakdown toxic material in cells through the presence of at least 50 digestive and oxidative enzymes. They also contain catalase (decomposes hydrogen peroxide). causes Zellweger syndrome (ZS) wich results in neurological, visual and liver issues that lead to death in infants

Contains thylakoids in stacks known as granum. Also contains enzymes responsible for carbohydrate synthesis. Also contains small double stranded DNA and ribosomes

Mg+ ion is central to chlorophyll molecules

An electron from H2O enters PSII which boosts e- from below energy level of H2O then it moves to PSI which boosts the e- to a level above NADP+. This process of flow of e- from H2O to NADPH+ is called the Z scheme

Explain the flow of e- from PSII (P680) to PSI (P700):

What is the difference between cyclic ad non-cyclic phosphorylation?

Cyclic phosphorylation:
- performed by PSI
- creates (additional) ATP
- e- source is P700
- oxygen is not produced
- photolysis does not occur

Non-cyclic phosphorylation:
- performed by PSII, bust PSI is involved
- e- source is water
- photolysis occurs
- NADPH, ATP and oxygen is produced
- is linear due to the linear movement by electrons from H2O to NADP+

$Light Reaction: * done by molecules in the thylakoid membrane * converts light energy into ATP and NADPH * splits H2O and releases O2 \ Calvin Cycle: * takes place in the stroma * uses ATP and NADPH to convert CO2 into C3P * Returns ADP, inorganic phosphate and NADP+ to the light reaction$

The C3 pathway, which is the reduction of PGA to GAP using NADPH and ATP and the regeneration of RuBP

Regulated by TIMPs (tissue inhibitor of metalloproteinases). TIMPs degrades ECM and directly inhibit ECM by proteolysis or indirect promote ECM deposition

When inactive the subunits of the integrin are in a close proximity bent state. When talin binds to the tails in the cytoplasm the alpha and beta subunits are separated and change into an upright position. This position allows for the integrin to the ECM ligands.

Rough ER: studded with ribosomes and produces proteins, attached to the nuclear envelope
Smooth ER: no ribosomes, produces steroids, hormones and lipids, also associated with metabolism and detoxification, found inn kidney tubule and skeletal muscles

$1. Autoradiography: helps to visualize biochemical process using radiolabeled materials 2. GFP based protein tracking: uses Green Florescence Protein (isolated from jelly fish, emits florescence light) to form a GFP-DNA chimera that can help observe the protein synthesis and movement in a cell. Can be also used to study protein traffic in viral genes 3. Biochemical analysis of subcellular fractions: uses centrifugation to separate fractions and then study them 4. Use of cell free systems: doesnt use cells just studies organelle 5. Utility of genetic mutants: take a gene and see how mutant functions$

- moves material from ER forward to the ERGIC and golgi complex
- anterograde transport

The physical properties of the proteins is the main reason that resident molecules in retention are left out of transport vesicles
Ex. Soluble lumen protein in the ER and membrane proteins with short transmembrane domain are excluded from transport vesicles

Each membrane protein has a retrieval signal (short amino acid sequence at C terminal) that makes sure they get sent back to the ER if they by mistake go to the ERGIC or golgi.
Retrieval signal is KDEL

- during this process an organelle is surrounded by a double membrane structure which produces an autophagosome. This is then fused with a lysosome to make an autophagolysosme. This is digested and leaves a residual body that can leave the cell