Biochem Exam 1 Review / Hard questions

What is the pH equation?

What is the pH equation?

pH = -log[H+]

What is the Henderson-Hasselbalch equation(s)?

pH = pKa + log([A-]/[HA])

[A-]/[HA] = 10^(pH-pKa)

What disease is caused by DNA replication problems?

Huntington’s disease is caused by trinucleotide expansion during DNA replication, a similar problem occurs in a gene in FTD/ALS.

Describe CRISPR/Cas9 genome editing.

Cas9 binds gRNA to the desired sequence and makes a double strand DNA break. This can lead to deletions or insertions or it can be used to add donor DNA into a system.

What is the structure and function of mRNA?

Has a 5’ cap and a poly A tail (allows RNA to be amplified witha poly T primer). It is modified during transcription.

What is the structure and function of tRNA?

It has an anti-codon end that recognizes the codon in mRNA, and has an amino acid attachment site that picks up amino acids, this is necessary for translation. Looks like a clover.

What fatty acids are essential and why?

Omega 6: linoleate and arachidonate and Omega 3: linolenate. Body does not naturally produce sufficient amounts for all processes, must be consumed in diet, synthesis of eicosanoids (20+ carbon FAs), synthesis of endocannabinoids (neurological function, mood regulation), lipid raft formation, act to activate transcription factors in the nucleus.

What is the effect of aspirin on arachidonic acid?

Aspirin blocks the action of enzyme COX-1, which leads to less arachidonic acid being converted into pro-inflammatory prostaglandin D2. Aspirin promotes the activity of COX-2 which makes anti-inflammatory compounds.

What is the structure of triglycerides and how it is converted?

A glycerol attached to 3 fatty acids. Lipase secreted by the pancreas does hydrolysis to convert the triglycerol into fatty acids and monoacylglycerol, which are then absorbed into the intestine.

What does degradation of phosphoglycerides?

Phospholipases, different kinds cleave different bonds. Phospholipase C yields diacylglycerol (DAG) which is a signaling molecule that activates protein kinase C (PKC). Phospholipase A is present in insect and snake venom, can cause inflammation and pain.

What are sphingolipids?

Has sphingosine backbone with sphingosine fatty acid tail and a fatty acid attached. Unlike glycerol, sphingosine already has a saturated fatty acid tail and one of the OH groups instead is an amino group.

What are ceramides?

Waxy sphingolipids with an additional fatty acid chain attached on the amine bond.

What are differences between omega 3 and 6?

Omega 3 stimulates the transcription of anti-inflammatory genes. Omega 6 is involved in endocannabinoid synthesis. Arachidonic acid derived by omega 3 leads to anti-inflammatory eicosanoids, but when derived from omega 6 leads to proinflammatory eicosanoids.

How are sphingolipids used in cellular signaling?

Ceramides create cell death-inducing signals, ceramidase uses hydrolysis to remove a fatty acid turning it into sphingosine, sphingosine kinase phosphorylates sphingosine using ATP, which results in sphingosine 1-phosphate which is involved in sending pro-mitotic signals. In cancer cells sphingosine kinase is upregulated to send more pro-mitotic signals.

What is the most common phospholipid found in cell membranes?

Phosphatidylcholine (lecithin).

What is the structure and function of glycolipids?

Sphingolipids with a sugar group(s) instead of the end OH group. Sugar residues are always on the outside membrane, crucial for cellular recognition and immune function.

Describe COX-1 and COX-2 and how aspirin interacts with them.

COX-1 and COX-2 are isozymes (very similar bt encoded by different genes) that both need Serine 530. Aspirin irreversibly inhibits COX-1 thus inhibiting the production of pro-inflammatory prostaglandin D2, it alters COX-2 to produce lipoxins and resolvins instead of prostaglandins (inflammatory).

Describe the process of lipoprotein transport.

Chylomicrons are stored as triglycerides in adipose tissue or converted to fatty acids and go to peripheral tissues with LDL receptors. Some peripheral tissues secrete HDL which gets transported back to the liver so cholesterol can be recycled. There are many feedback loops to maintain homeostasis of fats in the bloodstream and recycle cholesterol. The liver synthesizes HDL which picks up cholesterol and brings it back to the liver.

What are precursors to aldosterone and what does it do?

Progestogens C21 to Mineralocorticoids C21 to aldosterone. Increases Na+ reabsorption in kidneys and excretion of K+ and H+.

What are precursors to cortisol and what does it do?

Progestogens C21 to Glucocorticoids C21 to cortisol. Promotes glucose and glycogen synthesis, enhances fat/protein degradation, inhibits inflammatory response.

How do steroid hormone receptors act as transcription factors?

Steroid hormones can fuse into membranes, protein receptors can bind to the hormones and act as transcription factors in the nucleus. Once Estradiol binds to the receptor it has a conformational change and dimerizes and is able to go through the nuclear membrane, once inside it binds to co-regulators which effect gene transcription. Specific DNA sequences can act as binding sites for the transcription factor. ERE (estrogen response element)- specific DNA sequence that the estrogen receptor binds to.

What is the similarity between inhibitors and sex hormones in cancer?

Exemestane is an aromatase inhibitor which inhibits the production of estradiol from testosterone by mimicking testosterone. Similarly, tamoxifen prevents the binding of estradiol to the estrogen receptor.

What are common features of bilayer membranes?

Self-sealed, closed, noncovalent structure, 2D fluid structure: the individual molecules are moving and jostling, asymmetric: the phospholipid composition of the inner and outer leaflets are different, most are electrically polarized due to ionic imbalances, leading to membrane potential.

Describe inner and outer membrane composition.

Outer leaflet: more sphingomyelin and phosphatidylcholine. Inner leaflet: phosphatidylethanolamine, only inner membrane has phosphatidylserine.

Why is membrane lipid composition asymmetric?

1) Transmembrane protein domains have evolved with the asymmetry present (needed for transmembrane protein structure and function), 2) Sphingomyelin and the myelin sheath have electrical insulation functions necessary on the exterior of the cell. 3) Phosphatidylserine is needed as a cofactor for some enzymes and if it “flips” to the outside it signals for phagocytes to engulf the cell (final stages of apoptosis)

How does phosphatidylserine act as a cofactor?

In the basal state of cell PS is on inside and XRP8 is inactive. During apoptosis caspases 3 and 7 activate XRP8 by cleaving it and it becomes a“scramblase” enzyme speeds up traverse diffusion of PS, this puts PS on outside of cell, which lets immune cells know to eat the cell because it’s going through apoptosis.

How do proteins mediate membrane function?

1) Membrane-anchored enzymes: often act on lipids 2) Porins: allow passive diffusion of small molecules, ions, and water 3) Growth factor receptors: receive and propagate signals 4) Endocytosis and exocytosis proteins 5) Ion channels and pumps: passive and active transport of charged ions

Glycosylphosphatidylinositol-anchored proteins (GPI-anchored proteins)

Proteins get synthesized from N to C-terminus. Protein C-terminus is covalently bonded to phosphoethanolamine, which is covalently bonded to a cluster of 3 mannose residues, which are covalently bonded to non-acetylated glucosamine, which are covalently bonded to PI (hydrophilic head of a phospholipid). Anchored to membrane by PI (a phospholipid).

What are porins?

Lots of B sheets, form a giant channel for things to pass through the membrane. Believed to be responsible for antibiotic resistance because when the bacteria become selective to what can enter the porins.

Growth factor receptors

Are transmembrane proteins. When a ligand binds to a receptor, dimerization occurs, and then it autophosphorylates each other (on tyrosine residues), signaling a cascade that goes to the nucleus, changing gene expression. Insulin-like growth factor (IGF) receptor is a kind of transmembrane protein known as receptor tyrosine kinase.

Endocytosis

Allows valid cargo to be brought into a cell. Ligand binds to a receptor and causes the membrane to bend inward (could be due to an accumulation of lipid rafts) until a circle is formed. Clathrin proteins on inner membrane bind to AP-2 complex and help form a cage (made of three heavy chains and three light chains).

Exocytosis

Neuronal synaptic vesicles need rapid recycling after exocytosis. SNARE complex forces vesicle fusion with the outer membrane for exocytosis, this is naturally slow so it requires ATP.

Vitamin A

Required for vision, growth, and reproduction. Deficiency can lead to night blindness, cornea damage, damage to respiratory and gastrointestinal tract. VItaimin A (retinol) is converted to retinal to reset receptor molecules and trigger the cascade of events that leads to depolarization of the photoreceptor cell. Beta-carotene (found in vegetables and fruits) is a precursor.

Vitamin D

It is required for absorption of calcium from dietary sources and regulates calcium and phosphate metabolism. Deficiency can lead to rickets (skeletal deformities, impaired growth) in children and osteomalacia (soft, bending bones) in adults. It is synthesized by photolysis (requires light) of cholesterol.

Vitamin E

Is an antioxidant, so it acts as a protective molecule against free radicals. Deficiency can lead to lesions in muscles and nerves (rare).

Vitamin K

Required for blood coagulation (clotting). Deficiency leads to subdermal hemorrhaging. Warfarin is structurally similar to vitamin K so it inhibits it (rat poison that causes bleeding out).

What is the membrane potential (voltage) caused by?

Entropy Diffusion- molecules want to move from a high to a low concentration. Electrostatic Repulsion- similarly charged molecules repulse each other.

What is SERCA?

Sarcoplasmic reticulum Ca2+ ATPase.
During muscle contractive, Ca2+ increases in the cytoplasm.
During muscle relaxation, Ca2+ decreases in the cytoplasm and is pumped against gradient into sarcoplasmic reticulum.
SERCA allows the muscles to relax, and is the most abundant membrane protein.
Concentration of Ca outside calls is MUCH higher than inside muscle cells.

Explain the SERCA pathway.

(In intracellular space of muscle) Two calcium ions from the cytosol bind to channel which causes confirmation change that exposes Asp 351 on P domain. Then ATP binds in N domain which causes a confirmation change and bends it towards Asp residue. ATP then hydrolyzes into ADP which phosphorylates Asp 351 (no immediate confirmation change). ATP leaves which causes a confirmation change where the N domain hinges towards the phosphate and pushes both Ca2+ ions out into the lumen. SERCA resets when the phosphate is hydrolyzed and returns to the initial confirmation.

What are ABC transporters and how do they differ from SERCA?

A transport protein that allows for antibiotics to enter a cell in bacteria. This is done by the antibiotic from inside the cell binds to the space, then ATP binds which opens the channel to the outside of the membrane and releases the antibiotic, the hydrolysis of ATP resets the transporter to the original state. The difference is that ATP hydrolysis is necessary to reset the protein, rather than driving something out.

What are mechanosensitive and thermo-sensitive channels?

Trp-family channels (ion channels) can open in response to changes in temp and mechanical stress. Merkel cells of the skin express a mechanosensitive ion channel that is responsive to feelings of gentle stress. Mice that lack TRPV3 (a protein) are unable to sense elevated temps (though they can sense cold and noxious heat).

What is the function of acetylcholine in muscle?

Every time a muscle contracts a synapse has been released it at the muscle where there is a receptor for it, once it binds the channel opens to Na+ ions.

What is maltose?

2 glucoses joined by a 1,4 alpha bond.

What is Chitin a homopolymer of? How does Chitin differ from glucose?

Chitin (Beta Linkage) is a homopolymer of N-acetylglucoseamine (GlcNAc). Unlike glucose, it has an acetylamine group at Carbon 2.

What are Glycosaminoglycans (GAGs)?

Repeating chains of disaccharides (not homopolymers). One unit is and amino sugar and one unit has a negative charge. They are almost always components of the extracellular matrix.

What is Erythropoietin?

It is secreted by the kidney and stimulates the production of red blood cells. Glycosylation of it helps prevent the kidney from filtering it out of the blood.

What are proteoglycans? What is a disease that can be caused when these can't be degraded?

They are glycoproteins that are linked to GAGs. They are mostly carbs, and are important components of the extracellular domain. Hurler disease can arise with they cant be degraded.

What should we know about proteoglycans?

They connect hyaluronan scaffold to other GAGs. They protect cells from mechanical damage, interact with growth factors, interact with the immune system, are crucial for the function of cartilaginous joints, and have altered expression in cancer by remodeling the tumor microenvironment.

What are mucins?

Proteoglycans that are components of mucus. They have a complex branching pattern. Mostly carbs.

What is the mannan-binding lectin?

A part of the innate immune sensing of fungi and bacterial glycoproteins.

What are velcro like interactions and how do they work?

Lectin has velcro like interactions. Glucose is able to velcro to mannose when calcium is present.

What are selectins?

A subtype of lectin that has a lectin domain. They help leukocytes of the inate immune system "roll" along endothelial cell membrane (inner blood vessel).