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Biochemistry I > Biochemistry Lecture Exam 4 > Flashcards

Biochemistry Lecture Exam 4 Flashcards

1
Q

What are saturated and unsaturated fatty acids?

A

Saturated Fatty Acids
-are waxy (solids) at room temperature
-have no C-C double bonds
Unsaturated Fatty Acids
-are liquids at room temperature
-have at least 1 C-C double bond

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2
Q

How does saturation affect structure and melting point?

A

-Saturated fatty acids have a higher melting point than unsaturated fatty acids
-Unsaturated fatty acids contain at least one C-C double bond

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3
Q

What configuration are the double bonds typically in for saturated and unsaturated fats?

A

-Saturated Fatty Acids have no C-C double bonds
-Unsaturated Fatty Acids have at least one C-C double bonds
-Most naturally occurring are in a cis confirmation

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4
Q

How does the naming of lipids work? (where do you start numbering carbons? How do you denote double bond numbers and positions?)

A

-Nomenclature for Unbranched Fatty Acids
-the chain length and number of bonds separated by a colon
-numbering begins at the carboxyl carbon
-positions of double bonds are indicated by a delta symbol and a superscript number

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5
Q

What are PUFAS and why are they essential?

A

PUFAs: polyunsaturated fatty acids; contain more than one double bond in the backbone
-They are essential because the body needs them to function but it can not make them naturally

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6
Q

What omega-3 do we typically get from our diet and what can we produce from it?

A

-alpha-linoleic acid (ALA)
-we must get this from our diet; it uses ALA to synthesize EPA and DHA

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7
Q

What is a triaglycerol? What purpose can it serve in organisms?

A

-Triacylglycerol: simplest lipids constructed from fatty acids; composed of three fatty acids; can be simple or mixed; nonpolar, hydrophobic
-they provide energy storage and insulation
-adipocytes in vertebrates
-triacylglycerols in seeds

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8
Q

What are phospholipids?

A

have hydrophobic regions composed of two fatty acids joined to glycerol or sphingosine

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9
Q

What are glycolipids?

A

contain a simple sugar or complex oligosaccharide at the polar ends

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10
Q

What are sterols?

A

compounds characterized by a rigid system of four fused hydrocarbon rings

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11
Q

What does it mean for a molecule to be amphipathic and how does this apply to membranes?

A

-Amphipathic: one end of the molecule is hydrophobic, the other is hydrophilic
-hydrophobic regions associate with each other
-hydrophilic region associate with water

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12
Q

What is the precursor of the glycerophospholipids? Name 3 examples of phospholipids

A

-Phosphatidic Acid is the precursor of the glycerophospholipids
-Examples: Cardiolipin, Phosphatidylcholine, Phosphatidylserine

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13
Q

What is the precursor of sphingolipids? Name 2 examples of sphingolipids

A

-Ceramide is the precursor of Sphingolipids
-Examples: Sphingomyelin, Lactosylceramide

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14
Q

Where are phospholipids and sphingolipids degraded? What happens when this system doesn’t work properly?

A

-They are degraded in lysosomes
-If the system doesn’t work properly (by lacking enzymes), the lipids can build up and cause lipid storage diseases (damage the cell, destroy the cell)

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15
Q

What are some basic structural features of sterols?

A

-consists of four fused rings
-almost planar
-relatively rigid

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16
Q

What is the most well known example of a sterol?

A

cholesterol

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17
Q

What are Eicosanoids and what are the main classes?

A

-Eicosanoids: paracrine hormones, substances that act only on cells near the point of hormone synthesis instead of being transported in the blood
-Four Major Classes
-Prostaglandins (PG)
-Thromboxanes (TX)
-Leukotrienes( LT)
-Lipoxins (LX)

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18
Q

Name 2 examples of molecules that are derived from cholesterol.

A

Testosterone and Cortisol

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19
Q

What processes are vitamins A and D involved in?

A

-Vitamin A is involved in the processes of development, cell growth, and differentiation, and vision
-Vitamin D is involved in the production of calcitriol?

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20
Q

What are vitamins E and K used for?

A

-Vitamin E is used in cell membranes, lipid deposits, and lipoproteins
-Vitamin K: undergoes a cycle of oxidation and reduction during the formation of active prothrombin

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21
Q

Lipid Bilayer

A
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22
Q

Micelle

A

-spherical structures containing amphipathic molecules arranged with hydrophobic regions in the interior and hydrophilic head
groups on the exterior
-Favored when the cross section areas of the head group is greater than that of the acyl side chain

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23
Q

What is the fluid mosaic and how does it describe the movement of lipids and proteins in a membrane?

A

-Fluid mosaic model: pattern formed by individual lipid and protein units in a membrane
-pattern can change while maintaining the permeability of the membrane

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24
Q

What are the functions of biological membranes?

A

`-Permit shape changes that accompany cell growth and movement, permit exocytosis, and cell division, serve as molecular gatekeepers

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25
Q

What are membrane proteins?

A

receptors, transporters, and enzymes

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26
Q

What is the difference between integral and peripheral membrane proteins?

A

-Integral: firmly embedded within the lipid bilayer
-Peripheral: associate with the membrane through electrostatic interactions and hydrogen bonding

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27
Q

Which organelles have a double vs a single bilayer?

A

-Single Lipid Bilayer: ER, Golgi, Lysosomes, various small vesicles
-Double Layer Bilayer: Nucleus, Mitochondria, chloroplasts (in plants)

28
Q

Membrane Trafficking

A

process by which membrane lipids and proteins that are synthesized in the ER move to their destination organelles or to the plasma membrane

29
Q

LTPs

A

lipid transfer proteins; soluble proteins that contain a hydrophobic lipid-binding pocket to carry a lipid from one membrane to another

30
Q

Hydropathy Index

A

expresses the free energy change associated with the movement of an amino acid side chain from a hydrophobic environment to water

31
Q

Lipid Raft

A

there’s a slide about lipid aggregation. It is called membrane raft in the slides. Basically there’s a bunch of lipids that make a very thick section in the membrane.

32
Q

What features of a protein sequence allow for a prediction of an integral membrane protein?

A

-How do we know if something is going to be in the membrane or not
-The type of amino acids makes the difference
-Hydrophobic amino acids represent a region that is buried inside the membrane
-Hydrophillic amino acids represent regions that are outside of the membrane
-Hydropathy Index: how well does that area interact with water
-can go through amino acids and “score” how positive or negative they are
-more positive in the membrane; more negative out of the membrane
-When reading the graph what is on the left is inside the cell and what is on the right of the integral protein is outside the cell membrane
· What proteins are involved in moving lipids from one face

33
Q

How can alpha and beta secondary structures be used in integral membrane proteins to cross the bilayer (ie, what amino acid compositions are part of these structures?)?

A

-Beta: tryptophan, tyrosine. Creates Beta barrels in the hydrophobic portion of the membrane

34
Q

What proteins are involved in moving lipids from one face to another?

A

“Flippases (moves lipid on outside to inside), floppases (moves lipid on inside to outside), and scramblases (moves either, involves Ca+)”

35
Q

What is simple and facilitated diffusion?

A

-Simple Diffusion: movement of a solute from the region of higher concentration to the region of lower concentration
-Facilitated diffusion: facilitate movement down a concentration gradient, increasing the transport

36
Q

What is primary active and secondary active transport?

A

-Primary: solute accumulation is coupled directly to an exergonic chemical reaction
-Secondary: endergonic transport of one solute is coupled to the exergonic flow of a different solute that was originally pumped uphill by primary active transport

37
Q

What do GLUT transporters do?

A

transports glucose into cells or across tissue barriers

38
Q

Antiporters

A

moves in opposite directions

39
Q

Symporters

A

moves in the same direction

40
Q

Uniporters

A

carry only one substance

41
Q

What is Na/K ATPase and what does it do?

A

-Na/K ATPase: couples phosphorylation-dephosphorylation of the critical Asp residue to the movement of Na+ and K+ against their electrochemical gradients
-maintains low [Na+] and high [K+]
-essential to the conduction of action potentials in neurons

42
Q

What are F-Type ATPases and what do they do?

A

-F-type ATPases: catalyze the uphill transmembrane passage of protons, driven by ATP hydrolysis

43
Q

What are ABC transporters and what do they do?

A

-ABC transporters: family of ATP-driven transporters that pump substrates across a membrane against a concentration gradient; has two ATP binding domains and two transmembrane domains

44
Q

What is a key example of ABC transporters involved in drug resistance?

A

-Example: Multidrug Transporter (MDR1): human ABC transporter with very broad substrate specificity
-encoded by ABCB1 gene
-removes toxic compounds
-responsible for resistance of tumors to drugs

45
Q

What are aquaporins?

A

provide channels for the movement of water molecules across plasma membranes

46
Q

What are ligand-gated and voltage-gated channels?

A

-Ligand-Gated: binding of extracellular or intracellular small molecule forces an allosteric transition in the protein, which opens or closes the channel
-Voltage-Gated: a change in transmembrane electrical potential causes a charged protein domain to move relative to the membrane, opening or closing the channel

47
Q

What is signal transduction?

A

-Signal Transduction: the conversion of information into a chemical change
-signal represents information that is detected by specific receptors
-conversion of the signal to a cellular response always involves a chemical process

48
Q

What does it mean for signal systems to be specific and sensitive?

A

-Specificity: achieved by precise molecular complementarity between the signal and receptor molecules
-mediated by weak (noncovalent) forces
-Sensitivity: results from the high affinity of signal receptors for their ligands
-Short Answer: Signal systems use specific signals for specific receptors and those receptors will only respond to the ligands that they are intended for

49
Q

What does it mean for signals to be amplified?

A

-Amplification: results when an enzyme is activated by a signal receptor and, in turn, catalyzes the activation of many molecules of a second enzyme, and so on, in an enzyme cascade

50
Q

What does it mean for signal proteins to be modular?

A

-Modular: has multiple domains that recognize specific features; allows cells to mix and match a set of signaling molecules

51
Q

What does desensitization, integration, and divergence mean in terms of signaling?

A

-Desensitization: no longer responsive to a signal; occurs when a signal is present continuously
-Integration: the ability of the system to receive multiple signals and produce a unified response
-Divergence: branched rather than linear; occurs when a signal is present continuously

52
Q

How does a G-protein coupled receptor work?

A

-GPCRs: receptors that act through a member of the gunaosine nucleotide binding protein (G protein) family
-Mechanisim:
-External Ligand binds to a receptor and activates an intracellular GTP-binding protein. This regulates an enzyme that generates an intracellular second messenger

53
Q

What is an agonist and an antagonist?

A

-Agonist: molecule that binds a receptor and produces the effects of the natural ligand
-Antagonist: analog that binds the receptor and blocks the effects of the agonist, including the natural ligand

54
Q

How does the B-andrenergic receptor pathway respond to epinephrine? What are the downstream effects?

A

-Methods of Termination:
-epinephrine concentration drops below the Kd for its receptor
-The GTPase activity of the G protein hydrolyzes the GTP bound to the alpha G subunit of
-cAMP is hydrolyzed to 5’ AMP by cyclic nucleotide phosphodiesterase

55
Q

What is a GTPase and why are they looked at like switches?

A

-GTPase: hydrolyzes GTP to GDP
-G s alpha has intrinsic GTPase activity that switches G s alpha to its inactive form by converting its bound GTP to GDP

56
Q

How does the PKA protein get activated by cAMP?

A

-cyclic AMP is an allosteric activator of PKA
-binding of cAMP yields two active C subunits

57
Q

What is CREB and what effect does it have?

A

-CREB: cAMP response element binding protein: alters the expression of specific genes regulated by cAMP
-in some cells, the catalytic subunit of PKA can also move into the nucleus, where it phosphorylates CREB

58
Q

What is a Ras and how does it get turned on and off?

A

-Ras: a ~20 kDa minimal signaling unit; is mutated to be “on” in 25% of cancers
-GTP hydrolysis flips the “switch” to turn Ras on and off
-when GTP is hydrolyzed, the loss of H bonds allows the switch I and switch II regions to relax into a buried confirmation

59
Q

What does Ca2+ do as a second messenger?

A

-In unstimulated cells, cytosolic [Ca2+ ] is kept very low by the Ca2+ pumps
-hormonal, neural, or other stimuli cause
-an influx of Ca2+ into the cell through Ca2+ channel
-the release of sequestered Ca2+ into the cytosol

60
Q

How does rhodospin work in vision?

A

-Rhodopsin: a GPCR in the disk membranes of rod cells in the vertebrate eye
-Opsin: the protein component of rhodopsin
-Rhodopsin absorbs photons

61
Q

How do receptor tyrosine kinases work?

A

-RTKs: family of plasma membrane receptors with protein kinase activity
-have an extracellular domain and a cytoplasmic Tyr kinase domain
-Autophosphorylation: each Beta subunit phosphorylates three essential Tyr residues near the C-terminus of the other Beta subunit
-opens the active site

62
Q

How does the insulin receptor pathway work?

A

-Insulin Receptor Substrate 1: becomes the point of nucleation for a complex of proteins that carry the message from the receptor to end targets
-Mech:
Insulin Receptor binds insulin and undergoes autophosphorylation on its carboxyl-terminal Tyr residues
Insulin receptor phosphorylates IRS1 on its Tyr residues
SH2 domain of Grb2 binds to the phosphate group of the Tyr of IRS1. Sos binds to Grb2, then to Ras, causing GDP release and GTP binding to Ras
Activated Ras binds and activates Raf-1
Raf-1 phosphorylates MEK on two Ser residues, activating it. MEK phosphorylates ERK on a Thr and a Tyr residue, activating it.
ERK moves into the nucleus and phosphorylates nuclear transcription factors such as Elk1, activating them
Phosphorylated Elk1 joins SRF to stimulate the transcription and translation of a set of genes needed for cell division
-SH2 domain: binds phosphorylated Tyr residues in a protein partner

63
Q

How does PIP3 play a role in signaling?

A

-activation of PI3K by phosphorylated IRS1 initiates movement of GLUT4 to the plasma membrane and activation of glycogen synthase
-once activated, PI3K converts the membrane lipid PIP2 to PIP3 by the transfer of a phosphoryl group from ATP

64
Q

How do adapter proteins allow different pathways to communicate?

A

-Extensive interconnections among signaling pathways allow integration and fine-tuning of multiple hormonal effects

65
Q

How do ion channels work?

A

-Ion channels open when a specific ligand binds to its associated receptor or there is a change in the transmembrane electrical potential (voltage-gated ion channel)

66
Q

How do nuclear receptors work?

A

-Hormone Response Elements (HREs): specific regulatory sequences in DNA that interact with receptor proteins following hormone binding

Biochemistry I (6 decks)

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