Biochem Lec 13-14-15

Question 1

What are some of the essential membrane functions

Answer 1

it acts as barrier that regulates the import and export of essential molecules
it is also used for compartmentalization of specialized processes which increases cellular efficacy
it also modulate cell-cell recognition due to presence of glycoproteins and glycolypidis and sugar

Question 2

what are membrane structural properties

Answer 2

biological membrane are composed of lipid bilayers that are imperable to polar or charged molecules
the hydrophobic effect drives memembrane formation or amphipathic molecules that assemble due to noncovalent interactions
membranes are also asymmetric and composed of lipids, proteins

Question 3

why is membrane fluidity important

Answer 3

because proteins will carry on the movement of molecules across the membrane and signals are also transmitted across membrane
lipids and cholestrol also play role in membrane fluidity

Question 4

What does Fluid Mosaic model stand for and how has it been recently modified

Answer 4

Fluid= membrane components moving rapidly in plane of membrane
mosaic= diverse mixture of lipids, embedded and peripheral proteins, and carbohydrates on surface
have been modified because movement of lipids and membrane proteins differ significant in samples of pure lipids vs biological membranes

Question 5

How to measure lipid dynamics in membrane

Answer 5

using fluorescence recovery after photobleaching (FRAP):
using high intensity laser to bleach fluorophore in small parts of membrane and measure mobility of other molecules into affected region and the recovery rate of the lipids/proteins using this method demonstrate their mobility in membrane

Question 6

What type of microscopy is used to monitor the movment of flurescent molecules throughout membrane

Answer 6

single molecule tracking flurescence microscopy

Question 7

What are some factors that affect memebrane lipids and proteins movement

Answer 7

the time they interact withing certain regions like lipid rafts, the interaction with other components of membrane

Question 8

How is asymmetry in membrane achieved

Answer 8

through help of enzymes that mediate the movement of lipids between the two bilayers
these enzymes are translocases: flippase which move lipid to inner layer and Floppase which move lipids to outer layer
another enzyme called scramblases will mix things up and undo what flippase and floppase do
all these enzymes are ATP dependant

Question 9

What are lipids

Answer 9

molecules involved in providing structural support for cells and organelles, for storing carbons for energy, and play role in information transduction and signalling
they are defined by their physical properties: they have low solubility in water but highly soluble in nonpolar solvents
these physical properties are due to presence of diverse chemical structures and functional groups

Question 10

What is meant by lipids self assembly

Answer 10

lipids spontaneously aggregate in water to bury their hydrophobic groups while polar grouos interact with water
and noncovalent forces are driving this assembly
structure that end up forming is based on structure of lipids and their chemical interactions

Question 11

what are the three big categories in which lipids are found and what type of lipids are in these categories

Answer 11

1- storage= triacylglycerides
2- structural= phospholipids, sphinglolipids, glycolypids, and sterols
3- signallying= sterols, omegas, and eicosanoids

Question 12

what does the fatty acids structure consist of on molecular level

Answer 12

fatty acid consist of hydrohpobic carbons bonded by single or double bond and has a hydrophilic carboxylic group at the end

Question 13

Why are unsaturated, omega, fatty acids good?

Answer 13

when it comes to bond in saturated fatty acid, because they are single bonded, the noncovalent interactions are like glue holding the chains together which decreases its fluidity so they are more solid and harder to melt (have high melting point)
while unsaturated fatty acids have kinks present due to the cis-double bonds which increase its fluidity and they have low melting point so they are better for the body as they won’t acummulate and cause issue

Question 14

why is it significant if the carbons of fatty acids are single or double bonded

Answer 14

single bonded means there are saturated, bad fats, as teh carbons are singl bonded so have maximum amount of hydrogen bonded to them while double bonded carbons means it is an unsaturated fatty acid, good fats, and these double bonds are numbered relative to the carboxylic group or relative to terminal methyl group for omega fatty acids

Question 15

What are omega fatty acids

Answer 15

these omega-3 and omega-6 fatty acids are polyunbsaturated fatty acids (meaning they contain more than one double bond) and they cannot be made by humans but they are essential so they must be obtained from our diet

Question 16

what is phase transitions of lipids

Answer 16

the melting of membrane lipids is teh phase transitions from gel-like solid phase to liquid-crystalline phase

Question 17

what is a triacylglycerol

Answer 17

it is an efficient and unlimited energy reserve of reduced carbon chains
3 fatty acids are bound to glycerol backbone by ester linkages=TAG
fatty acyl tails can be unsaturated creating mixed triglycerides

Question 18

what are amphipathic molecules and some examples

Answer 18

amphipathic molecules are made by attaching fatty acyl chains to polar head groups
ex) glycerophospholipids and sphingolipids

Question 19

how is structure of glycerophospholipids different from sphingolipids

Answer 19

glycerophospholipids consist of glycerol head with 1 saturated fatty acid chain, another 1 unsaturated fatty acid chain, and last chain is phosphate group with some head group attacehd to it that contribute to charge of molecule
sphingolipides consist of three chains different from each other, one is saturated fatty acid chain, another is sphingosine chain, and last is the head group that will contribute to charge of moelcule

Question 20

why is cholestrol an important steroid

Answer 20

can be metabolized to other hormones and needed for dietary lipid absorption
can form complexes with sphingolipids and some lipid anchor-proteins to form lipid rafts and these rafts help moderate membrane fluidity and also have role in signal transduction so cholestrol can modulate membrane fluidity

Question 21

What are the three types of membrane proteins

Answer 21

peripheral membrane proteins, integral membrane proteins, and lipid anchored proteins

Question 22

what are charcteristics of peripheral membrane proteins

Answer 22

they adhere to surface of lipid membranes or integral membrane proteins through non-covalent interactions and can be easily removed using milder conditions

Question 23

what are characteristics of integral membrane proteins

Answer 23

they completly span the membrane, transmembrane segments, and require harsher conditions to be removed
need to dirupt the membrane to purify them

Question 24

what are characteritics of lipid anchor proteins

Answer 24

also require harsh detergents or solvants for membrane removal as the lipid chains are covalently attached to amino acid functional groups and side chains
GPI-anchored proteins (glycosyl phosphatidylinositol) are oen that covalently link through sugar chain and lipid anchor

Question 25

how does using detergents to remove the memebrane proteins changes shape of membrane

Answer 25

the detergents create micelles around hydrophobic regions of membrane to solubilize the membrane proteins

Question 26

What is critical micelle concentration

Answer 26

it is the concentration at which the detergent spontaneously forms the stable micelle strcutures and some of these detergents are mild while others are way harsher like SDS which denature the proteins

Question 27

How can we predict the membrane spanning segments

Answer 27

using DNA sequencing and protein prediction algorithms as transmembrane segments are primarily made of hydrophobic amino acids so the strategy is to scan the priomary sequence for long stretches of hydrophobic amino acids representing the TM segments

Question 28

how to determine protein topology

Answer 28

find the hydropathy index for streatch of amino acids by averging the Kyte-Doolittle hydrophobicity values of all of the aminoi acids found in the segment then move one residue over to the right and repeat the same step and plot all of these values to look at the graph and see which is more, polar vs nonpolar

Question 29

How to identify the type of TM segment from the plotted graph of hydrophiobicity indexes

Answer 29

if it is glycophorin A (GPA) which contain single transmemebrane segment between amino acid 72-91, then there will be one wide wave on top of line
if it is bacteriorhodopsin which contain 7 TMs, there will be 7 peaks over the line that span at least 20 amino acids

Question 30

what are the common components in any signal transduction cascades

Answer 30

binding specifically to signalling molecules as a response to stimulus
reception of the message by receptor
relay of primary message to cell interior by generating secondary messenger
amplification and transduction of signal
response and then termination of signal cascade

Question 31

what are the GPCR

Answer 31

the G-protein coupled receptores are family of membrane proteins and contain 7v transmembrane proteins
when they undergo conformational change, they releaase the G proteins

Question 32

What is ligand for B2-adrenergic receptor and how does the ligand binding this GPCR afffect it

Answer 32

epinephrine is the ligand for B2-adrenergic receptor and when it binds, it induces small changes in TM5 on the extracellular side and movement in TM6 will transmit the signal inside as it promote the release of G-alpha GTP which activates adenylyl cyclase and produce cAMP which go to activate PKA and other enzymes

Question 33

What are some unique characteristics about Ras proteins

Answer 33

they are G-proteins which are memebers of GTPases that bind and hydrolyzes GTP to GDP which inititae cell proliferation and apoptosis and defect in GTP hydrolysis can lead to uncontrolled signalling and cancer

Question 34

What are two other types of signalling

Answer 34

Enzyme-linked receptores which contain 1 TM segment that may dimerize when ligan binds and its activation lead to auto-phosphorylation or phosphorylationb by tyrosine kinase
phospholipid mediated signalling is the other one which is a phospholipase that hydrolyze phospholipids to produce other secondary messengers like DAG or IP3 causing Ca release

Question 35

How do integral membrane proteins mediate transport

Answer 35

using facilitated diffusion or active transport (with or without ATP)

Question 36

what are important feature of chanel proteins

Answer 36

channel proteins are membrane transporters that facilitated diffusion and important features are : selectivity, rapid conductance of ions, and they can be gated

Question 37

What are characteristics of potassium ion channels

Answer 37

they are essential for cellular processes like regulating cell volume, secreting hromones, and electrical impulse formation
each subunit contribute selectrivity filter of 5 amino acids that contribute to K+ binding where the 4 backbone carbonyls and threonine side chain hydroxyl bind the K+ ions
changing the sequence alters selectivity for other cations

Question 38

What are the two types of reactions involved in metabolism and how do they differ

Answer 38

anabolic and catabolic reactions are the two methods
anabolic= reductive and endergonic, need energy, as the take the precursor molecules and make macromolecules
catabolic= oxidative and exergonic, gives energy off, as it takes the energy yielding nutrients(macromolecules) and break them into energy poor end products

Question 39

what are some of the factores that influence the metabolic flux (conversion of metabolites through the pathways)

Answer 39

gibbs free energy difference and enzmyes,
(metabolite concentration and ATP availability)

Question 40

How does coupling work

Answer 40

enzyme will couple favourable and unfavourable reaction to produce an overall favourable reaction

Question 41

Why does hydrolysisng different phosphoanhydride bonds release different amount of free energies

Answer 41

that is because of stabilization of teh product as AMP is more stable than ADP so it will release more energy than ATP to ADP

Question 42

what are some of the unique features of ATP

Answer 42

it is a nucleotide made of adenine, ribose, and three phosphates where the alpha, beta, and gamma phisphates are linked by phosphoanhydride bonds and another ester bond to sugar
it is involved in bothe catabolic and anabolic due to its phosphate group transfer reactions

Question 43

how does ATP hydrolysis affect muscle contraction

Answer 43

ATP hydrolysis by ATPase will contract the muscle

Question 44

What enzyme is involved in phosphoryl transfer potential in muscle

Answer 44

creatine kinase which during rest convert ATP and creatine into ADP and phoshphocreatine but during exercise, the phosphocreeatine and ADP are converted into ATP and creatine by also creatine kinase but creatine kinase prefer the forward reaction that gives ATP and creatine