Biochem Lec 13-14-15 Flashcards
What are some of the essential membrane functions
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
what are membrane structural properties
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
why is membrane fluidity important
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
What does Fluid Mosaic model stand for and how has it been recently modified
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
How to measure lipid dynamics in membrane
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
What type of microscopy is used to monitor the movment of flurescent molecules throughout membrane
single molecule tracking flurescence microscopy
What are some factors that affect memebrane lipids and proteins movement
the time they interact withing certain regions like lipid rafts, the interaction with other components of membrane
How is asymmetry in membrane achieved
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
What are lipids
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
What is meant by lipids self assembly
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
what are the three big categories in which lipids are found and what type of lipids are in these categories
1- storage= triacylglycerides
2- structural= phospholipids, sphinglolipids, glycolypids, and sterols
3- signallying= sterols, omegas, and eicosanoids
what does the fatty acids structure consist of on molecular level
fatty acid consist of hydrohpobic carbons bonded by single or double bond and has a hydrophilic carboxylic group at the end
Why are unsaturated, omega, fatty acids good?
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
why is it significant if the carbons of fatty acids are single or double bonded
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
What are omega fatty acids
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
what is phase transitions of lipids
the melting of membrane lipids is teh phase transitions from gel-like solid phase to liquid-crystalline phase
what is a triacylglycerol
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
what are amphipathic molecules and some examples
amphipathic molecules are made by attaching fatty acyl chains to polar head groups
ex) glycerophospholipids and sphingolipids
how is structure of glycerophospholipids different from sphingolipids
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
why is cholestrol an important steroid
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
What are the three types of membrane proteins
peripheral membrane proteins, integral membrane proteins, and lipid anchored proteins
what are charcteristics of peripheral membrane proteins
they adhere to surface of lipid membranes or integral membrane proteins through non-covalent interactions and can be easily removed using milder conditions
what are characteristics of integral membrane proteins
they completly span the membrane, transmembrane segments, and require harsher conditions to be removed
need to dirupt the membrane to purify them
what are characteritics of lipid anchor proteins
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
how does using detergents to remove the memebrane proteins changes shape of membrane
the detergents create micelles around hydrophobic regions of membrane to solubilize the membrane proteins
What is critical micelle concentration
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
How can we predict the membrane spanning segments
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
how to determine protein topology
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
How to identify the type of TM segment from the plotted graph of hydrophiobicity indexes
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
what are the common components in any signal transduction cascades
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
what are the GPCR
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
What is ligand for B2-adrenergic receptor and how does the ligand binding this GPCR afffect it
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
What are some unique characteristics about Ras proteins
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
What are two other types of signalling
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
How do integral membrane proteins mediate transport
using facilitated diffusion or active transport (with or without ATP)
what are important feature of chanel proteins
channel proteins are membrane transporters that facilitated diffusion and important features are : selectivity, rapid conductance of ions, and they can be gated
What are characteristics of potassium ion channels
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
What are the two types of reactions involved in metabolism and how do they differ
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
what are some of the factores that influence the metabolic flux (conversion of metabolites through the pathways)
gibbs free energy difference and enzmyes,
(metabolite concentration and ATP availability)
How does coupling work
enzyme will couple favourable and unfavourable reaction to produce an overall favourable reaction
Why does hydrolysisng different phosphoanhydride bonds release different amount of free energies
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
what are some of the unique features of ATP
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
how does ATP hydrolysis affect muscle contraction
ATP hydrolysis by ATPase will contract the muscle
What enzyme is involved in phosphoryl transfer potential in muscle
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
