Exam Prep MCB2021F membrane lipids and proteins

functions of plasma membrane

physical barrier

selective permeability

organelle delineation and individuality

cell recognition

what is membrane bilayer made of

a mosaic of lipids, proteins

what makes membrane bilayer fluid and dynamic

constituents that make up the membrane are capable of movement

what forms the structure of the membrane bilayer

lipids, proteins and carbohydrates

membrane lipids

phospholipids, glycolipids, cholesterol

membrane proteins

integral, peripheral, lipid-anchored

phospholipids are divided into

glycerophospholipids and sphingolipids

glycerophospholipids

glycerol backbone

2 FA at c1 and c2

saturated or unsaturated

phosphate at C3

no alcohol

what is an example of a glycerophospholipid

phosphatidic acid

the OH group making up glycerophospholipids gives rise to what

phosphatidylserine, phosphatidylcholine and phosphatidylethanolamine

phospholipases

enzymes that cleave glycerophospholipid bonds

what do PLC and PLD hydrolyse

either side of the polar head

what does phospholipase A2 in snake venom cause

release of FA at C2 ultimately causing breakdown of phospholipids

what does sphingosine contain

an amino group and a unsaturated hydrocarbon chain

how are ceramides formed

by an amide linkage of 1 fatty acid to the amino terminal of sphingosine

what do ceramides do

signal molecules

regulate structure

differentiate cells

proliferate cells

what is sphingomyelin

the sphingolipid in membrane bilayer of nerve cells

what are glycolipids

ceramides bound to 1 or more sugar residues in a glycosidic linkage

Where are glycolipids found?

on outer portion of leaflet

ceramide structure

sphingosine backbone and fatty acide residue

sphingomyelin structure

Sphingosine backbone + FAs + Phosphocholine/ethanolamine

cerebroside structure

sphingosine backbone

FA

single sugar residue

ganglioside

sphingosine backbone

FA

oligosaccharide residue

sialic acid

what is the most common steroid

cholesterol

what makes up cholesterol

4 fused HC rings

one end of ring has a HC chain and the other end has an OH group

interaction of cholesterol with cell membrane

hydrophobic end embedded in membrane with FA chain

OH interacts with H2O and polar heads of phospholipids and sphingolipids

transverse asymmetry

different lipid or protein compositions in the two leaflets or monolayers of a bilayer membrane

lateral heterogeneity

different lipid or protein compositions in plane of 1 leaflet of a bilayer membrane

membrane lipid movements

lateral diffusion, rotational diffusion and transverse diffusion

which lipid movements are fast

lateral and rotational diffusion

which lipid movements are slow

transverse motion

ATP-dependent flippases

transport lipids from outer leaflet to inner leaflet

ATP-dependent floppases

transport lipids from inner leaflet to outer leaflet

ATP-independent bi-directional scramblases

moves lipids between bilayers

lipid raft function

concentrates molecules to aid in cellular processes such as signalling, signal transduction, protein trafficking

integral polytropic proteins

span entire width of membrane

integral monotropic proteins

attached to one side of bilayer but do not span entire width of membrane

what are integral proteins in contact with the lipid bilayer dominated by

alpha helices and beta sheets

where are alpha helices found

in all types of biological membranes

where are beta sheets found

in membrane of bacterial cells

Beta sheet transmembrane domains

beta sheets arrange in an antiparallel fashion to make a beta barrel

how many amino acids are needed per beta sheet to cross membrane

9-11

orientation of beta sheet transmembrane domains

AA orient toward the exterior and hydrophilic residues orient toward the aqueous interior pore

alpha helical transmembrane domains

proteins can have 1 to 12 TM segments

hydrophobic AA cross membrane

need to 21-25 to cross

membrane helix distortions

kinks at proline residues

what do proline residues distort

the helix

what do pro-induced kinks create

weak points in the PM helix, which facilitates movement of PM

how can transmembrane alpha helical domains be revealed

by hydropathy plots based on its amino acid sequence

where are porins found

in outer membrane of bacteria

what do porins acts as

pore through which some molecules can diffuse

porin orientation

polar residues face inside and non-polar face the membrane

beta strand advantage over alpha helices

can code more transmembrane segments on the same amount of genetic material

peripheral proteins

don't penetrate the membrane

How are peripheral proteins attached to the membrane?

ionic and H-bond interactions

amphipathic alpha helix

hydrophobic loop

association with integral protein

where are peripheral proteins temporarily bound

to plasma membrane

why can peripheral proteins dissociate from the membrane

due to weaker interaction

Lipid-anchored membrane proteins

proteins on the surface of the bilayer are linked to lipid in membrane bilayer and achors protein to membrane

4 linkages defined to link protein to lipid

n myristoylation

s palmitoylation

prenylated anchors

glycosyl phosphatidylinositol anchors

N-myristoylation

FA is myristic acid

myristic acid forms an amide linkage with glycine amino acid in protein at N terminal

S-palmitoylation

palmitic acid linked via an ester linkage to SH group of cysteine residue of protein

prenylated anchors

linking of prenyl groups - farnesyl and geranylgeranyl to carboxyl terminal cysteine of proteins

how are lipid anchored membrane proteins switching devices

they alter the affinity of a protein to the membrane and signal transduction pathways

three important factors that determine how transport occurs

size, polarity and charge

4 types of transport across biological membranes

passive diffusion

facilitated diffusion

primary active transport

secondary active transport

passive diffusion

small uncharged molecules

energy independent

facilitated diffusion

large or polar molecules

energy independent

facilitated diffusion: carrier proteins

glucose binds to GLUT1 transporter protein

causes GLUT1 transporter to shift to its T2 conformation

binding site open to inside of cell

glucose released to cell interior

second conformational change in GLUT1

loss of bound glucose causes GLUT1 to return to T1

active transport

movement of molecules against the concentration gradient

energy dependent

requires specialized integral ATPase proteins

concentration gradient

unequal distribution of molecules

electric gradient

unequal distribution of charged molecules between 2 sides of a membrane

what do A and T share

2 H bonds

what do G and C share

3 H bonds

why are G:C regions more stable

due to more H bonds between them

how is the helix anti-parallel

sugar phosphates outside

bases stack inside

helix dimensions

10 bp per turn

bp space = 0.34 nm

diameter = 2.37nm

pitch = 3.4nm

how do major grooves accomodate a protein

regulatory proteins can recognize the pattern of bases and H bonding possibiliteies in major groove

heat DNA to >80C

results in denaturation from disrupted base-pairing interactions

why does denaturation cause a 30-37% increase in UV absorbance reflecting strand separation

pi-electrons of unstacked bases

hyperchromic effect

an increase in UV absorption due to denaturation

Tm

midpoint of absorbance increase

how else can DNA be denatured

using an alkali and/or pH

why does the absorbance drop when temperature is lowwered

re-establishment of stacking

Why does the Tm increase as the G-C content increases?

G:C pairs have more bonds

how many bp/turn in helix of linear DNA

10

what enzymes introduce or remove supercoils

topoisomerases and gyrases

how is DNA condensation made possible

by wrapping DNA around nucleosomes and then packing them with DNA into helical filaments

DNA in eukaryotic cells exists as

chromatin

chromatin consists of

histones and non-histone chromosomal proteins

histone octamer structure

8 core histones make up a core

DNA helix to chromosome

DNA helix

nucleosomes

filament

DNA loops

miniband unit of a chromosome

chromosome

central dogma

DNA -> RNA -> Protein

why does replication of DNA give identical progeny molecules

base pairing is the mechanism for determining the nt sequence

semi-conservative replication

in each new DNA double helix, one strand is from the original molecule, and one strand is new

features of DNA replication

ORI

bidirectional

occurs 5 to 3

double helix must be unwound by helicases

semi-discontinuous

leading strand synthesis

replication moves 5 to 3

parent antisense acts as template for continuous strand synthesis

lagging strand synthesis

replication moves 5 to 3

parent sense acts as template for discontinuous strand synthesis

pol 1 needs

all 4 deoxynucleotides

a template

a primer

pol 1 has 3 active sites:

polymerase activity

proof reading

editing function

pol 3

chief DNA-replicating enzyme of E.coli

where is pol 3 found

sits at each replication fork