1
Q
Polymers
A
- polymers formed from monomers via condensation/dehydration reactions
- water made as byproduct
- for 2 monomers to join, they are usually coupled to a carrier molecule
- once coupled to a carrier molecule, the monomer is activated
- enzymes and ATP required to activate monomers
-hydrolysis reactions break polymers into monomers and water is required for the reaction
2
Q
Lysosome
A
- intracellular digestion
- hydrolytic enzymes
3
Q
Carbohydrates
A
- (CH2O)n
- molar ratio of 1:2:1
- n=number of carbons
- monosaccharides are the monomer for carbohydrates
- 2 monosaccharides = disaccharide
- glycosidic bond between monomers
- lactose has beta-glycosidic bonds
- sucrose has alpha-glycosidic bonds
- oligosaccharides = small chains 3-10
- always covalently attached to lipids or proteins
- polysaccharides = hundreds/thousands monosaccharides
4
Q
Starch
A
- polysaccharide
- stores chemical energy in plants
- amylose and amylopectin
- alpha glycosidic bonds
5
Q
Glycogen
A
- polysaccharide
- stores chemical energy in animals
- linked by alpha glycosidic bonds
6
Q
Cellulose
A
- structural polysaccharide
- beta glycosidic linkage
7
Q
Lipids
A
- fats (triglycerides)
- phospholipids
- steroids
8
Q
Fatty acid
A
- hydrocarbon chain with a carboxy group on the end
- building block for some classes of lipids
- saturated: no double bonds
- unsaturated: has at least one double bond
- causes kink in 3D shape
9
Q
Triacyglycerols
A
- function is to store energy
- sometimes for insulation against the cold
- 1 glycerol + 3 fatty acids joined via condensation rxn
- connected by ester linkage
10
Q
Saturated triacylglycerols
A
- usually called fats
- no double bonds
- solid at room temperature because of linearity
- pack together tightly
- most animal fats are saturated
11
Q
Unsaturated triacylglycerols
A
- oils (fish and plants)
- liquid at room temp due to kinks that create gaps in structure
- has double bonds
- can be cis or trans
- cis (same side) will form a bend
- trans (opposite side) has no bend… so similar to saturated FA
12
Q
Hydrogenated veg oil
A
- artificially making saturated or trans fats from cis fats
- shoot hydrogen atoms at molecule (hydrogenation)
- trans fats will taste better and last forever
13
Q
Phospholipids
A
- phosphoglycerides
- sphingolipids
14
Q
Phosphoglyceride
A
- found in cell membranes
- has a polar head group, glycerol backbone, 2 FA tails
- amphipathic (hydrophobic and hydrophilic regions)
- form a lipid bilayer in membranes
15
Q
Steroids
A
- derived from 4-ringed hydrocarbon skeleton
- cholesterol precursor for all steroids
- amphipathic due to OH group
- examples: estradiol, testosterone, cortisol, aldosterone
16
Q
Proteins
A
- monomers are amino acids
- amino acids contain: an amino group, carboxyl group, H, and R group attached to a carbon
- amino acids classified by R groups
17
Q
Amino acids
A
- non-polar: side chains are hydrophobic
- associate via van der waals forces and hydrophobic interactions
- always on inside
- polar, uncharged: at physiological pH, side chains have partial charge
- will form hydrogen bonds with other molecules, including water
- polar, charged: at physiological pH, side chains will have a full charge
- will form ionic bonds with other charged species
18
Q
UNIQUE amino acids
A
- Cysteine: will form a covalent bond with another cysteine to form a DISULFIDE BOND
- proline: will form a disruptive kink in a polypeptide
19
Q
Peptide bonds
A
-amino acids join via condensation reactions to form peptide bonds between carboxy group and amino group
- N terminus: amino group
- C terminus: carboxyl group
20
Q
Protein structure
A
-if a protein doesn’t fold correctly it can cause functional problems including diseases
- primary structure: order of amino acids
- peptide = 20-30 aa
- polypeptide = 30-400 aa
- secondary: 3D shape in a localized area
- alpha helix or beta pleated sheets (proteins under a lot of pressure like silk)
- stabilized by H bonds
- tertiary structure: overall 3D shape
- due to interactions between side chains
- stabilized by disulfide bonds, H bonds, ionic bonds, van der waals
21
Q
Fibrous proteins
A
- often outside of cell
- elongated
- structural
- filamentous
-examples: fibroin, keratin, collagen, elastin
22
Q
Globular proteins
A
- most proteins
- compact shape
- folding unique to specific function
- consists of a number of domains
-examples: most enzymes, many cell structure proteins
23
Q
Protein domains
A
- protein segments with a distinct structure and predictable function
- each domain functions in a semi-independent manner
- can mix and match different domains to create custom protein with multiple functions
24
Q
Quaternary structure
A
- not possessed by all proteins
- multiple polypeptides associate to work as one functional protein
- eg. Hemoglobin
- some multiple functional proteins come together to make a multi protein complex or molecular machine
- pyruvate dehydrogenase
25
Protein folding
- Christian anfinsen (1956)
- destabilized disulfide bonds using urea and mercaptoethanol
- then used dialysis to remove urea and mercaptoethanol
- protein refolded all on its own
- demonstrated that all the information needed for correct folding is contained within the amino acid sequence
26
Molecular chaperones
- also called heat shock proteins
- prevent inappropriate interactions by binding to the nascent polypeptide to give it time to fold
- role is to assist folding and assemble
- as proteins come out of the ribosome, chaperones stick mostly to hydrophobia AA exposed in non-native proteins but buried in proteins with a native conformation
- during increased heat, proteins unfold and hydrophobic sites become exposed
- heat shock response: altered gene expression when cell exposed to high temps
-chaperoning has a barrel shape and provides a space where the new protein can fold properly without disturbances from other proteins
27
Hsp70/BiP
-sticks to hydrophobic AAs to allow nascent polypeptide to fold into Native conformation
28
Membrane facts and functions
-5-10nm thick
- functions:
1. Boundary and permeability barrier (separates activities and reactions)
2. Sites for specific proteins
3. Regulate solute transport (gate keepers)
4. Signal transduction (receptor molecules)
5. Cell-to-cell interaction
29
Membrane composition
- lipids
- phospholipids
- glycolipids
- steroids
- protein
- often outweigh lipid composition
- carbohydrates
- found in glycolipids and glycoproteins
- never found alone, always attached to lipid or carbo
30
Phosphoglycerides
- type of phospholipid
- contains a polar head group
- glycerol backbone
- 2 fatty acid tails
- can have different polar head groups (eg. Choline)
31
Head groups of phosphoglycerides
1. Choline = phosphotidylcholine
2. Serine = phosphotidylserine
3. Ethanolamine = phosphotidylethanolamine
4. Inositol = phosphotidylinositol
- different membranes have different distributions of phosphoglycerides
- inner leaflet vs outer layer have very different compositions
- ASYMMETRIC DISTRIBUTION
32
Asymmetric distribution
-different competitions of outer layer of membrane vs inner layer
33
Sphingolipids
- similar to phosphoglycerides, but sphingosine backbone instead of glycerol
- fatty acid tails are usually longer
- due to L shape of sphingosine, only one additional FA tail attached
- cerebrosides and gangliosides
- prominent in membranes of brain and nerve cells
34
Gorter and Grendel
- 1952
- phospholipid bilayer experiment using red blood cells
- isolated phospholipids and put them on water
- the phospholipids arranged themselves to that only hydrophilic areas on water
- discovered that the cells covered 2x as much water as they had calculated it should have -> discovered bilayer
35
Phospholipid bilayer
- will spontaneously form in water
| - contains a cytoplasmic (inner) leaflet and an exoplasmic (outer) leaflet
36
Movement of lipids
- rotation (rotate in one place)
- lateral diffusion (move laterally throughout one side of membrane)
- transverse diffusion (flip flop to other side of membrane)
- thermodynamically unfavourable so rarely occurs
- requires flipases
37
FRAP
- fluorescence recovery after photo bleaching
- a technique to study lipid mobility
- must label cell surface molecules with fluorescent dye
- bleach an area of cell surface with laser beam
- watch fluorescent labeled molecules diffuse into bleached area
38
Membrane fluidity
- critical to membrane function
- transport of solutes across membrane depend on membrane fluidity
- too fluid can cause problems (ions leaking in and out)
- at high temps membrane is MORE FLUID
- at low temps membrane is LESS FLUID
- movement of molecules slows down
39
Fatty acid saturation and membrane fluidity
- UNSATURATED fatty acids = INCREASED FLUIDITY
- more kinks creates less compact structure
- SATURATED fatty acids = DECREASED FLUIDITY
- more organized structure/compact arrangement
40
Homeoviscous adaption
- ability for cell to change lipid content to adapt for temperature
- can increase or decrease the amount of saturation
- can change the length of fatty acid chains
41
Fatty acid length and membrane fluidity
- LONGER hydrocarbon chains = LESS FLUID
- SHORTER hydrocarbon chains = MORE FLUID
- think of spaghetti analogy
42
Cholesterol and membrane fluidity
- at WARM temps = DECREASE FLUIDITY
- Acts as walls to prevent movement making it rigid
- at COLD temps = INCREASE FLUIDITY
- bumpy shape makes gaps and prevents tight packing
-cholesterol usually evenly distributed between two leaflets
43
Fluid mosaic model
-proposed by singer and Nicholson (1972)
- described a fluid bilayer of lipids
- containing mosaic of proteins within it
44
Freeze fracture
- technique to demonstrate existence of proteins in membranes
- freeze membrane and cut with diamond to separate leaflets
- examine layer under microscope
45
Types of membrane proteins
- integral
- peripheral
- lipid-anchored
46
Integral proteins
- penetrate into the hydrophobic region of the bilayer
- securely positioned... dont move
- they are:
1. Asymmetric
2. Amphipathic
3. Alpha-helices (usually)
-transmembrane domains contain AAs with hydrophobic chains
47
Peripheral membrane proteins
- loosely attached to surface through electrostatic bonds
- they are dynamic and move around
- asymmetric distribution across leaflets
48
Lipid-anchored proteins
- on the surface of the membrane
- covalently attached to lipid (strong bond)
- in the EXOPLASMIC leaflet, usually attached to GPI
- in CYTOPLASMIC leaflet, usually attached to fatty acid
49
GPI
- glycosylphosphatidylinositol
| - protein is attached to a sugar that is attached to a phosphotidylinositol
50
Lipid rafts
-localized areas with unique lipid composition that sequester signalling proteins
- 4 features:
1. Tightly packed (many saturated FAs)
2. Sphingolipids (higher % than rest of membrane)
3. Cholesterol
4. GPI proteins
51
Membrane carbohydrates
- ALWAYS on exoplasmic leaflet
- important in cell-cell interactions and sorting proteins to different compartments
- always attached to something
- attached to lipid = GLYCOLIPID
- attached to proteins = GLYCOPROTEIN
52
Glycoproteins
1. N-linked: carbohydrate attached to asparagine amino acid
| 2. O-linked: carbohydrate attached to a serine or threonine AA
53
Glycolipids
- glycolipids in red blood cell membranes determine blood type
- antigens
54
Glycocalyx
- sugar coat
- carbohydrates from glycolipids and glycoproteins stick out from the cell surface and make a sticky surface coat
- important for
1. Cell to cell adhesion
2. Adhesion
3. Protection
- body doesnt recognize some bacteria due to glycocalyx surrounding it/hiding it
55
Membrane protein movement
- Larry Frye and Michael Edidin
- 1970
- “Classic experiment”
- fusion of human and mouse cells that contain different proteins
- exposed to fluorescent antibodies
- after 5 mins the proteins began to mix
- within 40 mins they were evenly distributed
56
Proteins don’t ALWAYS move in membrane
- reasons why a protein might not move:
1. May be anchored to cytoskeleton below
2. May be wedged between other immobile proteins
2. May be attached to something in extracellular matrix
BIOL 2020
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