bio 362

co factor addition vs ptm addition

ptm- covalent addition of one phosphate sourcing off rna atp

cfa-noncovalent addition of rna nucleotide that changes conformation of protein it binds to

GTP and ATP are about what

conformation, NOT ENERGY

cofactor binding is not limited to what

gtp,, atp can also be a cofactor

cofactor nucleotide transport

co factor binding completely changes comformation of protein so it lets small molecule through

\-also activates enzymatic energy

what do proteins do

bind to biological stuff to induce an effect

effect of proteins

-acct upon substrate, enzymatic activity, scaffold, transport

X-ray crystallography

protein structure

\-make ribbon diagrams

\-requires very pure protein sample and all proteins in identical conformation(so refraction pattern is the same through every protein)

x ray crystallography drawn

\-proteins must create crystals (not floppy)

\-solid structure

\-done by dehydrating them

western blotting

protein size, abundance, location

\-show how much protein is present

\-uses gel electrophoresis

western blotting image

-compare between control group and another group (treatment or disease)

immunohistochemistry

protein location and abundance

\-uses color to distinguish between different properties

antibodies

use these proteins to help find proteins in tissue, determine how much of them are in a sample

\-used recently for medications

antibody state

they are proteins!-y shape

antibody function

bind to stuff

\-when a bunch of antibodies bind to a toxin, your body will recognize that the clump of antibodies is surrounding something that is trying to kill you

what happens when body recognizes antibody cluster

\-activates immune system

\-makes it unable to kill you

\-activates phagocytic cells in your body so they will ingest the toxin and destroy it

other applications for antibodies

-can be developed for therapy, diagnostics, and discovery

antibodies and immunohistochemistry drawing (left side only)

-finds exactly where the one protein is located

common features of all cells

\-all cells store hereditary info in dna

\-dna is replicated through templated polymerization

\-dna is transcribed into rna

\-rna is translated into proteins

\-all cells are enclosed by a plasma membrane

what is a membrane

selective barrier

\-thin sheet acting as a boundary, lining, or partition

\-filter water through membranes

membranes have to be what

modifiable and have limits

what are plasma membranes made up of

lipids and proteins forming the cell boundary

what makes up legs of phospholipids

fatty acid chains (20 diff)

fatty acids make up what

fats, lipids, and membranes

are fatty acids bad?

fatty acids\=bad but fats\=super bad

no cells can exist without what

phospholipid bilayer, fats, and fatty acids

\-life giving unit!

how are fatty acids stored

as triglycerides (fats)

fatty acids as energy

* way better than glucose for energy
* because every 2 carbons get us an acetyl coA, NADH, and an FADH2
* these are all necessary to power our cells/mitochondria

3 types of fat cells

brown, beige, and white

brown fat cells

convert chemical energy into heat to protect against cold weather

beige fat cell

immature cell in white fat tissue matures to burn fat

white fat cell

most common fat cell, used to store fat and found beneath the skin and abdomen

smooth er and fats

makes and stores all lipids

smooth er making and storing lipids

1. phospholipid bilayer forms at surface of er
2. phospholipid monolayer begins separation with triglycerols and cholesterol esters in middle (forming circle) and proteins involved on the outside
3. circle detaches from er, creating the full, circular lipid

fat

glycerol backbone linked to 3 fatty acids

fatty acid

long chain hydrocarbon bound to a carboxyl group

how are fatty acids stored as an energy reserve

through an ester linkage to glycerol to form triglycerides

lipid aggregates(structure)

\-fatty acids have a hydrophilic head and a hydrophobic tail

\-in water, they can form a surface film or small micelles

\-their derivatives can form larger aggregates held together by hydrophobic forces

triglycerides

can form large spherical fat droplets in the cytoplasm

phospholipids and glycolipids

form self-sealing lipid bilayers that are the basis for all cell membranes

common fatty acids

stearic acid, palmitic acid, and oleic acid

saturated fat

A lipid made from fatty acids that have all single bonds between carbon atoms

unsaturated fat

A lipid made from fatty acids that have at least one double bond in its hydrocarbon tail between carbon atoms.

double bond in unsaturated fats

rigid and creates a kink in the chain

\-rest of the chain is free to rotate about the other c-c bonds

how are fatty acids distinct

\-length of hydrocarbon chain (how many hydrocarbons-between 16 and 18)

\-saturated or unsaturated

carboxyl group on fatty acids

only hydrophilic part (cooh)

phospholipid drawing

-choline is smtg phosphate bonded to-changes

saturated lipids only

not very permeable, tighter

Mixed Saturated and Unsaturated lipids

more permeable

longer hydrocarbons

less permeable

Phosphatidylserine

only polar head group that has net charge on it (negative)

\-almost always only a cytoplasmic phospholipid

phospholipid names

1st is phosphatidyl (because of 2 fatty acids)

2nd is polar head group

fatty acids building blocks

stored as fats, used to make lipids, which make up membranes

cholesterol

sterol/ringed lipid, small polar head group

\-rigid ring structure makes it so can't work like phospholipid

\-can move between polar and hydrophillic zones to change character of phospholipid membrane

\-amount affects how changes

shape of phospholipid

like a cylinder, can pack them tightly

lipid bilayer

collection of phospholipids

* set limit and restricted access to cytoplasm
* like wall (stuff can get through-water and gas)

internal lipid bilayers

establish limit and restricted access to inside of organelles

\-fluid bilayer

fluidity of phospholipid bilayer types

\-lateral diffusion

\-flexion

\-flip-flop sides

\-rotation

things that affect membrane fluidity

\-long vs short chains

\-saturated vs unsaturated

\-cholesterol

\-phospholipid shapes

\-composition

easier fluid movement

with more unsaturated chains (cis-double bonds)

membrane fluidity restrictions (high to low permeability)

high permeability

\-hydrophobic molecules (o2, co2, n2, steroid hormones) (go straight through)

\-small, uncharged polar molecules (h20, urea, glycerol, nh3) (go through sometimes

\-large, uncharged polar molecules (glucose/sucrose) (rarely go through)

\-ions (H+, Na+, HCO3-, Ca2+) (never go through

low permeability

sugar modified lipids

only extracellular lipids

lipid rafts

\-zones in bilayer that are not very fluid

\-embedded with proteins grouped together

\-important if need to bring in smtg that usually can't get through

\-fluid but not homogenous

another name for the plasma membrane

fluid mosaic membrane

types of proteins that associate with the lipid bilayer

integral, lipid-anchored, and peripheral

integral proteins

Integral proteins that span the membrane(also transmembrane)

\-fully through membrane with functional units on both sides

integral membrane proteins that aren't transmembrane

alpha helix will span half of membrane but double back to the same side

\-doesn't go completely across membrane

lipid-anchored proteins

covalent attachment of a lipid to an amino acid side chain within a protein

\-PTM

\-permanent

\-not coded in our gene

peripheral proteins

The proteins of a membrane that are not embedded in the lipid bilayer; they are appendages loosely bound to the surface of the membrane

\-either intra or extracellular side

\-not physically connected to membrane (work at outside of membrane)

What are GPI anchors?

\-sugar coated

\-LIPID ANCHOR that is added if we have smtg in the er that needs to move to the outer leaflet

\-sugars=important outside of cell

\-holds protein to fatty acid and adds sugar residue in this one place

hydropathy plots

* how much does this protein hate water
* predict where and how many membrane spanning regions are

what is a beta barrel

A structural form of beta sheet, in which it forms a PORE to transport materials

\-makes easy to move stuff through body of membrane

protein intra/erchain bonds

disulfide bonds

\-outside cell or need to alter structure w another protein

integral proteins in more detail

\-have inter and intra chain disulfide bonds

\-have oligosaccharides attached to the protein(in exoplasm)

\-have sulfhydryl groups attached in cytosol(outside)

\-transmembrane alpha or beta helices

apical plasma membrane

absorbs substances from the lumen

lateral plasma membrane

interacts with neighboring epithelial cells

basal plasma membrane

has binding sites for basal lamina

factors that affect charge separation

lipids, proteins, and concentration

electrochemical gradient

gradient of electrochemical potential that can move ions/small molecules across a membrane

2 parts of the electrochemical gradient

\-chemical gradient (diff in solute concentration across membrane)

\-electrical gradient (diff in charge across membrane)

Types of membrane transport

passive and active

passive transport

movement down concentration(uncharged) and electrochemical(charged) gradient (both involved)

\-move based on conc., pulled based on charge

membrane potential

the voltage difference across a membrane

active transport

the movement of materials through a cell membrane using energy and enzymes

channel mediated transport

\-Passive transport

\-Allows only one type of solute to pass through

\-Allows membranes to be selectively permeable

channel vs transporter

-both passive, but transporters can be active

channel vs transporter graph/relationship

\-rate they move stuff across

\-transporters take a bit longer to get to max potential

states transporter proteins can be in

outward-open, occluded, inward-open

channel protein

protein that forms a channel to allow a particular molecule or ion to cross the plasma membrane

\-for molecules that can't do diffusion

\-open=movement through (regulated)

transporters

both passive and active transport

\-open on one side or open to neither

symport

same direction

antiport

opposite direction

uniport

carries only one type of solute

types of coupled transport

symport and antiport

light driven pump

uses light as energy

atp-driven transport

Transport of solute against gradient by utilizing energy derived from ATP hydrolysis

atp-driven transport types

p-type, ABC transporter, V-type proton pump, F-type ATP synthase

p-type pump

\-used for ions

\-establish charge gradient

\-active

ABC transporters

\-use atp to transport small molecules

\-atp binding casette

\-not as specific as p-type pumps

\-pull out small molecules quickly

V-type proton pump

ATP drives transport

F-type proton pump

works in reverse