day 3 Flashcards
4 parts of an amino acid
amino group
side chain (R)
carboxyl group
alfa carbon
what bonds exist with a non-polar side chain (R)
london forces + hydrophobic interactions
what bonds exist with an UNCHARGED polar side chain (R)
hydrogen bonds + hydrophylic interactions + london forces
what bonds exist with a CHARGED polar side chain (R)
electrostatic attraction + hydrophylic interactions + hydrogen bonds + london forces
true/false: polypeptide chains (proteins) have directionality
TRUE
always have an amino group on one end (n-terminus) and a carboxyl group on the other end (c-terminus)
c-terminus
carboxyl group on end of polypeptide chain. new amino acids are added to this end of the chain
n-terminus
amino acid group on end of polypeptide chain. first amino acid that started the chain (new amino acids added to c-terminus)
primary structure
a sequence of amino acids linked by peptide bonds. always in the N-C-C order
secondary structure
local regions of polypeptide chains form 3D shapes. either alfa helix or beta sheet. formed by backbone interactions
2 types of secondary structures formed
alfa helix + beta sheet
tirtiary structure
final folding of polypeptide innitiated/involves mostly side chain (R) interctions
quaternary structure
only in multimeric proteins, the association between 2 or more peptides as they interact to form the final and functional protein
alfa helix formation
formed by hydrogen bonds between oxygen and hydrogen from seperate amino acids four units away on primary backbone
beta sheets
hydrogen bonds between oxygen + hydrogen on the primary backbone from adjacent regions forming rows (antiparallel or parallel)
chaperones
chaperones make polypeptide folding more efficient and reliable
2 ways chaperones work
- binding to partially folded chains
- form folding chambers
conformation
final 3D shape of polypeptide chain. determined by interactions between amino acids that forms the lowest free energy state
what 3 components can make up a tirtiary structure?
alfa helixes, beta sheets, random coils/unstructured regions
domain
segment of a polypeptide chain that folds into discrete and stable structure.
NOT the same as multimeric proteins
multimeric proteins
proteins made from more than one polypeptide chain which form ONE final functional protein
ligand
any substance bound by protein at a specific binding site
antibodies
bind antigens (ligands) at the interface of the heavy and light chains with high specificity
imunohistochemistry
detecting proteins (antigens) in cells or tissue using antibodies tagged with florescent labels.
demonstrates where a specific protein exists in a cell or tissue
substrate
ligand in an enzymatic reaction
active site
a pocket/grove in an enzyme with chemical + structural properties that accomodates the substrate (essentially the binding site for substrate)
explain lock/key model and induced fit model
lock/key model: specific shape of substrate matched exactly with specific shape of active site on enzyme
induced fit model: the enzyme and substrate mold around eachother to fit perfectly (through electrostatic attraction/positive and negative charges) and then the enzyme returns to original form once products are formed
conformational change
binding of the substrate to enzyme induces a conformational change in both enzyme and substrate that helps catalize rxn
competitive enzyme inhibitors
substrate and inhibitor compete for the same active site (if inhibitor is there, substrate cannot bind and trigger a reaction)
allsteric inhibition
there exists both an allosteric site and an active site. when the substrate binds to the active site, the products are produced, if allosteric site is filled with allosteric inhibitor the substrate does not fit and the reaction cannot occur. only one (either substrate or allosteric inhibitor can bind at once)
allosteric activation
there exists both an allosteric binding site and an active site. when nothing is bonded to this molecule (no allosteric activator), the shape of the molecule is incorect and the substrate does not fit. when the allosteric activator binds to the allosteric site, the substrate can fit and the product is produced
kinase
enzyme that adds a phosphate to a molecule (phosphorization)
phosphatase
enzyme that removes a phosphate group (dephosphorylation)
do fatty acids that make up membrain lipids make up polypeptide chains?
NO THEY DO NOT.
still a macromolecule though
lipid functions
energy storage, membrain structure, chemical signaling
types of lipids
fatty acids
tryglicorides
phospholipids
glycolipids
steroids
terpines
fatty acid
long, unbranching hydrocarbon chain with a terminal carboxyl group
saturated fat
no double bonds, written as straight squigly line. solid at room temperature + easy to stack.
unsaturated fat
contains at least one double bond, written as straight squigly line with bend at the double bond. liquid at room temperature, harder to stack.
three main types of membrain lipids
phosphatidylcholine (PC), cholesterol, glycolipids
amphipathic
a molecule containing both hydrophobic and hydrophilic regons
phosphatidylcholine (PC)
most common phospholipid in cell membranes
hydrophilic head:
choline group
phosphate group
glycerol group
hydrophobic tails:
hydrocarbon tail (2)
cholesterol
packs between unsaturated fatty acid chains (polypeptides) to add rigidity to the membrain and reduce permiability
hydrophilic head:
polar head group (OH)
rigid planar steroid ring structure
hydrophobic tail:
hydrocarbon tail (1)
glycolipids
have sugars (carbohydrates) exposed to the extracellular (outside) environment which serve as markers for cell recognition
what ennzyme is used to ‘flip’ phopholipids from one side to the other
flippase
flippase
uses energy from the hdrolysis of ATP to keep phosphatedylserine on the ‘inside’/cell side of the plasma membrane
membrane organization and asymetry is organized where
the golgi aparatus – organized oppositly in golgi membrane, fliped when in real cell membrane
aptosis
programmed cell death/intercellular death program
what does phosphatidylserine (PS) signal when on the OUTSIDE of a cell membrane
EAT ME! (distroy me and recycle organelles etc inside)
small non-polar molecules pass BLANK through the cell membrane
(O2, N2, CO2)
EASILY + QUICKELY
small uncharged polar molicules pass BLANK through the cell membrane
(H2O, ethinol, glycerol)
LESS QUICKELY + EASILY (than small non-polar molecules)
larger uncharged polar molecules pass BLANK through the cell membrane
(amino acids, glucose, nucleosides)
INFREQUENTLY (usually moved through by transport)
ions pass BLANK through the cell membrane
(H+, Na+, K+, etc)
NEVER pass through cell membrain on their own (need help, atp)
types of proteins imbedded in membrane (4)
transporters and channels
anchors
receptors
enzymes
passive transport
molecules move with concentration gradient (still need help moving through channel for example but is still moving with concentration gradient so no ATP needed)
active transport
molecules moving against concentration gradient. needs energy to drive movement against gradient, ATP
simple difusion
freely moving through membrane (down conc. gradient)
voltage gradient
difference in charge accross a membrain
concentration gradient
difference in concentration accross a membrain
electrochemical gradient
a combination of voltage and concentration gradients
sodium/potassium pump
uses ATP to pump 3Na+ ions out and 2K+ ions in to maintain correct eletrochemical gradient across the cell membrane
symport
moves 2 molecules at same time (one down its gradient, the other up) by using the energy released from the movement of one molecule down its gradient (ex. Na+) to simultaniously move the second molecule up its concentration gradient (ex. glucose)
