BIOCHEM EXAM 2

• -specific
• -regulated in several ways
• -transform energy
• -don't move equilibrium
• -stabilize transition state
• -active site cleft
• -change in response to correct substrate

• Oxidoreductases
• Transferases
• Hydrolases
• Lyases
• Isomerases
• Ligases

oxidation- reduction

group transfer

hydrolysis reactions

add/remove bonds to form double bonds

intramolecular group transfer

ligation of 2 substrates at the expense of ATP hydrolysis

• 1. a rxn can only take place spontaneously if changeG<0
• 2.if changeG=0 system is at equilibrium; no net change
• 3. if changeG>0 an input of free energy is required to drive the rxn
• 4.changeG of a rxn is independent of the path of transformation
• 5.changeG provides no information about the rate of the rxn

• changeG = changeH - TchangeS
• (not at equilibrium)
• at equilibrium changeG=0

• Standard free energy change
• changeG⁰'

V_o=V_max([S]/[S]+K_M)

• S=substrate
• V_max=maximal rate
• V₀=slowest rate of reaction

• lowercase k
• only look at a rxn in a single direction

• CAPITAL K
• look at rxn in both directions

rectangular hyperbola

• sigmoidal curve
• multiple interacting active sites

double reciprocal plot

• turnover number: duration of contact between enzyme and substrate.
• high turnover means a fast enzyme and vice versa.

• Michaelis constant
• substrate concentration at which the reaction rate is half of its max value.

maximum rate of the reaction

• inhibitor combines with enzyme at the active site
• V_max gets lower as if less enzyme were present

• doesn't prevent substrate from binding
• K_m DOESN'T CHANGE
• decrease turnover number

sugars that are diastereomers and differ at only one asymmetric center

isomers that are NOT mirror images

isomers that are mirror images of each other

differ in order of attachment

two alkoxy groups to the same carbon

two hydroxyl groups to the same carbon

• one hydroxyl
• one alkoxy

sugars that react all called reducing sugars

• attachment at the anomeric carbon
• bond formed between the anomeric carbon and the oxygen of an alcohol

lactose.

• nutritional resevoir in plants
• is a storage form of glucose
• polysaccharide

• major polysaccharide found in plants
• most abundant
• structural role

• major polysaccharide found in plants for storage of energy
• storage form of glucose

• alpha: OH group is on opposite side of the ring as the anomeric carbon (CH₂OH)
• beta: OH group is on the same side of the ring as the anomeric carbon

change the aldo form from -ose to -ulose

the chemical inversion of alpha and beta anomers

COOH at C-1

COOH at C-6

COOH at c-1 and c-6

5 membered ring

6 membered ring

• 1. joined by ETHERS rather than ESTERS (more resistant to hydrolysis and extreme environments)
• 2. alkyl chains are BRANCHED not linear (resistant to oxidation)
• 3.central glycerol is INVERTED. Have different lipids (no fatty acids).

• 1.sheetlike
• 2.lipids and proteins
• 3.hydrophilic and hydrophobic
• 4.specific proteins mediate functions
• 5.noncovalent assemblies
• 6.asymmetric
• 7.fluid structures
• 8.electrically polarized

• not attached to the membrane itself
• attached to membrane elements

• attached permanently to the living cell
• PART of the membrane

• found in bee and snake venom
• frees arachonoic acid- causes pain

• 20 carbons and 4 double bonds 5,8,11,16
• gives rise to inflammation process
• fatty acids stick together
• aspirin interferes with the process
• activated by prostaglandin

• fights pain and inflammation
• blocks cyclooxygenase which is an enzyme that activates prostaglandin synthesis and cause pain, shock and immobilization

lateral diffusion but not able to flip flop or leave the membrane

• promotes inflammation
• integral protein
• activated by arachonoic acid

ions and most polar molecules

outside of the cell

• "i am positively blue over you"
• stained blue
• primitive bacteria; first to exist
• large cell membrane
• ONLY ONE CELL MEMBRANE
• must stay at source of food to eat

• have a small cell membrane
• two cell walls; one for protection one for permeability
• have prions (stomachs) can take food to go and digest

active

passive

• form of passive transport
• has a V_max which means there is a max rate of exit or entry so graph is a rectangular hyperbola
• uses channels; ligand-gated which means door must be opened by something

• requires energy to take place
• moves against the gradient
• usually involves ions
• utilizes pumos

• doesnt require ATP
• carries molecules uphill
• associates unfavorable molecules with ones that are more favorable
• antiporters or symporters

• allows ions to flow across membranes 
• gated by needing a certain ligand or voltage
• central to the functioning of our nervous systems

• allows the flow of metabolites or ions between cells
• made up of 12 molecules of connexin

there is an unequal distribution of molecules

1.0

• 2 different species flowing in opposite directions
• ex: Na+ can only enter when K+ leaves

• use the flow of one species to drive another species into the cell in the same direction
• "you can only come to the party if you bring a date"
• ex: glucose usually moves against the gradient but it can go inside the cell if it goes with sodium

inhibits dephosphorylation disrupts Na+ equilibrium and makes there have more INSIDE the cell which leads to a slower extrusion of Ca+ which leads to heart problems (enhanced heart contractions)

• removes drugs that enter the cell by pumping them out before it has an effect
• ex: P-glycoprotein

• have an ATP binding cassette (2 ATP binding domains)
• 1. MDR
• 2. CFTR
• are in contact but dont bind strongly without ATP
• mechanism involves scissoring of 2 subunits

• transports Na and Cl
• in cystic fibrosis the Cl- transporter malfunctions which causes  NaCl on the skin which causes problems

• enables ion conductance measurement through the path of a cell membrane
• pipette with two electrodes and the part of the cell that the electrode is suctioned to will have the same ion conductance read by the electrodes
• the flow through a single channel can be measured with time resolution in microseconds

• detachment via pulling in the patch clamp technique
• dont know how many channels you're getting can see channel opening and find out how many ions go through per second

• entire cell and plasma membrane monitored
• suctioning the whole cell
• less useful than excised, less precise

• best understood ligand-gated channel
• binding of acetylcholine leads to the opening
• densely packed receptor (20,000 μm)

• Acetylcholine is released from the pre-synaptic membrane inresponse to depolarization.
• It travels across the synapse and "pushes a button" on the receptor which opens a ligand gated sodium channel, allowing Na+to flow in.
• Then potassium channels open, allowing K+ to flow out.

• composed of 5 subunits
• anchored to post synaptic membrane (glycolipid tethered there)
• rotation effect; all units break right then opens up
• turnover 25,000/sec
• VERY IMPORTANT
• binding two causes receptor to open

• inhibits acetylcholinesterase
• will kill you

• responsible for transmitting information initiated signals such as hormones, smells, taste
• when ligands bind to this receptor they initiate G-proteins
• passes through the membrane 7 times

• activates adenylate cyclase
• activated by 7TM receptors bind with ligands

• turns cyclicAMP to ATP
• increases concentration of cAMP

• activated by g proteins
• cleavage of Phosphatidyl Inositol Bisphosphate into 2 parts
• 1.IP3
• 2.DAG

opens calcium channels

activates protein kinase c

• phosphatidyl inositol bisphosphate
• cleavage results in release of calcium and activation of protein kinase C

calcium

• detects influx of Ca2+
• binds 4 ions that changes it shape

• activated by cleavage of pip2
• stimulates expression of other genes by phosphorylation of the CREBS transcriptional activation cycle
• phosphorylates target proteins

• enzyme looks for RRGSI but finds close match, RRGAI, but enzyme cant phosphorylate this so RRGAI acts like a chew toy
• presence of S is real substrate

calcium resevoir in cell

ATP, NAD+, NADH, NADP+, NADPH, FAD, FADH2, FMN, FMNH2,Coenzyme A

-7.3 kCal/mol which dramatically changes K_eq

couple favorable with unfavorable to drive the reaction

• 1. digestion- proteins hydrolyzed to AA, polysaccharides to simple sugars, fats to glycerol & fatty acids. NO USEFUL ENERGY. Prep stage.
• 2. conversion to acetyl units in acetyl CoA. Some ATP generated but not much compared to 3rd. 2 ATP

• 3.complete oxidation of acetyl unit in acetyl CoA to ATP
• . acetyl coa brought into the citric acid cycle where it is completely oxidized proton gradient is created which is used to synthesis ATP. 28-36 ATPS.

forms covalent bonds but requires free energy from ATP cleavage

• energy charge regulates metabolism
• ATP generating pathways (catabolic) are inhibited by high energy charge whereas ATP utilizing pathways (anabolic) pathways are stimulated by high energy charge