biochem Flashcards
amino acids are what
molecs with two functional groups - amino group (NH2) carboxyl group (COOH)
chiral centres mean what
four different groups attached to it (except glycine)
major sites of metabolic activity in body
liver, skeletal and cardiac muscles, brain, adipocytes
ahti-hypertensive medications are called what
ACE inhibitors
ACE does what
catalyzes reaction that converst peptide angiotensin I to angiotensin II
angiotensin II does what
directly causes constriction of blood vessels to raise blood pressure, and also stimulates release of hormon aldosterone
do catalysts impact the thermodynamics of a biological reaction?
no
equilibrium position doesn’t change
oxidoreductases
catalyze redox reactions
often have cofactor that acts as e- carrier such as NAD+ NADP+
reductant is electron ______
donor
oxidant is the electron ________
acceptor
transferases
catalyze movement of functional group from one molecule to another
kinases catalyze the transfer of a phosphate group, generally from ATP, to another molecule
hydrolases
catalyze breaking of compound into two molecules using the addition of water
phosphatase - cleaves phosphate group from another molecule
lysaes
catalyze cleaage of a single molecule into two products
do not requre water as a substrate and do not act as oxidoreductases
isomerase
catalyze rearrangement of bonds within a molecule
catalyze rxns between steroisomers as well as constitutional isomers
ligases
catalyze addition or synthesis reactions, generally between large similar molecules and often require ATP
remember nucleic acid synthesis and repair
endergonic rxn
requires nrg
exergonic rxn
nrg is given off
enzymes lower the activation energy of a reaction by what
stabilizing the transition state
lock and key theory
enzymes active site (lock) is already in appropriate conformation for substrate (key) to bind
induced fit
more scienifically accepted
stats with substrate and enyme active site that don’t seem to fit together but once subbstrate is present and ready to interact with active site, molecules find induced fit is comfy for both
apoenzyme
enzyme without its cofactor
holoenzyme
enzyme with necessary cofactor
tightly bound cofactors or coenzymes that are necessary for enzyme function
prosthetic groups
cofactors are generally __ molecs or________ ions, and coenzymes are small ______ groups
inorganic
metal
organic
the only way to increase vmax is to what
increase enzyme conc
michaelis menten equation is what
describes how the rate of the rxn depends on the conc of both the enyzyme and substrate which forms product
km is conc at what
1/2 the enzyme’s active sites are in use and the velocity of rxm is half of vmax
it is substrate concentration
michaelis constant
a low km is what and a high one is what
low high affinity for substrate
high is low affinity for enzyme
kcat is what
equilibrium constant for a rxn that is being catalyzed by an enzyme
ratio of kcat/km is what
catalytic efficiency of enzyme
higher catalytic efficiency is what
more efficient enzyme
lineweaver burk plot is a
double reciprocal graph of the michaelis menten equation
x axis of lineweaver burk is what
-1/km
intercept of the line with y axis in lineweaver burk is what
1/vmax
where is the lineweaver burk plot useful?
when determining the type of inhibition that an enzyme is experiencing bc vmax and km can be compared without estimation
cooperative enzymes
have multiple subunits and mutliple active sites
hill’s coefficient is what
mathematical representation of the cooperativeness of an enzyme
cooperative enzymes are subject to activation and inhibition, both________ and through______ sites
competitively
allosteric
if hills coefficient is:
> 1
<1
=1
positively cooperative binding is occuring - such that after one ligand is bound the affinity of the enzyme for further lingans increases
negatively cooperative bidning is occuring, such that after one ligand is bound the affinity of the enzyme for fruther ligands decreases
the enzyme does not exhibit cooperative binding
enzyme catalyzed rxns tend to double in velocity for every ____ increase in temp until optimum temp is reached
10 degrees celsius
pH affects the ___ of the active site, but also because changes in pH can lead to _ of the enzyme
ionization
denaturation
increasing levels of salt can disrupt what causing what
hydrogen and ionic bonds
causes partial change in the conformation of the enzyme and can cause denaturation
feed forward regulation
regulated by intermeiates that precede the enzyme in the pathway
competitive inhibition
how to overcome as well
involves occupancy of active site
can be overcome by adding more substrate so that the substrate to inhibitor ratio is higher
does adding a competitive inhibitor alter vmax?
no, because if enough substrate is added, it will outcompete the inhibitor and be able to run the reaction at maximum velocity
what does a competitive inhibitor increase
measured value of km - bc substrate concentration has to be higher to reah half the maximum velocity in the presence of the inhibitor
noncompetitive inhibitor
binds to allosteric site instead of active site, which induces a change in enzyme formation
cannot be overcome by adding more substraatewh
what does a noncompetitive inhibiotr do
decreases measured value of vmax becauee there is less enzyme avaiblable to react - it does not alter value of km bc any copies of enzyme that are still active maintain same affinity for their substrate
mixed inhibition
results when an inhibitor can bind to either the enzyme or the enzyme ubstrate complex, but has different affinity for each
bind at allosteric sites
what does mixed inhibition alter?
experimental value of km depending on prefernece of inhibitor for enzyme vs enzyme substrate complex
if mixed inhibitor preferentially binds to enzyme, it increases the __ value and lowers afiniity, if the inhibtor binds to the enzyme substrate comple, it ____ the km value and increases finity . in either case, ___ is decreased
km
lowers vmax
uncompetitive inhibitors
bind only to tne enzyme substrate complezx and essentially lock the substrate in the enzyme preventing its release
irreversible inhibiton
active site is made unavailabe for a prolonged period of time or enzyme is permanently altered
example of irreversible inhibtion
aspirin
allosteric enzymes
alternate btwn an active and inactive form
actiavator will result in shift that makes active site more available for binding to substrate where as inhibitor will make it less availbal e
covalently modified enzymes
activated or deactivated by phosphorylation or dephosphorlyation
zymogens
contain catalytic active domain and regulatory domain
regulatory domain must either be removed or altered to expose the ative site
apoptotic enzymes exnhibit similar regulation
most zymogens have sufix - ogen
collagen
characteristic trihelical fiber
makes up most of the EM of connective tissue
elastin
important component of EM
strethc then recoil like a sping
keratin
intermediate filamnt proteins - found in epithelial cells
contribute to mechanical integrity of cell and function as regulatory proteins also
actin
microfilmamtns and thin filaments in myofibrils
most abundant protein in eukaryotic cells
positive and negative side - polarity allows motor proteins to travel unidirectionally along an actin filamenttu
tubulin
microtubules
structure, chromosome separation
negative end = adjacent to nucleus
positive end = perihpery of cell
primary structural proteisn in body
collagen
elastin
keratin
actin
tubulin
cold elephants kill angry tigers
motor proteins
use ATP to power conformation changes associated necessary for motor function
myosin
interacts with actin
celluar transport
single head and neck
mvmt at neck = sarcomere contraction
kinesins and dyenins
kinesins align chromosomes during metaphase and depolymerize microtubules during anaphase of mitosis
dyneins involved in sliding movement of cilia and flagerlla - both important for vesicle transport
kinesins bring vesicles toward positive end
dyneins bring vesicles toward negative end
cell adhesion moleculs
protins found on surface of most cells and aid in binding cell to em or other cells
cadherins
glycoproteins that mediate calcium dependent cell adhesion
often hold similar cell types tgt , like epithelial cells
integrins
two membrane spannin chains alpha beta
cellular signalling
selectins
bind to carb molecs that project from other cell surfaces
expresssed on white blood cells and endothelial cells that line blood vessels
host defence
when antibodies bind to target antigens, three outcomes
neutralize antigen making pathogen or toxin unable to exert effect on body
marking pathogen for destruction by other wbc immediatley - opsonization
clumping together he antigen and antibody into large insoluble protein complexes that can be phagocitozed and digested by macrophases
3 main types of proteins responsible for biosignalling
ion channels
enzyme linked receptros
g protein coupled receptors
faiciliated diffusion
passive transpot - diffiusion of molecs down concentration gradient through pore in membrane created by transmmebraneprotein
used for molecs that are impermeable to membrane
enzyme linked receptors domains
membrane spanning domain
ligand binding domain
catalytic domain
membrane spannign domain
anchors receptor in cell membrane
ligand binding domain
stimuated by appropriate ligand and induces conformational charge that activates catalytic domain
three main types of g proteins
gs - stimulates adenlyate cyclase - increases lvls of cAMP in cell
gi inhibits adenylate cyclase - decreases lvls of cAMP in cell
gq activates phospholipase C which cleaves phospholipid from membrane to form PIP2 - which is then cleaved into DAG and IP3 - iP3 can open calcium chanels in ER increasing calcium lvls in cell
5 major classes of non enzymatic protins
structural proteins
motor proteins
binding proteins
immunoglobins
biosignalling proteins
native PAGE
type of electrophoresis
method for analyzign proteins in native states
limited by varying mass to charge and mass to size ratios of celllar proteins
most useful to compar molecular size or chare of proeins known o be similar in size from other analytica methods SDS PAGE or size exclusion chromatography
in isoelectric focusing, a protein stops moving when what
pH = pl
SDS PAGE
separates proteins on babses of relative molecular mass alone
isoelectric focusing
exploids acidic and basic properties of AA by separating on basis of isoelectric point (pI)
anode in isoelectric focusing
A+
has Acidic (H+ rich gel) and a plus charge
all chromatography is about what
affinity of substance for the mobile and stationary phases except for size exclusion chromatorgraphy
4 most common forms of chromatography
column chromatography
ion exchange chromatography
size exclusion chromatography
affinity chromatography
after protein is isolated, next step of analysis is what
study protein structure
activity
conc
a a composition
protein structure can be determined through
x ray crystallogaphy and nuclear magnetic resonance spectroscopy
amino acid composisiotn of protein can be determined how
complete protein hydrolysis and subsequent chromatographic analysis
small proteins best analyzed with edman degradation
uses ccleavage to sequence proteins of up to 50 to 70 aa
larger proteins digestion ith chymotrypsin, trypsin, cyanogen bromid, etc..
2 main ways to determind conc of protein in a sample
UV spectroscopy
bradford protein assay
bradford protein assay
mixes protein in solution with coomassie brilliant blue dye
gives up protins upong bdigin to amino acid groups, turning blue in process
ionic attractions between dye and protein then stabilize this blue form of the dye
bradford protein assay colours meaning
acidic form = brown
basic form = blue
simplext monosaccharides
three carbon atoms - trioses
three types of seteroisomers
same sugars in dif optical families are enantiomers - D-glucose and L-glucose
two sugars that are in the same family - that are not identical and are not mirror images of each other are diastereomers
special subtype of iastereomers are those that differ in configuration at exactly one chiral center - epimers - D-ribose and D-arabinose which only differ at C-2
mutarotation
spontaneous change of configuration about C-1
two standard reagents used to detect presence of reducing sugars
tollens reagent and benedicts reagent
tollens: frehsly prepared - starting with silver nitrate which is mixed with NaOH to produce silver oxide - silver oxide is dissolved in ammonia to produce [Ag(NH3)2]+ - actual tollen’s reagent
benedict’s: aldehyde group of an aldose is readily oxidized, indicated by a red precipitate of Cu2O
tautomerization
rearrangement of bonds in a compound, usually by moving a hydrogen and forming a doubl bond
enol
compound with double bond and alcohol group
glycogen is what in animals
carbohydrate storage unit
3 types of lipids
structural
signalling
energy storing
3 types of structural lipids
phospholipids
sphingolipids
waxes
phospholipids
phosphate and alcohol that compirse the polar head group joined to hydrophobic fatty acid tail by phosphodiester linkages
fully saturated fatty acid tails will have what
only single bonds
unsaturated fatty acid includes what
one or more double bonds - double bonds introduce kinks into the fatty acid chain, which makes it difficult for them to stack and solidify
glycerophospholipids
contain a glycerol backbone bonded by ester linkages to two fatty acids and by a phosphodiester linkage to a highly polar head group
sphingolipids
hve sphingosine or sphingoid backbone
also have long chain nonpolar fatty aid tails and polar head groups
four major subclasses of sphingolipid
ceramide - single hydron atom as its head group
sphingomyelins - major class of sphingolipids that are also phospholipids - either phosphocholine or phosphoethanolamine as head group - contains phosphodiester bond
glycosphingolipids - not phosphlipids bc they contain no phsophodiester linkage
cerebrosides - single sugar, globosides have two or more
gangliosides - glycolipids that have plar head groups composed of oligosaccharides with one or more n-acetylneuraminic acid - NANA
waxes
esters of long chain fatty acids with long chain alcohols - form pliable solids at room emprature
4 types of signalling lipids
terpenes and terpenoids
steroids
prostaglandins
fat soluble vitamins
terpenes and terpenoids
metabolic precursors to steroids and other lipid signaling molecules - vried independent functions
strong scented
terpenoids - derivatives of terpenes that have undergone oxygenation or rearrangment of the carbon skeleton
steroids
characterized by having four cycloalkane rings fused together - three cyclohexane and one cyclopentane - steroid functionality is determine by the oxidation status of these rings, as well as the functional groups they carry
cholesteroal
steorid of primary importance
responsible for mediating membrane fluidity
amphipathic molecule containing both hydrophilic and hydrophoboiv omponnents
prostaglandins
20-carbon molecules unsaturated carboxylic acids derived from arachidonic acid contain one five carbon ring
act as paracrine or autocrine signalling molecules
fat soluble vitamins
a d e k
vit a
carotene - unsaturated hydrocarbon - vision
vit d
cholecalciferol - consumed or formed in uv light driven reaction
lack can result in rickets - condition seen in children and characterized by underdeveloped curved long bones as well as impeded growth
vit e
tocopherols and tocotrienols
substicuted aromatic ring with long isoprenoid side chains
vit k
koagulation
saponification
ester hydrolysis of triacylglycerols using strong base
base used is lye
surfactant
- lowers surface tnesion at surface of liquid
miceelles
tiny aggregates of soap w hydrophobic tails turned inward and the hydorphilic heads turned outward thereby shielding the hydrophobic lipid tails and allow for overall solvation
colloid
when 2 or more different phases combine to form what appears to be a single phase
central dogma of molecular biology
the way proteins are made in our body - first dna is transcirbed into rna and then ran is translated into protein
mRNA
transcribed from template dna strands by RNA polymerase enzymes in nucleus of cells
in eukaryotes, mRNA is what
monocistronic - each mRNA molecule transltaed into only one protein product
in prokaryotes it can be polycistronic
wobble position
variable third base in codon - evolutionary development designed to protect aginast mutations in the coding regions of our dna
3 types of point mutations
silent / degenerate
missense
nonsense
3 main steps of translation
initiation
elongation
termination
3 binding sites for trnas in robosomes
a - amino acylcite
p - peptidyl site
e - exit site
necessary requirements for each step of ranslation
initation - IF ad GTP
elongation - EF and GTP
termination - RF and GTP
4 types of post transltion processing
phosphoryatoin
carboxylation
glycsylation
prenylation
two types of operons
inducible systems and repressible systems
inducible systems
repressor is bonded tihglty to operator system and thereby acts as roadblock
rhna polymerase is unable to get from promotor to structural gene bc repressor is in the way
negative control - binding of protein reduces transcirption actvity
basically, the system is normally off but can be made to turn on given a particular signal
positive control
binding of protein to DNA icnreases transcirtipion
___ operon is negative inducible system whereas ___ operon is negative repressible system
lac
trp
cis regulators vs trans reglatorus
cis - same vicinty as gene they control - enhancers
trans - travel through cell to their point of action - transcirptio factor
acetylation of histone proteins does what
decreases positive charge on lysie residues and weakens the ineteraction of tehe histone with the dna
results in open chromatin conformation that alows for easier access of transcirptional machinery to dna
fluid mosaic model
states the plasma membrane is mostly a loose fluid membrane that is studded and held together by protesin cholesterols, and other groups
lipid rafts
similar liids with or without associated proteins that serve as attachment points for other biomolecules - often serve roles in signaling
micelle
- single layered phospholipi vesicles
liposoms
double layered phospholipid vesicles
chylomicrons
transport fatty acids fromt he diet as triacylglycerols from the intesitne
cholesterol necessar why
regulates membrane fluidity and also necessary in syntehsis of all steroids
gap junctions
aka connexons - formed by alignment and interaction of pores composed of six molecules of connexin
desmosomes and hemidesmosomes
desmosomes - bind adjacent cells by anchoring to their cytoskeletons - formed by interactions between transmembrane proteins associated with intermediate filaments inside adjacent cells
hemidesmosomes - similar function, but main function is to attach epithelial cells to underlying structures, especially the basement membrane
negative change of g IS HWHAT AND POSITIVE IS WHAT
passive transport
active transport
primary v secondary active trasnport
primary - uses ATP or another energy molecule to diretly power the transport of molecules acorss and membrane
secondary - coupled transport - uses energy to transport particles across membrane, however in conrast to primary active transport, there is no direct coupling to ATP ydrolysis
symport and anitport
when both particles flow the same direction across membrane
opposite directions - antiport
endocytosis
when cell memrane invaginates and engults material to bring it into the cell
micelles are what
water soluble spheres with a lipid soluble interior
they have a hydrophobic centre
at the end of the ilieum, what happens to bile salts?
actively reabsorbed and recycled - any fats that remains in the intestine will pass into the colon and ultimately ends up in the stool`
ratio of free fatty acids to gycerol
3:1
triacylglycerol molec is composed of glycerol and three fatty acids
classes of lipoprotiesn
chylomicrons
vldl
idl (vldl remains)
ldl
hdl
chylomicrons and vldl primarily carry what and ldld and hdl primarily charry what
triacylglycerls
cholesterol
citrate shuttle
carries mitochondrial acetyl-coa into cytoplasm where synthesis occurs
what is the rate limiting step in cholesterol biosynthesis?
synthesis of mevalonic acid in smooth ER
fatty acid synthesis and beta oxidation are what
reverse processes
four steps of beta oxidation
oxidation of fatty acid to form double bond
hydration of double bond to form hydroxyl group
oxidation of hydroxyl group to form a carbonyl (beta keoacid)
splitting of the beta keoacid into shorter acyl-coa and acetyl co-a
ketone bodies
transportable forms of acetyl coA
produced by liver and used by other tissues during prolonged starvation
flavoproteins
most notable for presence in mitochondria and chloroplasts as electron carriers
also involved in modification of other b vitamins to active forms
3 main metabolic states:
postprandial (absorptive) state
greater anabolism than catabolism
postabsorptive (Fasting) state
counterregulatory hormones
prolonged fasting (Starvation)
lipolysis rapid resulting in excess acetyl co A
two types of cells insenstiive to insulin
nervous tissue
rbc
insulin is secrted by what
beta cells of pancreatic islents of langerhans
tissues in whic glucose uptake is not affected by insulin
nervous tissue
kidney tubules
intestinal mucosa
rbs
beta cells of pancrease
insulin increases
glucose and triacylglycerol uptake by fat cells
lipoprotein lipase activity, which clears VLDL and chylomicrons from the blood
tracylglycerol synthesis in adipose tissue and the liver from acetyl co a
insulin decreases
tiacycygcerol breakdown in adipose tissue
formation of ketone bodies by the liver
glucagon is secreted by what how
alpha cells of pancreatic islets of langerhans
cortisol
steroid hormone that promtes mobiliatzation of energy stores through the degradation and increased delivery of aminoa cids and increase lipolysis
catecholaimes do what
increasae activty of liver and muscle glycogen phosphorylase thus promoting glycogenolysis
glut 2 and 4 are what
primary receptors responsible for transport of glucose into and out of cells
glut 2
low affinity transporte in hepatocytes and pancreatic cells
glut 4
in adipose tissue, and muscle and respnds to glucose concenrtario in peripheral blood
adipose tissue requires glucose to form what
DHAP
glycolysis is what
cytoplasmic pathway that converts glucose into two pyruvate molecules relasing a modest amount of energy captuerd in two substrate level phosphyrlations and one oxidation reaction
investment phase
consumption of ATP in steps 1 and 3 - cell has actually made an energy investment to metabolize glucose, which pays off later when ATP is released by substrate level phsophsyrlation
five important enzymes for glycolysis
hexokinase and glucokinase
phosphofructokinase
glyceraldehyde3phosphate dehydrogenouase
3 phosphoglycerate kinase
pyruvate kinase
liver and skeletal muscle glycogen roles
liver: broken down to maintain a constant level of glucose in the blood
muscle: broken down to provide glucose to muscle during vigorous exercise
AMP will activate things that _____ energy, and inactivate things that _____ it
produce
consume
