biochem meow meow meow

cytosine

uracil baby

thymineee with that methyl group aye

adedeninee

guanine

dna structures orders levels

1. linear nucleotides 5 to 3’

2. base pairings!, cruciform (double stranded four way junction, two closed hairpin, occurs in palindromic regions of dna); helixes forms a, b, z, h

3. 3-d folding, circular dna (supercoils- roles in gene expression) trna

4. nucleosomes bead on string histone, fibers, loops, mini bands, sister chromatids, chromosome

nucleosides

base with pentose sugar beta N1/9 glycosidic bond

nucletides

phosphate acid esterfied at 5’ sugar - strong acid 

high energy- phosphoric anhydrides link extra phosphates

nucleic acids

3 to 5’ phosphodiester bridges forms that phosphate sugar backbone

dna

two antiparallel polynucleotides in double helix with base pair interchain h bonds and stacking, elextrostatic phosphate repulsions, recognizes and replaces uracil with cytosine

greater resistance to alkaline hydrolysis, strong base may denature but dna won’t cleave the phosphodiester bond

transcribed to rna

types of dna

A: short fat dehydrated right duplex (double strand), most common for double stranded RNA, no common in vivo

B: right duplex rings stack, most common physiological DNA

Z: left duplex, interchanges with B with methylation of cytosine bases; CG rich, may be physiologically relevant in dna expression regulation

H: triple helix, 1 purine 2 pyrimidine

rna

single strand, more flexible, less stable under alkaline conditions and promotes alkaline hydrolysis

rna structure levels

1. nucleotides

2. stems, loops, bulges (mismatches), multi branched junctions (intrastrand base pairing), hairpin are stem loop from imperfect base pairs,

3. psuedoknots ( single strand with hairpin loop) formed by coaxial stacking

   1. ribosome RNA and their proteins

mRNA

carries genetic info from dna to ribosomes for pan synthesis

eukaryotes have splicing and polyadenylation intron removal

tRNA

reads mRNA, translates, AA attaches to invariant 3 CAA

cloverleaf: acceptor stem, anticodon loop, D loop, TPC loop

3D L shape

rRNA

forms ribosomes for translation, synthesizes proteins, has large and small subunits

structure and functional core of ribosomes

catalytic power

how fast enzyme reaction occurs vs uncatalyzed

competitive inhibitors

increase Km max constant 

uncompetitive

same factor decrease of km and vmax

noncompetitive

km constant, vmax decrease

proteolytic activation

zymogens need proteolytic cleavage to activate, irreversible and only as needed, to prevent premature enzyme activity that could harm tissues or cells

Ex: chymotrypsinogen activates to chymotrpysin to help digest ptns in small intestines

covalent NA catalysis

ES bind together, E nucleophile residue (ser, cys, lys, his) attacks and covalent bonds S electrophilic center, transition state reactive high energy, E stabilizes with H bond and lower Ea increases reaction rate, chymotrypsin cleaves carboxyl of large hydrophobic aa (phe, met, tyr, trp) to form EP complex, another nucleophile like water then NA and forms P

acid base catalysis

nucleophile attacks base, proton transfer stabilizes transition state, product forms

metal ion catalysis

enzyme cofactor that interacts with S, stabilizes transition state, orients S for run, leaving group leaves

water acitivated

thermolysis- endoprotease with catalystic Zn that stabilizes negative charges on peptide carbonyl oxygen as Glu deprotonates water, promotes attack on carbonyl carbon 

active sites

small 3d pockets on E where catalysis happens, enforces S specificity and stereoselectivity, oreients R, stabilizes transition state, regulates E activity, perform chemical reactions

atp hydrolyssis not required for ES bind but can modulate ES affinity

yas queen now repeat what I just said

irreversible inhibitiors

lower vmax

active site or other

permanently covalent bonds (aspirin acetylation of ser, penicillin inhibits cell wall synthesis)

taq polymerase

thermos aquatics functions at 72 degrees

MM

hyperbolic shape

holoenzyme

fully assembled, catalytically active form of E that has coenzyme or metal ion bound

without is called apo enzyme

Glycogen phosphorylase

active site and allosteric site regulation,

covalent modification- hormone converts inactive GP to active

cleaves glucose from nonreducing ends of glycogen through phosphorolysis reaction to convert to cellular fuel, glucose 1 phosphate

allosteric activators AMP (signals low energy)

inhibitors ATP and glucose 6 P

pyridoxal 5 phosphate acid base catalyst

5 phosphate (acid) protonates and weakens bond of glycosidic oxygen of glucose, (base) help attack inorganic phosphate on C1 glucose, promotes cleavage of glycosidic bond, forms G1P!

phosphofructokinase 1 PFK1

active site and allosteric site regulation

commits glucose to glycolysis by forming fructose 1, 6 biphosphate

activators AMP ADP fructose 26 biphosphate

inhibitors ATP citrate

absolute specificity favors binding of one substrate

aspartate transcarbamoylase ATCase

catalytic and regulatory subunits with allosteric sites (regulates and cooperatively)

activated by ATP

inhibitor CTP (end product)

HEMOGLOBINNN

tetramer a2b2 four prosthetic heme group 

sigmoidal cooperative (essentially for efficient o2 transport)

oxygen binding: shifts F helix because iron is pulled into the heme plane, one ab rotates 15 degrees (t to R aye) break salt bridges

CO2 hydration and glycolosis make protons which increase o2 dissociation

bicarbonate dehydration consumes protons, decrease o2 dissociation, binds o2, releases CO2

BPG allosteric effecter ionic bonds in central cavity has negative charges with 8 positive charges (2lys, 4 his, 2 n term)

fetal hemoglobin

a2y2, His instead of Ser in 143, higher affinity to oxygen than BPG, lacks 2(+) charges binds loosely, hyperbolic curve, depends on mother for o2 and gas exchange

sickle cell disease

Glu6 turned to Val in B globin, causes deoxyHbS polymerization which distorts rbcs to sickle cell shape under lower oxygen or acidic conditions.

rigidity and aggregations leads to blockage of capillaries, circulation impairment, tissue damage, and premature rbc death (anemia)m

myoglobin

metalloprotein with one heme group

stores o2 in muscle tissues

hyperbolic noncooperative binding

local structural changes with o2 bind

higher affinity to o2 than hb

unaffected by pH or pressure

transferases

phosphate from ATP to substrate

Kinases: hexokinase- transfers phosphate from ATP to glucose to form glucose 6 phosphate (group specificity)

tyrosine kinase phosphorylates tyrosine with phosphate from ATP to make ADP

ligases

joins two substrates together with ATP breaking down to release energy

catalyzes phosphodiester bonds of two DNA strands

DNA ligase- covalent bond of 3 hydroxyl and 5 phosphate terminal

oxireductase

adds molecular oxygen to single substrate, movement of electrons

alcohol dehydrogenase catalyses conversion of primary or secondary alcohol to aldehydes or ketones and reduces NAD+ to NADHp

isomerases

intramolecular group transfer, epimerication, racemization of chiral carbon

converts carotenoid double bond from cis to trans

lyases

add or remove groups from double bond without h2o

decarboxylase aldolases

hydrolases

hydrolysis (cleave bond with h20)

proteases ptns to peptides or AA

lipases - lipid substrate hydrolyzed to components (glycerol and FA), ester bond cleaved

lactase- hydrolyzes lactose to glucose and galactose

relazed confomation

binds to activator and increase S binding pr

protoporphyrin IX

uses four pyrites N atoms to bind to iron, and also a proximal histidine

BPG

allosteric effector shifts o2 bind curve to the right decrease Hb affinity for o2, stabilizes t state, promotes o2 release

bohr effect

increase co2, decrease pH decrease Hb affinity for o2