MT1 Flashcards
nucleic acids
make up genetic info and encode proteins
lipids
energy storing, signaling and structural components of cell membranes
carbohydrates
energy storing, structural componenets
water’s 3 highs
high heat capacity -> stable temp to support life
high heat of vaporization -> cool down the body of organisms
higher density than its solid form-> prevents lakes from freezing over
water structure
bent and polar, 104.5 between the H’s meaning the dipoles can’t cancel (make net dipole!)
O has partial -
dipole-dipole int
attractive int between 2 permanent dipoles
H bonding
special dipole-dipole for H atom bonded to only O, N, or F
happens in water is is what causes the 3 highs
bond length is long
weaker than covalent bonds
water can bond with up to 4 neighbors (actually though at rm temp 3.4 other water molecs)
ionic interactions
ion-ion and ion-dipole
metal ion and anion group
opposite charges (anion wants positive side, cation wants negative of polar molec)
water dissolves because hydration (shell!)
van der Waals
weakest but more universal intermolecular force
transient, induced dipole-dipole
need close enough proximity, but if too close they become repelled
longer radius than covalent
hydrophobic int
major driving force for protein folding and cell membrane assembly
entropy! water makes cages around hydrophobic stuff, which also wanna bind so with aggregatopn, more entropy ebcause less ordered water because less esxposed nonpolar surface
COO- pKa
~2
NH3+
~10
lys pKr
10.5
arg pKr
12.5
his pkr
6.0
asp pkr
3.7
glu pkr
4.3
tyr pkr
10.1
cys pkr
8.2
size exclusion chromatography
small proteins flow through the beads’ channels whereas large flow around the beads (small proteins elute slower)
ion exchange chromatography
cation: + proteins interact more with a neg matrix > + proteins elute slower
anion: - proteins interact more with a + matric > neg proteins elute slower
phosphoylation
thr, ser, tyr in eukaryotes; his in bacteria/plants
critical for regulation of enzyme activity, protein protein int, and signal transduction
Ubiquitination
protein degradation, translation regulation, etc: lys
Lipidation
(target proteins to membranes): gly, cys
Acetylation
(epigentic regulation, histone structure, and int with DNA): lys
Carboxylation
(increases affinity for Ca): glu
Glycosylation
(protein stability, recognition (40 human diseases are caused my mis-this): ser, thr, asn
phi angle
N-Ca
psi angle
Ca-COOH bond
ramachandran plot
B sheets at top left
L a helix off to the right
R a helic at bottomer area on left
glycine rama plot
symmetric, all the way down 2 sides
proline rama plot
on the left, down, but smaller than gly
pre-proline
also rigid like proline, just not as much so a tad messier
a folds
helix bundle (like a bundle) helix-loop-helix (EF hand) (like 2 a helices in an L like formation~) what do they look like?
helix bundle
4 helices amphipathic helices the inward side is hydrophobic other faces (exposed) are polar/charged example: human growth hormone 4 a helices with each other
B folds
beta barrel (cylinder-like) beta propeller (propeller shape)
B barrel
formed from antiparallel beta sheets
lots of sizes and topologies, neighboring strands are often not adjacent in aa seq
strandds tilted 40 degrees to the barrel axis
fns: nutrient transport, signaling, motility, and survival
eg. retinol binding protein: vit A is hydrophobic so needs help to move through blood stream, and B barrel is that, can hold it inside!
alpha helix
spiral structure of polypep with 3.6 residues/turn and 5.4 rise/turn
side chains point out
helical turns held by 3-4 H bonds (from the cOoh and the nH)
macro dipole because all pep have dipoles with similar orientation
amino always + and carboxyl always -
can be right/left handed (use your hand and the whichever matched the curve is the anser) (proteins mostly R) (R is most stable for L aa)
ala very likely to be a helix
gly no (too flexible) and pro no (not flexible)
stability affect by: interactions between R groups, steric hindrance, pro/gly, end int
beta strand
zig-zag shape, alt side chains point in opp dir, 2/more segments of poly-pep run alongside each other
nearby are either // or anti//
B sheet stabilized by inter-strand H bonds
anti//: same side spacing of side chains is 7, perpendicular to strands are teh H bonds, aa forms 2 H boonds with another aa on neighbor strands
//” same side spacing of side chains is 6.5, H bonds are angled, less stable, aa forms 2 H boonds with another aa on neighbor strands
a/B fold
a/B horseshoe (horseshoe shape) (leu repeaters)
a/B Rossmann fold (pyramid~like)
a/B barrel (circuclar)