Mcb Exam 1 - Mdq # 2 Topics

Front 1

Ice is enthalpically _____ and entropically ______

Back 1

favored (-H)
opposed (-S)

Front 2

Water is entropically _____

Back 2

favored (+S)

Front 3

Hydrophobic effect is _____ driven. What does is cause and give 3 examples

Back 3

entropically (+S)
desolvation of nonpolar compounds to reduce solvated SA
micelle, lipid bilayer, enzyme/substrate intermolecular interaction

Front 4

Henderson Hasselbach's equations

Back 4

pH = pKa + log [A-] / [HA]

pKa = pH where 1/2 of acid is dissociated
small changes in [H+] cause big changes in pH

Front 5

Buffers

Back 5

weak acids and bases resist pH changes by provided a large resivour of H+
works best at pKa of buffer

Front 6

Buffer system of blood

Back 6

Low pH (acidosis) - shift in eq. to increase Co2
High pH (alkalosis) - shift to increase bicarb (HCo3-)
much more bicarb that H2Co3

Front 7

relative pKa values

Back 7

low pKa means high dissociation of acid (gives up H+ easier) = stronger acid!

Front 8

Fully differentiated cells live in what cell cycle stage?

Back 8

Go

Front 9

Regeneration of liver after surgical removal

Back 9

nonprolif., diff. cells re-enter cell cycle and resume mitosis

Front 10

2 distinguising characteristics of stem cells

Back 10

self-renewal (able to maintain pop. size indefinitely)

potential to differentiate into mature cells with specialized fxn

Front 11

transit-amplifying stage

Back 11

daughter cells of stem cells that divide several times to increase diff. cell pop. before losing ability for mitosis

Front 12

toti- vs. pluri- vs. mutli- vs. unipotent

Back 12

toti - all cells and tissues (zygote)
pluri - all 3 germ layers (inner cell mass)
multi - several lineages in a single tissue/organ (hematopoietic bone marrow)
uni - one cell type

Front 13

challenges of use of adult stem cells in therapy (x4)

Back 13

determning presence of stem cells
limited # of stem cells
maintaining stem cell prop. in culture
stimulating/controlling differentiation

Front 14

where do embryonic stem cells come from?

Back 14

inner cell mass

Front 15

challenges of use of embryonic stem cells use

Back 15

how to increase pop. and maintain pluripotency
need "feeder" cells
control of diff./spec.
find a inhibitor of diff. in humans (use leukemia inhibitory factor in mice)
access to enough ESC for research
ethical considerations

Front 16

therapeutic cloning

Back 16

nucleus from adult stem cell transplanted into enucleated egg to make an embryo in culture.

low success rate

Front 17

potency of adult stem cells

Back 17

multipotent

Front 18

stem cell niche

Back 18

location where an adult stem cell is located. Neighbor cells secrete factors to maintain stem cell phenotype

Front 19

induced pluripotent stem cells (iPSCs)
challenges?

Back 19

transfect mouse fibroblast cell with reterovirus carrying 4 genes to induces pluripotency without the use of embryos

may cause cancer (oncogenes), low yeild, time consuming and expensive, unpredictable

Front 20

proteins are made of ____ -amino acids of the ______ isomer variety

Back 20

alpha
L

Front 21

what charged form are aa's typically in a biological neutral pH

Back 21

Zwitteron

Front 22

Peptide bond

Back 22

formed by condensation rxn; broken by hydrolysis rxn
NOT thermodynamically favored, but kinetically favored
stable - need heat and acid to break
planar & rigid - due to partial double bond character of C-N

Front 23

Homolog?
What are the 2 types of homologs?

Back 23

homo: protein from common ancestor with similar structures/sequences
paralog - same species, different fxn
ortholog - different species, similar fxn

Front 24

Consensus sequence

Back 24

shows the most common amino acids at each position in homolog proteins
{residue} = any aa but that listed aa
[residue] = any of the aa listed

Front 25

dihedral angles

Back 25

Phi (ϕ) = rotation around Cα-N
Psi (Ψ) = rotation around Cα-Carbonyl

Front 26

Ramachandran Plot

Back 26

plot favorable (due to H bond stablization) and unfavorable (due to steric clash) phi psi angles for a protein

Front 27

α-helix

Back 27

right-handed
held together by H-bonds
3.6 aa/turn
aa 1 and 8 stack on top of each other
short

Front 28

β-sheet

Back 28

parallel - h-bonded strands in same direction. weak

antiparallel - strands in opposite direction. strong

mixed

twisted

Front 29

β-turn

Back 29

4 aa long connection b/w secondary structures
AA1 and AA4 H-bond to stablizes
AA2 = Pro
AA3 = Gly

Front 30

Loops

Back 30

greater than 4 aa long connection that links secondary structures

Front 31

forces that stabilize tertiary structure

Back 31

hydrophobic and polar interactions

Front 32

2 tertiary structure types

Back 32

fibrous - long, filamentous, water-insoluble protein aggregates, structural proteins (tendons, CT, bone)

Globular - hydrophobic core, more compact than α-helixes or β-sheets

Front 33

2 types of fibrous proteins

Back 33

α-keratin - L-handed coil of 2 R-handed α-helixes. Heptad repeat of Leu. Rich in hydrophobic aa

Collagen - R-handed coil of 3 L-handed helixes. Strechy. Gly-x-Pro/Hyp common sequence with Gly facing inside of coil. Hydroxyproline forces Pro into exo conformation to stablize collagen fiber

Front 34

Tertiary structure of myoglobin

Back 34

Globular.
8 α-helixes connected by β-turns.

Front 35

Super secondary structure (motiffs)

Back 35

b/w secondary and tertiary
several secondary structures connected in a stable conformation (ex: helix-loop-helix)

Front 36

Domain

Back 36

unit of tertiary structure.
40-400 aa

Front 37

Denaturing agents

Back 37

urea (disrupts H bonds)
Guanidinium Cl
β-mercatoethanol (disulfide bonds)

Front 38

Cummulative selection

Back 38

each correct folding sequence is retained because folded intermediate is much more stable than previous unfolded state

Front 39

Molten globule state

Back 39

discrete folding state that initiates proteins folding
hydrophobic aa's collapse on themselves

Front 40

2 types of environmentally-effected conformation proteins

Back 40

intrinsically unstructured proteins - no structure until they interact with other molecules

metamorphic proteins - have several folded forms equal in energy and in equilibrium

Front 41

heme structure

Back 41

4 pyrole rings with N's forming coordinate bonds with Fe that is covalently bonded to prox. His

Oxygen binding to Fe oxidizes it to Fe3+ = superoxide ion - stablized by distal His

Front 42

Mb and Hb affinities

Back 42

Mb has a greater affinity for O2, but cooperativity of Hb allows for more O2 to be delivered to tissues

Front 43

2 Hb states

Back 43

T (tense) state - deoxy Hb with low O2 affinity. Contains a center pore)

R (relaxed) state - oxy Hb with high O2 affinity

Front 44

2 models of Hb configurational changes

Back 44

concerted - Hb exists in equilibrium b/w fully T or fully R states with T state favored when O2 is low and R state favored when O2 is high

sequential - binding of O2 causes one subunit of Hb to change from T to R state until all subs are R-state and occupied by O2

Front 45

2,3-BPG

Back 45

allosteric modulator (doesn't bind in O2 binding site) that stabilizes T state in Hb
decreases O2 affinity
highly negative - interacts with Lys and His in Hb

Front 46

Fetal Hb

Back 46

α2γ2 - γ sub has a Ser in place of His so 2,3-BPG can't bind to Hb
greater O2 affinity than maternal Hb

Front 47

Bohr effect

Back 47

decrease in pH causes a Right-shift (lower O2 affinity)
- increaseing Co2 causes a decrease in pH to release more O2 to tissues
- caused by protonation of His to change pKa to 7 and stabalize T state
- Co2 dissociates to H+ in HCo3- in RBC and is transported as HCO3- in blood to lungs