Biochem Chapter 5

Front 1

Electron Configuration of Fe and Fe2+

Back 1

Fe: [Ar]4s2 3d6

Fe2+: [Ar] 3d6

Front 2

deoxyhemoglobin VS oxyhemoglobin

Back 2

deoxy: Fe bubble big and Fe below the plain, "puckered"

oxy: ring not puckered as much (.4 angstroms higher), Fe bubble is smaller

Front 3

________ spin deoxy Hb is

Back 3

paramagnetic

Front 4

_________ spin oxy Hb is

Back 4

diamagnetic

Front 5

what is heme made up of?

Back 5

Porphyrin and Fe

Front 6

the concerted or MWC* or Symmetry Model

Back 6

deoxy = larger central cavity
oxy = smaller central cavity

T-state & R-state
*Monod, Wyman, & Changeux

Front 7

Networking of hydrogen bonds in deoxy-Hb

Back 7

IN TISSUES: HIgher [H+] causes protonation of AAs causing formation of salt bridges which stabilize the T-state

IN LUNGS: higher pH, lower [H+], don't have salt bridge interactions so favor R-state

Front 8

2,3-BPG binding pocket

Back 8

BPG binds to and stabilizes the T-state (because cavity is larger); will not bind to R-state because cavity too small

**binding pocket is between β1 and β2 subunits**

Front 9

What is the adaption to high altitude?

Back 9

produce more 2,3-BPG and lower Hb's affinity for oxygen

-allows us to DELIVER 37% O2 to our tissues versus 30% without it

Front 10

Fetal VS normal adult hemoglobin

Back 10

Fetus hemoglobin = 2 gammas
Normal adult = 2 β subunits

Fetus does not bind 2,3-BPG as well (will not stabilize the T-state); therefore, has a higher affinity for O2 then normal adult

Front 11

Which structure of heme subunits/myoglobin is more conserved? Tertiary or Primary

Back 11

Tertiary

If single AA needed to form correct tertiary structure is changed it will affect the folding of the protein

Front 12

What factors influence the binding of O2 to myoglobin?

Back 12

partial pressure of oxygen, pO2

NOT [HCO3-], [hemoglobin], [2,3-BPG]

Front 13

What factors influence the binding of O2 to hemoglobin?

Back 13

[2,3-BPG], [CO2], pH, partial pressure of oxygen, pO2,

NOT [hemoglobin present], [HCO3-] ?

Front 14

Sickle-Cell Anemia

Back 14

-a molecular disease
-Linus Pauling's term
-results from an AA change in β subunit from Glu (polar) to Val (non-polar)
-effects the DEoxy hemoglobin
-Val interacts with hydrophobic patch of deoxy hemoglobin forming rods

Front 15

What type of interaction does the Val residue and hydrophobic patch of deoxy hemoglobin undergo?

Back 15

polymerization reaction forming rods

Front 16

Sickle-cell carriers are

Back 16

-protected against Malaria
-carriers (heterozygotes) of disease do have some RBCs that are sickled (2%)
-RBCs infected with malaria are prone to sickling
-spleen removes sickled cells from the circulation naturally, which also takes out RBCs infected with Malaria

Front 17

Mutation of Sickle-Cell

Back 17

NORMAL: 5'..GAG..3' coding
5'..GAG..3' mRNA
GAG --> Glu (polar)

DISEASE: 5'..GTG..3' coding
5'..GUG..3' mRNA
GUG --> Val (non-polar)

Front 18

Structural Proteins

Back 18

1. Microfilaments
2. Intermediate Filaments
3. Microtubules

Front 19

Diameter Size of Microfilaments

Back 19

70 angstroms

Front 20

Diameter Size of Intermediate Filaments

Back 20

100 angstroms

Front 21

Diameter Size of Microtubules

Back 21

240 Angstroms

Front 22

Size of structural proteins: smallest to largest

Back 22

microfilaments (smallest)
intermediate filaments (middle)
microtubules (largest)

Front 23

Microfilaments are made up of

Back 23

ACTIN

F-actin (filamentous actin) = polymerized

G-actin (globular monomeric form)

Front 24

What do Microfilaments do?

Back 24

1. determine cell shape
2. drive cell locomotion (help cell move)
3. generate tensile force (mm contractions)

Front 25

G-actin contains

Back 25

ATP-binding clefts

Front 26

F-actin contains

Back 26

(-) end = contain ATP-binding cleft

(+) end =

Front 27

Subunits add to and dissociate from

Back 27

ONE or BOTH ends of the microfilament

Usually, ADD more rapidly to the (+) end though

Front 28

treadmilling

Back 28

when rate of assembly at one end is balanced by the rate of disassembly at the other end

Front 29

Actin

Back 29

is a double chain of subunits and each subunit contacts 4 neighboring subunits

F-actin (filamentous actin) = polymerized

G-actin = (globular monomeric form)

Front 30

Ends of actin can be _____ by a __________

Back 30

capped; capping protein

if capping protein is removed from end -->end can resume polymerization

Front 31

Microtubules are formed from

Back 31

alpha-tubulin and beta-tubulin heterodimers

Front 32

Beta-tubulin

Back 32

has bound GTP

The GTP can be hydrolized into GDP upon incorporation into a microtubule

Front 33

Alpha-tubulin

Back 33

has bound GTP that is effectively buried

Front 34

Assembly of a Microtubule

Back 34

1) Protofilaments form from α & β-tubulin heterodimers
2) Many protofilaments connect together
3) Circle of protofilaments forms a microtubule

Front 35

Action of Microtubules

Back 35

1) reinforce cytoskeleton
2) construct cilia and flagella
3) separate pairs of chromosomes during mitosis

Front 36

Types of Intermediate Filament Proteins

Back 36

Keratin and Collagen

Front 37

Keratin

Back 37

-composed of TWO right handed α-helixes intertwined

-forms a left-handed superhelix = α coiled coil

-contains disulfide bonds
-found in hair and nails

Front 38

In Keratin: Amino acids ___ and ___ of α-helix are _______

Back 38

1 and 4 = non-polar

-align with 1 & 4 (also non-polar) of adjacent alpha helix

Front 39

Keratin is ____ residues per turn

Back 39

3.5 residues per turn

(instead of 3.6 like α-helix) because 2 α-helixes together

Front 40

Levels of Organization

Back 40

1) Monomer
2) Dimer (coiled-coil)
3) Tetramer = Protofilament
4) Octamer = Protofibril
5) Intermediate Filament = Microfibril

Front 41

Dimers (coiled-coils) are ____ angstroms long

Back 41

~450

Front 42

The sequence of Collagen

Back 42

-every 3rd AA is Gly
-often abbreviated Gly-X-Y
*where often X = Pro and Y = Hyp

FORMATION: Originally, is it Gly-Pro-Pro then post-translationally the 2nd Pro converted to Hyp (requires Vit C)

Front 43

Action of Collagen

Back 43

-structural role in extracellular matrix (the material that helps hold cells together

-in connective tissues and bones

Front 44

Hyp

Back 44

hydroxyproline

-emzyme: prolyl hydroxylase catalyzes formation of Hyp which indirectly requires Vitamin C

-w/o Hyp collagen does not form stable helices, and connective tissue is weakened

Front 45

Vitamin C deficiency

Back 45

related disease called Scurvy

-causes a reduction in collagen formation which results in weakened connective tissue (bleeding gums)

Front 46

Collagen

Back 46

-a fibrous, extracellular protein

-chain is a LEFT-handed helix (NOT an α-helix)

-3 left-handed chains twist about each other

-forms a right-handed coiled-coil

Front 47

Collagen Helix (Coiled-Coil)

Back 47

-Gly residues end up in the middle of the coiled-coil

-even an Ala with distort the tight packing of the triple helix

-Each Gly N-H makes a

Front 48

Collagen helix is stabilized by

Back 48

HYDROGEN BONDS

-each Gly N-H makes a hydrogen bond with the C=O of an X (Pro) on a NEIGHBORING chain

Front 49

Cross-linking the side chains in Collagen

Back 49

Lysine Residues bind together and Histidine involved at the end

-NOT disulfide bonds because sulfur is too bulky and wouldn't be affective

Front 50

Reasons for Collagen's high tensile strength is...

Back 50

DEBATED

1) Author of text: helix prevents other N-H and C=O groups from forming hydrogen bonds with each other, so they interact with a highly ordered network of H2O molecules surrounding the triple helix like a sheath

2) Holmgren, Taylor, Bretscher & Raines: Water bridges unlikely to contribute significantly to collagen stability b/c entropic (ΔS) cost enormous & would immobilize more than 500 H2O molecules

Front 51

Experiment of Collagen Helix by Holmgren, Taylor, Bretscher, & Raines

Back 51

Tested melting points of collagen containing:
1. unmodified (ProProGly)
2. regular (ProHypGly)
3. synthetic analog (ProFlp*Gly)
*Fluoroproline in place of hydroxyproline

-(ProFlpGly) had highest melting point, then ProHypGly, then (ProProGly)
-increased stability of collagen upon substitution of Flp for Hyp
****because F is more electronegative than O

Front 52

RESULTS of Collagen Stability Experiment suggest

Back 52

INDUCTIVE EFFECTS contribute significantly to the stability of collagen

-inductive affects arise from differences in electronegativity btwn two atoms forming a sigma bond

Front 53

Motor Proteins

Back 53

Myosin (~15 different types) and Kinesin

Front 54

Myosin

Back 54

-we focus on muscle myosin
-chemical energy --> mechanical energy

*Head region (2) - contains actin and ATP-binding site
*Neck region (2) - is an α-helix acts as lever
*Tail region - single coiled-coil

Front 55

Muscle cell is made up of

Back 55

muscle cell = myofibril

thick and thin filaments

Front 56

thick and thin filaments

Back 56

THICK = myosin

THIN = actin

*during mm contraction filaments slide past each other and actin get closer together
*myosin moves toward the (+) end of actin

Front 57

Mechanism of Myosin and Actin

Back 57

1. myosin head bond to actin subunit and ATP binding to myosin head alters the configuration of the myosin head so it releases actin

2. hydrolysis of ATP --> ADP + Pi triggers a confirmational change that cocks the myosin head back and increases the affinity of myosin for actin

3. Myosin binds to an actin subunit

4. binding to actin causes ADP and Pi to be released from myosin head --> power stroke (thin filament moves)

Front 58

Kinesin

Back 58

-moves along microtubule tracks

*Head region (2) - consist of 8-stranded β-sheets and 3 α-helices include tubulin-binding & nucleotide-binding site

*light chains (2) - opposite end to heads; bind to proteins in membrane shell of vesicle ("cargo")

-moves cargo towards (+) end of microtubule by stepping along the length of a single protofilament

Front 59

processivity

Back 59

the # of cycles of ATP hydrolysis and protein advancement (along something) that take place before the motor protein dissociates

Kinesin = HIGH
Myosin = LOW

Front 60

Heads of Myosin VS Kinesin

Back 60

Myosin work INDEPENDENTLY and has LOW processivity

Kinesin work TOGETHER and has HIGH processivity

Front 61

Permanent waving of hair (Steps)

Back 61

Chemical Reduction --> shape remodeling --> Chemical Oxidation

**disulfide bonds**