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Biochemistry > Lecture 2, 3 - Proteins & Hemoglobin, Myoglobin > Flashcards

Lecture 2, 3 - Proteins & Hemoglobin, Myoglobin Flashcards

1
Q

Functions of proteins (7)

A 
catalysis
transport (in and out of cell; metabolites)
contractile mechanism
protection
hormones
regulation
structural
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2
Q

What is catalysis?

A

speed up reactions that typically involve changing chemical identity of a substance

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3
Q

What are the types of proteins? (5)

A 
simple
membrane
conjugated
globular
fibrous
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4
Q

What is a simple protein?

A

one single polypeptide chain (ex: myoglobin)

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5
Q

What’s special about membrane proteins?

A

they are hydrophobic (why they can undergo lipid addition)

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6
Q

What do conjugated proteins have?

A

tightly bound covalent factor (ex: Hb with it’s Heme covalently attached so Hb can bind to oxygen)

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7
Q

What are globular proteins?

A

alpha helical structures, globular in shape (ex: Hb)

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8
Q

What are fibrous proteins?

A

Long and strong, extracellular proteins (ex: collagen)

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9
Q

What are the 4 levels of protein structure?

A

primary, secondary, tertiary, quaternary

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10
Q

what is the primary protein structure?

A

linear sequence of AA covalently linked by peptide bonds - determines rest of protein structure

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11
Q

What is the secondary protein structure?

A

alpha helix, include H-bonding

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12
Q

what is the tertiary protein structure?

A

3D arrangement of side chains, including non-covalent interactions like hydrophobic interactions, electrostatic interactions (ionic), salt bridges, and covalent bonding (disulfide bonds)

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13
Q

What is the quaternary protein structure?

A

ONLY applies if more than one polypeptide chain (subunits). 2, 3, or 4.

non-covalent interactions b/w chains

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14
Q

What are the characteristics of the peptide bond?

A 
COO- + NH3+ (lose H2O) 
determines structure
partial double bond character 
rigid and planar molecule 
can rotate (cis, trans (more stable)) 
main chain carbons (2 alpha C and C bound to N) determines secondary structure
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15
Q

What are the two amino acids that can assume cis formation?

A

glycine and proline

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16
Q

carbonyl and amino make?

A

peptide bond

uncharaged but polar so can form H bonds

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17
Q

why are peptide bonds important?

A

important for secondary structure b/c it determines how the polypeptide chains will fold to form their secondary structure due to limitations of bond angles around bond

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18
Q

What is the N terminus?

A

free NH3+ (first part of AA chain)

last AA is COO- group

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19
Q

How often is there H-bonding in an alpha helix strand?

A

every 4 AA’s

R2 and R6

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20
Q

What is a beta sheet? stabilized by?

A

parallel or anti-parallel protein strands

stabilized by H-bonds b/w strands

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21
Q

What are supersecondary structures?

A

protein combinations b/w secondary and tertiary structures - combo of secondary structures (B-a-B, Greek key, B-meander, B-barrel)

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22
Q

What is the tertiary structure?

A

3D structure

AA chain and 3D arrangement of side chains

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23
Q

What are the factors stabilizing tertiary structure?

A

non-covalent interactions (H-bond, ionic, salt bridges, hydrophobic interactions)

covalent - disulfide bonds

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24
Q

What is non-covalent binding also known as?

A

solvation

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25
Covalent bonding v non-covalent bonding?
sharing e- v not sharing e-
26
What is denaturation?
loss of secondary, tertiary (and quaternary) structure unfolding and loss of disulfide bonds protein becomes inactive and nonfunctional
27
What are hemoglobin and myoglobin?
major transport proteins for oxygen
28
Where is myoglobin found? What is its function?
found in muscle cells stores oxygen and transports oxygen to mitochondria able to bind oxygen tightly at low oxygen tension
29
What is Hb's function?
oxygen carrier in blood binds oxygen at high oxygen tension in lungs and releases it in systemic tissues at low tension carries CO2 from tissues to lungs
30
Similarities and differences in Mb and Hb tertiary structure
both have alpha helix secondary structure (globular and hydrophobic AA interior), both bind Heme interiorly (which allows O2 binding), both are conjugated proteins Mb has 1 polypeptide chain, Hb has 4 chains
31
What is the structure of heme?
extended aromatic ring with a reduced Fe in middle that binds to 4 nitrogens and forms pyrrole rings and has 2 COO- groups on edge, close to surface of protein
32
What binds oxygen in Hb and Mb? What doesn't?
O2 binds only to Fe2+ heme (reduced form of Fe) | Fe3+ (ferric form) heme aka methemoglobin does not bind O2
33
Fe3+ aka?
methemoglobin
34
Heme group
Fe ion held in heterocyclic ring (porphyrin), which consists of 4 pyrrole mlcs cyclically linked with Fe bound in center
35
How many hemes are in Hb?
4; each polypeptide chain has one that can bind O2 quaternary structure is impt for O2 delivery
36
How many hemes are in Mb?
1; Mb is a single polypeptide (up to tertiary structure only) so can only bind 1 O2
37
what does saturation curve tell?
how much O2 is bound to molecule | If 1, Mb and Hb completely saturated
38
For Mb, 50% saturation at low pressure indicates?
Mb has high affinity for O2; hb has lower affinity for O2
39
Why isn't Mb effective in delivering O2 from lung to tissue?
Mb wouldn't release O2 at level of tissues whereas Hb would deliver nearly 75% of O2
40
S shaped curve for Hb in linear plot indicates?
cooperativity (which requires more than 1 site)
41
Explain positive cooperativity
multiple binding sites - affinity of the binding sites for a ligand is increased, positive cooperativity, or decreased, negative cooperativity, upon the binding of a ligand to a binding site. Hb has 4 sites
42
Hb and + cooperativity
1st oxygen has low affinity (T confirmation) - taut | 2nd oxygen has high affinity (R confirmation) - relaxed
43
What confirmation is Hb in in absence of oxygen?
T confirmation once O2 binds, confirmation changes to R and Hb undergoes positive cooperativity; next 3 O2 binds easily
44
As O2 binds, what happens to bonds b/w 2 dimers?
fewer ionic and H-bonds
45
What does O2 binding do to heme plane? What is link?
pulls Fe2+ into heme plane coordination site with proximal histidine - without O2, Fe is out of plane. When O2 is bound to Fe, Fe is pulled into plane and changes interface
46
what do allosteric modifiers do?
changes conformation - when ligand binding at one site influences ligand binding at a different site
47
What are some allosteric modifiers?
pH, CO2, 2,3-bisphospoglycerate (BPG)
48
If you increase 4 things, saturation will shift to the right - what are they and what do they do?
increased temperature, H+ (dec in pH), CO2, 2,3 BPG will increase P50 and decrease O2 affinity for Hb - aka O2 more easily released
49
What is 2,3 DPG or BPG?
product of glycolysis in order to form ATP when low, Hb has hi affinity for O2 when hi, Hb has lo affinity for O2 and Hb releases O2 more easily
50
at high altitudes, how does saturation curve shift?
down and to right
51
Explain how CO2 is an allosteric modifier.
BPG stabilizes T confirmation (low affinity confirmation) CO2 does not bind Mb or heme CO2 binds Hb (carbamino-Hb) and stabilizes T confirmation During metabolism, CO2 reduces Hb affinity for O2, O2 released from Hb to tissue, which has low tension of O2
52
effect of pH and CO2 binding and release of O2 by Hb is called what? Where does it occur mostly? where is the opposite effect seen?
Bohr effect in systemic capillaries reverse of Bohr effect will occur in lung capillaries
53
What does Bohr effect do?
changes Hb from R confirmation to T confirmation (lowers affinity for O2)
54
What is carbon monoxide poisoning?
CO kills b/c it changes O2 binding at other Heme sites in Hb so Hb is in constant R confirmation - which wants to bind O2, so O2 is not released
55
Why is CO potent?
produced naturally from incomplete combustion of organic matter it is 200X more affinity at heme site than O2
56
CO poisoning and sickle cell anemia
RBCs are fragile and only have 50% functional heme - CO competes for Hb, and changes other sites to R so O2 is not released (inc affinity of O2) --> allosteric effect
57
is fetal Hb more or less susceptible to CO poisoning?
more b/c they have a different type of Hb
58
What are the types of Hb?
HbA - major adult form (alpha2B2) HbA2 - minor (2%, alpha2delta2) HbF - major Hb in fetus and newborn - much higher affinity for O2 then HbA and does not bind will to BPG (alpha2gamma2)
59
What is special about fetal Hb?
Fetal Hb needs to extract O2 from mother's Hb b/c lungs are non-functional in fetus
60
What is used for diagnosis and treatment of diabetes mellitus?
hemoglobin glycations Hb is a long-lived protein and is susceptible to non-enzymatic glycosylation - glucose aldehyde forms Schiff base with free amines in protein
61
what is a predictor of sustained hyper-glycemia?
glycosylated Hb levels in blood
62
What are some hemoglobinopathies?
sicke cell anemia (HbS) HbC HbM (methemoglobin, (Fe3+, oxidized) Thalassemias - Hb is not synthesized (one of the polypeptide chains)
63
thalassemia
Hb is not synthesized
64
What happens in sickle cell anemia HbS?
glutamate to valine mutation on protein surface (point mutation) - presents hydrophobic patch Hb polymerizes forming long strands RBC's have sickled shape in low O2 conditions, Hb goes in T confirmation (lo affinity) and RBC's aggregate Hb polymerizes b/c of valine on surface - creates long strains within RBC, which produces elongated shape RBC is more fragile, breaks down, and gets sticky --> stuck in capillary beds --> hypoxia
65
What happens in HbM?
histidine to tyrosine mutation this stabilizes Fe3+ (oxidized form which won't bind O2) so O2 can't bind to Fe3+ in heme --> cyanosis normally, Hb has Fe2+ (reduced form) so oxygen can bind to reduced Fe2+

Biochemistry (5 decks)

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