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biochemistry and molecular biology > module 3 protein function > Flashcards

module 3 protein function Flashcards

1
Q

what is the geometry of the 2 Hb

A

tertramer of 2 subunits which are a2B

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2
Q

is Hb a monomer or polymer

A

polymer

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3
Q

is Mb is monomer or polymer

A

monomer

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4
Q

Hb and Mb are what is each other

A

they are anologues and paralogues

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5
Q

how many subunits does Hb have

A

4 subunits with a Fe2+ heme group

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6
Q

interpret this graph

A
  • As the concentration of oxygen goes up more binding sites get filled
    • Myoglobin fill rapids and get close to saturation
      Haemoglobin is sigmoidal happens due to allosteric interactions which leads to cooperative bind
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7
Q

what are the 5 structural differences between Hb and Mb

A

Quaternary Structure:

Myoglobin: Myoglobin is a monomeric protein, meaning it consists of a single polypeptide chain.
Hemoglobin: Hemoglobin is a tetrameric protein, composed of four polypeptide subunits:

Heme Binding:

Myoglobin: Myoglobin contains a single heme group, which is the site where oxygen binds.
Hemoglobin: Hemoglobin contains four heme groups, one in each subunit, providing multiple binding sites for oxygen.

Binding Affinity:

Myoglobin: Myoglobin has a higher binding affinity for oxygen than hemoglobin. This high affinity allows myoglobin to store oxygen in muscle tissues, releasing it when oxygen levels are low.
Hemoglobin: Hemoglobin has a lower binding affinity for oxygen compared to myoglobin. This allows hemoglobin to efficiently transport oxygen from the lungs to tissues and release it where needed.

Tertiary Structure:

Myoglobin: Myoglobin has a single polypeptide chain folded into a compact globular structure.
Hemoglobin: Each subunit of hemoglobin has its own tertiary structure, and these subunits come together to form the quaternary structure of the protein.

Function:

Myoglobin: Myoglobin is primarily found in muscle tissues and is involved in storing oxygen for use during periods of low oxygen availability, such as during muscle contraction.
Hemoglobin: Hemoglobin is found in red blood cells and is responsible for transporting oxygen from the lungs to tissues throughout the body and carrying carbon dioxide from tissues back to the lungs for exhalation.

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8
Q

what are the 2 functions of Mb

A

1) Storage of oxygen
2) Release oxygen when rapidly contracting muscle needs energy (oxygen concentration drops

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9
Q

where is Mb abdunat in an organism

A

in muscle cells

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10
Q

describe the correlation of diving animals and Mb

A
  • Mb concentration in muscles of diving mammals is 10x higher then others
    • Mb in elephant seals is positively charges on its surface so the molecules repel each other and do not clump together at higher concentrations
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11
Q

oxygen is a what for Mb

A

a ligand!!!!

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12
Q

where does oxygen attach to in Hb and Mb

A

O2 binds to the Fe2+ which is attached to the binding site of the protein

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13
Q

what is the heme prosthetic group

A

a histidine residue

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14
Q

what is the equilibrium dissociation constant

A
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15
Q

what is biotin

A

Biotin is a vitamin and it must be provided in diets

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16
Q

the relationship between ligand binding affinity and the equilibrium dissociation constant Kd

A

The relationship between ligand binding affinity and the equilibrium dissociation constant (Kd) is crucial in understanding how tightly a ligand binds to its receptor or protein. Kd represents the concentration of the ligand at which half of the binding sites on the receptor are occupied.

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17
Q

what happens at higher and lower kd values and ligand binding

A

Lower Kd values indicate higher binding affinity, meaning the ligand binds tightly to the receptor, while higher Kd values indicate lower binding affinity, meaning the ligand binds less tightly.

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18
Q

Myoglobin’s Oxygen Binding:
- Heme Group with Iron (Fe)
- Histidine Residue (His) near heme
- Oxygen binds to iron, forms oxy-myoglobin
- Heme pocket shields oxygen
- High affinity for oxygen

A
  • Heme Group: Iron in protoporphyrin ring
  • Histidine Residue: Fifth ligand to iron
  • Oxygen Binding: Induces conformational change
  • Heme Pocket: Hydrophobic crevice
  • High Affinity: Efficient oxygen storage and delivery
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19
Q

what is the t state of Hb and what does it mean

A
  • T= tense state
    -More interactions, more stable
    Lower affinity for O2
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20
Q

what is the r state of Hb

A
  • R= relaxed state
    -Fewer interactions, more flexible
    High affinity for O2
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21
Q

oxygen binding to the heme group triggers what

A

O2 binding triggers T–>R conformational change

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22
Q

Hemoglobin (Hb) Affinity States:
- Tense (T) State: Low Affinity
- Relaxed (R) State: High Affinity
- Oxygen Binding Induces Transition

A

Tense (T) State:
- Iron less accessible
- Stabilized interactions
- Low Affinity for Oxygen

Relaxed (R) State:
- Conformational change
- Straightened heme groups
- High Affinity for Oxygen
- Cooperative Binding

Oxygen Binding Induces Transition:
- From Tense (T) to Relaxed (R) State

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23
Q

Oxygen Binding to Hemoglobin (Hb):
- Heme Group
- Iron (Fe)
- Histidine (His) Residue

A
  • Heme Group: Contains Iron (Fe)
  • Iron Coordination: Histidine Residue (His)
  • Oxygen Binding: Induces Conformational Change
  • Tense (T) State: Low Affinity
  • Relaxed (R) State: High Affinity
  • Cooperative Binding
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24
Q

what does each term of the hill expression mean

A
  • θ: Fractional saturation of binding sites
  • n: Hill coefficient (cooperativity)
  • Kd: Dissociation constant
  • Positive cooperativity when n > 1
  • Hyperbolic binding curve when n = 1
25
Q

If nH >1 (eg Hb/O2

A
  • Positive cooperativity
    Binding at one site increases binding at other sites on other subunits
26
Q

If nH=1

A
  • Binding is not cooperative
    Sites are independent
27
Q

Is nH<1 (rare)

A
  • Negative cooperativity
    Binding at one site decreased binding at another site on another subunit
28
Q

what is the end product of metabolism in tissues

A

H+ and Co2 are end products of metabolism in tissues

29
Q

do H+ and CO2 compete with Oxygen for the binding of the heme group

A

no cunt they do not!!!!!!!

30
Q

as O2 binds to Hb what happens to pH

A

pH increases as O2 binds to the heme groupn

31
Q

Effect of pH on Hb Affinity for O2:
- Histidine Protonation
- Protein Structure Changes
- Bohr Effect

A
  • Histidine Residues: Coordinate iron in heme
  • Protonation: Alters charge distribution
  • Tertiary Interactions: Salt bridges, stability
  • Bohr Effect: Lower pH reduces O2 affinity
  • Protonation destabilizes T state
  • Facilitates O2 release in tissues
32
Q

what is the bohr effect

A
  • Bohr Effect: Lower pH reduces O2 affinity
33
Q

what is BPG

A

BPG is derived from an intermediate in glucose metabolism

34
Q

what is the relationship between BPG and Hb

A

BPG interacts with Hb at a separate site to the O2 binding site and affects O2 binding

35
Q

where is BPG present

A

present in red blood cells

36
Q

what is the mechanism for BPG binding to the central cavity

A

BPG binds to Hb and decreased the affinity of Hb for O2
§ HbBPG + O2 <–> HbO2 + BPG
* Hb has a single binding site for BPG at the central cavity which is larger in the T state then in the R state
* BPG binding to residues around the cavity stabilises the T state

37
Q

Explain why BPG is important for oxygen release

A

(BPG) is important for oxygen release from hemoglobin because it stabilizes the T state of hemoglobin, decreases its affinity for oxygen, and promotes efficient oxygen unloading in tissues with high metabolic activity. This ensures that oxygen is delivered to cells where it is needed for cellular respiration and energy production.

38
Q

Explain why higher BPG concentration is advantageous at high altitude

A

(BPG) at high altitudes are advantageous because they enhance oxygen unloading from hemoglobin, compensate for reduced oxygen availability, help adapt to hypoxic conditions, and regulate oxygen affinity, ensuring efficient oxygen delivery to tissues despite the challenging environmental conditions.

39
Q

what is the Functional Effect of Carbon Monoxide (CO) Binding to Hb:

A
  • CO binds to hemoglobin (Hb) with much higher affinity than oxygen (O2)
  • Forms carboxyhemoglobin (COHb), reducing O2 transport
  • Shifts oxygen dissociation curve to the left
  • Decreases O2 release to tissues
  • Causes tissue hypoxia and potentially lethal poisoning
40
Q

Describe 3 broad areas for lipid functions and provide examples

A
  • Storage
    • Structure
      Signals
41
Q

Define the term lipid

A

Lipids are organic molecules characterized by insolubility in water and solubility in nonpolar solvents.
- They serve essential functions including energy storage, membrane structure, and signaling.

42
Q

what are the essential componets of a storage lipid

A
  • Fatty acids are essential components of other important lipids
    § Waxes
    § Phospholipids
    Triacyclglycerols
43
Q

what are biological lipids used for

A

□ Energy storage
□ Structural components of biological membranes
Signals and cofactors

44
Q

Fatty Acid Melting Points trends

A

Melting points increase with chain length and decrease with unsaturation.

Longer, saturated fatty acids have higher melting points due to stronger intermolecular forces. Unsaturated fatty acids with cis double bonds have lower melting points due to kinks in the chain.

45
Q

Fatty Acid Solubility trends

A

Fatty acids are insoluble in water but soluble in nonpolar solvents. Solubility decreases with increasing chain length.

Longer hydrocarbon chains make fatty acids more hydrophobic, reducing solubility in water. Shorter chains and polar functional groups increase solubility in water to some extent.

46
Q

Explain trends in melting temperatures of natural fats

A

Influenced by fatty acid composition, chain length, and degree of saturation.
- Saturated fatty acids have higher melting points due to stronger intermolecular forces.
- Longer fatty acid chains generally have higher melting points.
- Unsaturated fats have lower melting points due to double bonds introducing kinks in the chains.
- Natural fats contain a mixture of saturated and unsaturated fatty acids, influencing their melting temperatures.

47
Q

identify an omega 3 fatty acid

A

Omega-3 Fatty Acids:
- Have a double bond at the third carbon from the methyl (omega) end of the fatty acid chain.
- Examples include α-linolenic acid (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA).
- Found in fatty fish (such as salmon, mackerel, and sardines), flaxseeds, chia seeds, walnuts, and algae.

  • 3rd carbon in the opposite direction of the carboxyl group
48
Q

identify an omega 6 fatty acid

A

6th carbon from the oppoite end of the carboxyl group (COOH)

49
Q

highlight the structure of triglycerides

A

they have a glycerol molecule with 3 OH groups that attach to 3 fatty acids via an ester link/bond. these can be the same fatty acid or they can be different

50
Q

are triglycerides storage molecules

A

yes they are storage molecules

51
Q

what are the biological functions of lipids (there are three)

A

Storage of energy
§ Reduced compounds: lots of available energy through oxidation
§ Hydrophobic nature: good packing

  • Insulation from environment
    § Low thermal conductivity
    § High heat capacity (can adsorb heat)
    § Mechanical protection (can absorb shocks)
  • Water repellent
    § Hydrophobic nature keeps surfaces of the organism dry
    § Prevents excessive wetting
    § Prevents loss of water via evaporation
52
Q

what are phospholipids

A

are defined by the phosphate group within their polar head

53
Q

what are the 2 categories of phospholipids

A

1) Glycerophospholipids (based on the glycerol molecule)
2) Sphingolipids (bases on sphingosine)

54
Q

what is a Glycerophospholipids

A

a Glycerophospholipids is a phospolipid where it has 2 fatty acids attach to a glycerol, however it has a phosphate group an an alochol group attach to where the third fatty acid would be

55
Q

what is the range of charges on a Glycerophospholipids

A

ranges -4 to 0 in charge

56
Q

what are Glycerophospholipids mainly used for

A

used in for structure and signalling

57
Q

what is a Sphingolipids

A

a phospholipid where the glycerol is an L shape (where one of the fatty acids would be), one fatty acid attach to the glycerol through an ester bond and a phosphate group and a chlorine group bonded to the phosphate group

58
Q

what are Sphingolipids used for

A

structure and signalling roles

59
Q
A

biochemistry and molecular biology (4 decks)

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