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Medicine Sem 1 > Biochemistry week3,4,5 > Flashcards

Biochemistry week3,4,5 Flashcards

1
Q

What is the extracellular matrix

A

A network of macromolecules in the extracellular space, forming a 3 dimensional framework for tissue and organs.

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2
Q

What is the role of the extracellular matrix

A

It regulates cellular processes

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3
Q

What is the extracellular matrix composed of?

A
  • Fibrilliar proteins
  • Non collagenous glycoproteins
  • proteoglycan
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4
Q

What are the major proteins in the Extracellular matrix

A

collagen

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5
Q

How are collagens classified?

A

As fibrillar and non-fibrillar

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6
Q

What is the function of collagen fibrils?

A

It provides flexibility and high tensile strength

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7
Q

What is the primry structure of proteins?

A

This is the linear sequence of amino acids in a protein

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8
Q

What is the secondary structure of proteins?

A

This refers to the folding of the polypeptide chain, which is stabilised by hydrogen bonding between carbonyl and amide group

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9
Q

Name the 2 types of secondary structure

A
  • Alpha helix
  • Beta pleated sheet
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10
Q

Describe the alpha helix structure

A
  • Rod like, righthanded spiral, coiled structure
  • Each amide carbonyl group in the helix forms a hydrogen bind with an amide hydrogen for residues away
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11
Q

Describe the beta pleated sheet structure

A
  • Forms lateral hydrogen bonds between the peptide bonds
  • It is an extended structure with tetrahedral C-C binds creating a pleated shape
  • It can be arranged in parallel or antiparallel
  • Beta turns or bends allow the polypeptide to reverse direction
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12
Q

What is the tertiary structure

A

A 3 dimensional conformation of a protein

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13
Q

What is the tertiary structure stabilised by?

A
  • It is stabilised by side chain interactions:
  • Disulfide
  • Hydrogen bonds
  • Salt bridges
  • Hydrophobic interactions
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14
Q

Where do salt bridges form in the tertiary structure

A
  • They form between the oppositely charged amino acids
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15
Q

Name hydrogen donors and acceptors in the tertiary sturtcure and their role

A

hydrogen donors:
- Tryptophan
- Arginine
hydrogen acceptors:
-Asparaginine
- Glutamine
They contribute to the structure

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16
Q

What do denaturants do to the tertiary structure and name one

A
  • Urea
    They distrupt the secondary and tertiary structure by blocking the stabilising interactions
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17
Q

What is the quaternary structure?

A

refers to the assembly of 2 or more peptide chains(subunits) in a protein

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18
Q

What are the subunits in the quaternary sturtcure held together by?

A

Covalent and non-covalent interaactions on their surface

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19
Q

In the quarternary structure what are multisubunit proteins with multiple chains described as?

A
  • Dimeric
    -Trimeric
    -Multimeric
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20
Q

Explain the structure of hemoglbin

A
  • Has a terameric structure, with 2 a and b globin chains, each with a non covalently bonded heme group
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21
Q

What is myoglobin

A
  • Single globin polypeptide chain
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22
Q

What happens in the secondary structure of mammalian globins

A

-It has a high alpha helix content, organised into eight segments form a spherical globin fold

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23
Q

What is the tertiary structure of mamalian globins?

A
  • A helix a tightly packed in a spherical structure kown as the globin fold
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24
Q

What is the structure if the Heme prosthetic group?

A
  • It is a porphyrin molecle with an iron atom at its center which binds to oxygen
  • It is plantar and mostly hydrophobic
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25
Q

What is the role of heme interms of colout

A
  • It gives globins the colour purple when it is deoxygenated in venous blood and it gives them the colour red when its oxygenated in arterial blood
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26
Q

What is the role of Globins

A

They increase the solubility of the hydrophobic heme, by enclosing it in a hydrophobic pocket, which protects the heme from oxidation.

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27
Q

What is the function of myoglobin

A
  • It stores and releases oxygen in the muscle cells.
  • Ensuring there is a supply for cellular organelles
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28
Q

Where is the myoglobin found?

A
  • Cytosol of skeletal, cardiac and muscle cells
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29
Q

Explain the oxygen-release mechanism in myoglobin

A
  • In the muscle cells, myoglobin readily binds to oxygen from the blood.
  • During metabolism , myaglobin releases the oxygen allowing it to diffuse to the mitochondria
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30
Q

What is the function of hemoglobin and its location

A
  • It transports oxygen in human blood
    Location: found in red blood cells(erythrocytes)
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31
Q

What is the structure of hemoglobin

A

–composed of 2 a and b globin subunits arranged in a tetrahedral structure

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32
Q

Explain the cooperative binding concept with hemoglboin and oxygen

A
  • It binds to oxygen cooperatively,
  • The cooperative binding means that hemoglobins affinity for oxygen insreases as more oxygen molecules bind to it.
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33
Q

Explain the function of hemoglobin in oxygen delivery

A
  • It binds to oxygen in the lungs and releases it in the tissues. Structural changes allow it to adjust its affnity for oxygen as moves from high low oxygen envirnoments
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34
Q

Explain the conformatinal changes that occur in hemoglobin when binding to oxygen

A
  • When it binds to oxygen, a structural shift occurs, within the heme pocketand extends across the entire protein. The changes include:
    -Rotation
  • Displacment of the Hb subunit
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35
Q

Explain the binding capacity and saturation cruve of hemoglobin

A
  • It can bind up to 4 molecules, leading to a S shape oxygen- binding curve due to cooperative binding.
  • The steep part of the curve aligns with typical tissue oxygen levels, so small changes in the oxygen can greatly effect hemoglobins in releasing or binding oxygen.
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36
Q

What does the allosteric nature of hemoglobin -mean?

A
  • Means that the hemoglobins oxygen affinity can be modulated by molecules binding to sotes other than the primary oxygen binding site
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37
Q

Name allosteric effectors in HB

A
  • H+, CO2 and 2,3bisphosphoglycerate(2,3BP)
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38
Q

What is the role of allosteric effectors on Hb

A
  • ## They bind at different locations on the hemoglobin and influence the o2 binding affinty through structural changes
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39
Q

What is the effect of homotrophic interactions?

A
  • They enhance hemoglbins abffinity for oxygen molecule
40
Q

What are heterophobic interactions on Hb affinity for oygen

A
  • Other effectos like ( H+ and CO2) affect the oxygen binding affinity

-They lead to a decrease in affinity

41
Q

What is the function of an enzyme?

A
  • Speeds up the rate of reaction, lowering the activation enrgy and speeding up the time it takes to reach equillibrium, without changing the equillibrium
42
Q

Explain the factors that affect enzymatic reactions

A

TEMPERATURE
- As the temperature increases the enzymatic reactions increases
- Enzymes have an optimal temperature for peak efficiency
PRESSURE
- Enzymes have an optimum PH level which is influenced by ionisable amino acids involved in catalytic reactions

43
Q

Explain the concept of enzymatic specificity

A
  • Enzymes are highly specific for both the type of reaction they catalyze and the substrate they act on
  • This specificty is determined by amino acids at the enzyes catalytic centre
44
Q

What is enzymes specifity determined by?

A
  • Amino acids at the enzymes catalytic centers
45
Q

What is the enzymes optimum Ph level influenced by?

A
  • ionisable amino acids involved in catalytic reactions
46
Q

1.Explain the enzymes active site structure 2.what does the substarte specificty depend on ?

A
  • Has a substrate binding site and the catalytic site
  • On properties like size, structure,polarity and hydrophobility of the substrate binding site.
47
Q

What are coenzymes?

A
  • They are helper molecules essential for many enzyme-catalysed reaction
48
Q

What are Haloenzymes?

A
  • Enzymes with a covalenlty or noncovalently bound coenzyme
49
Q

What are Apoenzymes?

A

Enzymes without a coenzyme

50
Q

Name 3 types of co-enzymes

A
  • Soluble enzymes
  • Prosthetic group
  • Coenzyme A
51
Q

What are co factors?

A
  • Some enzymes need inorganic ions(cofactors) like( ca2+,fe,cu+, Mn for activity especially in blood clotting and oxidation-reduction reaction
52
Q

Give examples of cofactors

A

Ca2+, fe, cu+, mn

53
Q

Explain vitamin derivatives in co enzymes

A

Most coenzymes are derived from vitamins, such as B vitamins (niacin and riboflavin) used in oxidoreductase reactions.

54
Q

Name 2 examples of B vitamins that co enzymes are derives from

A

niacin, riboflavin

55
Q

Explain first type of coenyzyme

A

SOLUBLE COENZYMES
- They bind reversibly to enzymes, that are modified during the reaction and they are recycled by other enzymes

56
Q

Explain the second type of coenzymes

A

PROSTHETIC GROUPS
- They are tightly, often covalently bound, staying with the enzyme through the catalytic cycle

57
Q

What is the role of coA

A

It assists in transfering intermediates between enzymes

58
Q

What does the Michaelis- Menton model of enzymes assume?

A
  • The model assumes that the substrate (S) binds to the enzyme (E) to form an enzyme-substrate (ES) complex, which then decomposes into enzyme (E) and product (P).
59
Q

What is the steady state assumption in the Michaelis- Menton model

A

Steady-State Assumption: ES is rapidly established in steady-state equilibrium, with the decomposition of ES to E + P being the rate-limiting step.

60
Q

What are enzymes?

A

They are specialised proteins that catalyse biological reactions

61
Q

Name 4 places where enzymes are found

A

Mitochondria
Nucleus
Cytosol
Lysosome

62
Q

Name the 6 ways in which enzymes can be classified

A
  • oxidoreductases
  • Transferases
    -hydrolases
    -lyses
    -isomerases
  • Ligases
63
Q

What are Isozymes

A
  • ## Different structural forms of a protein that catalyze the same reaction
64
Q

What is km

A

The afinity of the enzyme for its substrate

65
Q

If enzymes have a high km what does that mean

A

It needs a high substarte concentration for efficent activity

66
Q

Name the types of Enzyme Inhibitors and what they lead to

A
  • Reversible inhibitors- Temporay inhibitiom
  • Irrevrsible inhibitors, permenant modication of an enzyme
67
Q

What is the function of the lineweaver-Burk plots in realtion to inhibition

A

They help to differentiate between, competitive, noncompetitive and uncompetitive inhibitons

68
Q

Explain the mechanism of competitive inhibitors

A
  • They resemeble and have a similar shap to the substrate, it bind to the enzymes active site, preventing the substrate from binding
69
Q

Explain the affect of competitive inhibitors on kinetics

A

-They increase the km, without affecting the maximum velocity, v_max

70
Q

1.What does the inhibition constant measure(k_i)?
2.What does a low k_i mean?

A
  • The binding strength of the inhibitor to the enzyme
  • Lower k_i means a stronger inhibiton
71
Q

How can the competitive inhibitors be overcome?

A
  • By increasing the substrate
72
Q

Explain the concept of uncompettitve inhibitors

A
  • They bind to the Enzyme substrate complex and not the free enzymes
73
Q

What is the uncompetitive inhibitors effects on kinetics

A

-It reduces the maximum velocity (v_max) and reduces km

74
Q

Explain the mechanism of non-competitive inhibitors

A

They bind to free enzymes or to the enzyme substrate complex, typically away from the active site

75
Q

Explain the non-compettitve inhibiton effect on kinetics

A

-Alter the km and the vmax

76
Q

What are the main points that regulate enzyme Activity

A
  • Gene expression
  • Proteolytic Activation
  • Allosteric regulation
  • Degradation
77
Q

What happens in Degradation, to do with regulating enzyme activity

A

controlled by intracellular proteases in lysosomes or proteasomes in the cytosol

78
Q

What is Proteolytic Activation of digestive ennzymes and example

A

When digestive enzymes are stored in an active form and activated in the gastrointestinal tract
- Trypsinogen is activated by entropeptidase

79
Q

Name the 2 types of Allosteric effects to do with enzymes

A
  • Homotrophic
    -Heterotrophic
80
Q

What is the behaviour of allosteric enzymes

A
  • Exhibit s shaped plots of reaction velocity vs substrate concentration
81
Q

Explain the process of Allosteric effectors in enzymes

A
  • Bind to a site different from the substrate binding site
    -Influences substrate binding or catalytic activity
82
Q

Exlain what happnes in the 2 types of allosteric effectors in enzymes

A

HOMOTROPHIC
-The substrate acts as an allosteric effector where binding at one active site affects substarte binding at another
HETEROTROPHIC
- A molecule other than the substrate acts as the effectore, altering nezyme activity or substrate binding.

83
Q

Name the types of connective tissue fibres

A
  • Collagen fibres
    -Reticular fibres
    -Elastic fibres
84
Q

What does the fibrillar structure contain?

A
  • Fibrillar
  • Network
    -FACITs
85
Q

What does the Nonfibrilar collagens contain?

A
  • Hexagonal networks
  • Broaded filaments
  • Beaded filaments
    -Anchoring fibrils
86
Q

Explain the structure of collagen molecules

A

-Cross linked between the lysine and hydroxylyseine aldehyde groups

87
Q

Explain the process of collagen synthesis

A

-Proline and lysine residues are hydroxylated and the profactor acsorbic acids is required
-The sugar groups are added to the hydroxylysine residues
- Triple A Helix is formed from 3 chains
- Intrachain and interchain hydrogen and disulfide bonds are formeed
- Triple molecule is stabilised by chaperone proteins
- Then proteoglycan is is formed

88
Q

What is the lock and theory?

A

Binding site for substate enzyme on the enzyme is a rigid entity and only a compund with a particular shape will fit

89
Q

What induced fit Theory?

A
  • Enzymes is flexible, and other susbstrates bind to the enzyme, the conformation of the protein changes so that a stable binary complex forms.
90
Q

What does Isosteric enzymes show compared to Allosteric enzymes?

A

–Isosteric enzymes show hyperbolic reaction rate curves in relation to substrate concentration.
Allosteric enzymes display sigmoidal reaction of velocity versus substrate concentration curves due to cooperative substrate binding

91
Q

What do Allosteric effectors alter in enzymes?

A

-Substrate binding affinity (Km).
-Catalytic rate (kcat).

92
Q

How are zymogens formed?

A
  • By digestove enzymes being stored in the pancrease as inactive forms
93
Q

What is the role of zymogens?

A
  • They prevent premature activation
  • Protect the pancrease from self digestion
94
Q

Explain the activation of zymogens in the gastrrintestinal tract

A
  • Zymogens are released In pancreatic juice after a meal
  • Trypsinogen is activated to trypsin by intestinal enteropeptidase, which is an enzyme located on the inner surface of the duodenum
95
Q

Where is eteropeptidase located

A
  • On the inner surface of the duodenum
96
Q

N terminal

Explain the mechanism of Trypsin Activation

A
  • Eteropeptidase removes an N-terminal peptide from typsinogen
  • This triggers a re arrangment in the Tertiary structure, forming active trypsin.
97
Q

What is Cascade amplification?

A
  • When active trypsin further activates other zymogens and trypsinogen moleules

Medicine Sem 1 (18 decks)

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