Biochemistry week3,4,5 Flashcards
What is the extracellular matrix
A network of macromolecules in the extracellular space, forming a 3 dimensional framework for tissue and organs.
What is the role of the extracellular matrix
It regulates cellular processes
What is the extracellular matrix composed of?
- Fibrilliar proteins
- Non collagenous glycoproteins
- proteoglycan
What are the major proteins in the Extracellular matrix
collagen
How are collagens classified?
As fibrillar and non-fibrillar
What is the function of collagen fibrils?
It provides flexibility and high tensile strength
What is the primry structure of proteins?
This is the linear sequence of amino acids in a protein
What is the secondary structure of proteins?
This refers to the folding of the polypeptide chain, which is stabilised by hydrogen bonding between carbonyl and amide group
Name the 2 types of secondary structure
- Alpha helix
- Beta pleated sheet
Describe the alpha helix structure
- Rod like, righthanded spiral, coiled structure
- Each amide carbonyl group in the helix forms a hydrogen bind with an amide hydrogen for residues away
Describe the beta pleated sheet structure
- 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
What is the tertiary structure
A 3 dimensional conformation of a protein
What is the tertiary structure stabilised by?
- It is stabilised by side chain interactions:
- Disulfide
- Hydrogen bonds
- Salt bridges
- Hydrophobic interactions
Where do salt bridges form in the tertiary structure
- They form between the oppositely charged amino acids
Name hydrogen donors and acceptors in the tertiary sturtcure and their role
hydrogen donors:
- Tryptophan
- Arginine
hydrogen acceptors:
-Asparaginine
- Glutamine
They contribute to the structure
What do denaturants do to the tertiary structure and name one
- Urea
They distrupt the secondary and tertiary structure by blocking the stabilising interactions
What is the quaternary structure?
refers to the assembly of 2 or more peptide chains(subunits) in a protein
What are the subunits in the quaternary sturtcure held together by?
Covalent and non-covalent interaactions on their surface
In the quarternary structure what are multisubunit proteins with multiple chains described as?
- Dimeric
-Trimeric
-Multimeric
Explain the structure of hemoglbin
- Has a terameric structure, with 2 a and b globin chains, each with a non covalently bonded heme group
What is myoglobin
- Single globin polypeptide chain
What happens in the secondary structure of mammalian globins
-It has a high alpha helix content, organised into eight segments form a spherical globin fold
What is the tertiary structure of mamalian globins?
- A helix a tightly packed in a spherical structure kown as the globin fold
What is the structure if the Heme prosthetic group?
- It is a porphyrin molecle with an iron atom at its center which binds to oxygen
- It is plantar and mostly hydrophobic
What is the role of heme interms of colout
- 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
What is the role of Globins
They increase the solubility of the hydrophobic heme, by enclosing it in a hydrophobic pocket, which protects the heme from oxidation.
What is the function of myoglobin
- It stores and releases oxygen in the muscle cells.
- Ensuring there is a supply for cellular organelles
Where is the myoglobin found?
- Cytosol of skeletal, cardiac smooth muscle cells
Explain the oxygen-release mechanism in myoglobin
- 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
What is the function of hemoglobin and its location
- It transports oxygen in human blood
Location: found in red blood cells(erythrocytes)
What is the structure of adult hemoglobin
–composed of 2 a and b globin subunits arranged in a tetrahedral structure
Explain the cooperative binding concept with hemoglboin and oxygen
- It binds to oxygen cooperatively,
- The cooperative binding means that hemoglobins affinity for oxygen insreases as more oxygen molecules bind to it.
Explain the function of hemoglobin in oxygen delivery
- 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
Explain the conformatinal changes that occur in hemoglobin when binding to oxygen
- 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
Explain the binding capacity and saturation cruve of hemoglobin
- 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.
What does the allosteric nature of hemoglobin -mean?
- Means that the hemoglobins oxygen affinity can be modulated by molecules binding to sotes other than the primary oxygen binding site
Name allosteric effectors in HB
- H+, CO2 and 2,3bisphosphoglycerate(2,3BP)
What is the role of allosteric effectors on Hb
- ## They bind at different locations on the hemoglobin and influence the o2 binding affinty through structural changes
What is the effect of homotrophic interactions?
- They enhance hemoglbins abffinity for oxygen molecule
What are heterophobic interactions on Hb affinity for oygen
- Other effectos like ( H+ and CO2) affect the oxygen binding affinity
-They lead to a decrease in affinity
What is the function of an enzyme?
- Speeds up the rate of reaction, lowering the activation enrgy and speeding up the time it takes to reach equillibrium, without changing the equillibrium
Explain the factors that affect enzymatic reactions
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
Explain the concept of enzymatic specificity
- 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
What is enzymes specifity determined by?
- Amino acids at the enzymes catalytic centers
What is the enzymes optimum Ph level influenced by?
- ionisable amino acids involved in catalytic reactions
1.Explain the enzymes active site structure 2.what does the substarte specificty depend on ?
- Has a substrate binding site and the catalytic site
- On properties like size, structure,polarity and hydrophobility of the substrate binding site.
What are coenzymes?
- They are helper molecules essential for many enzyme-catalysed reaction
What are Haloenzymes?
- Enzymes with a covalenlty or noncovalently bound coenzyme
What are Apoenzymes?
Enzymes without a coenzyme
Name 3 types of co-enzymes
- Soluble enzymes
- Prosthetic group
- Coenzyme A
What are co factors?
- Some enzymes need inorganic ions(cofactors) like( ca2+,fe,cu+, Mn for activity especially in blood clotting and oxidation-reduction reaction
Give examples of cofactors
Ca2+, fe, cu+, mn
Explain vitamin derivatives in co enzymes
Most coenzymes are derived from vitamins, such as B vitamins (niacin and riboflavin) used in oxidoreductase reactions.
Name 2 examples of B vitamins that co enzymes are derives from
niacin, riboflavin
Explain first type of coenyzyme
SOLUBLE COENZYMES
- They bind reversibly to enzymes, that are modified during the reaction and they are recycled by other enzymes
Explain the second type of coenzymes
PROSTHETIC GROUPS
- They are tightly, often covalently bound, staying with the enzyme through the catalytic cycle
What is the role of coA
It assists in transfering intermediates between enzymes
What does the Michaelis- Menton model of enzymes assume?
- 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).
What is the steady state assumption in the Michaelis- Menton model
Steady-State Assumption: ES is rapidly established in steady-state equilibrium, with the decomposition of ES to E + P being the rate-limiting step.
What are enzymes?
They are specialised proteins that catalyse biological reactions
Name 4 places where enzymes are found
Mitochondria
Nucleus
Cytosol
Lysosome
Name the 6 ways in which enzymes can be classified
- oxidoreductases
- Transferases
-hydrolases
-lyses
-isomerases - Ligases
What are Isozymes
- ## Different structural forms of a protein that catalyze the same reaction
What is km
The afinity of the enzyme for its substrate
If enzymes have a high km what does that mean
It needs a high substarte concentration for efficent activity
Name the types of Enzyme Inhibitors and what they lead to
- Reversible inhibitors- Temporay inhibitiom
- Irrevrsible inhibitors, permenant modication of an enzyme
What is the function of the lineweaver-Burk plots in realtion to inhibition
They help to differentiate between, competitive, noncompetitive and uncompetitive inhibitons
Explain the mechanism of competitive inhibitors
- They resemeble and have a similar shap to the substrate, it bind to the enzymes active site, preventing the substrate from binding
Explain the affect of competitive inhibitors on kinetics
-They increase the km, without affecting the maximum velocity, v_max
1.What does the inhibition constant measure(k_i)?
2.What does a low k_i mean?
- The binding strength of the inhibitor to the enzyme
- Lower k_i means a stronger inhibiton
How can the competitive inhibitors be overcome?
- By increasing the substrate
Explain the concept of uncompettitve inhibitors
- They bind to the Enzyme substrate complex and not the free enzymes
What is the uncompetitive inhibitors effects on kinetics
-It reduces the maximum velocity (v_max) and reduces km
Explain the mechanism of non-competitive inhibitors
They bind to free enzymes or to the enzyme substrate complex, typically away from the active site
Explain the non-compettitve inhibiton effect on kinetics
-km stays the same and decrease the vmax
What are the main points that regulate enzyme Activity
- Gene expression
- Proteolytic Activation
- Allosteric regulation
- Degradation
What happens in Degradation, to do with regulating enzyme activity
controlled by intracellular proteases in lysosomes or proteasomes in the cytosol
What is Proteolytic Activation of digestive ennzymes and example
When digestive enzymes are stored in an active form and activated in the gastrointestinal tract
- Trypsinogen is activated by entropeptidase
Name the 2 types of Allosteric effects to do with enzymes
- Homotrophic
-Heterotrophic
What is the behaviour of allosteric enzymes
- Exhibit s shaped plots of reaction velocity vs substrate concentration
Explain the process of Allosteric effectors in enzymes
- Bind to a site different from the substrate binding site
-Influences substrate binding or catalytic activity
Exlain what happnes in the 2 types of allosteric effectors in enzymes
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.
Name the types of connective tissue fibres
- Collagen fibres
-Reticular fibres
-Elastic fibres
What does the fibrillar structure contain?
- Fibrillar
- Network
-FACITs
What does the Nonfibrilar collagens contain?
- Hexagonal networks
- Broaded filaments
- Beaded filaments
-Anchoring fibrils
Explain the structure of collagen molecules
-Cross linked between the lysine and hydroxylyseine aldehyde groups
Explain the process of collagen synthesis
-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
What is the lock and theory?
Binding site for substate enzyme on the enzyme is a rigid entity and only a compund with a particular shape will fit
What induced fit Theory?
- Enzymes is flexible, and other susbstrates bind to the enzyme, the conformation of the protein changes so that a stable binary complex forms.
What does Isosteric enzymes show compared to Allosteric enzymes?
–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
What do Allosteric effectors alter in enzymes?
-Substrate binding affinity (Km).
-Catalytic rate (kcat).
How are zymogens formed?
- By digestove enzymes being stored in the pancrease as inactive forms
What is the role of zymogens?
- They prevent premature activation
- Protect the pancrease from self digestion
Explain the activation of zymogens in the gastrrintestinal tract
- 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
Where is eteropeptidase located
- On the inner surface of the duodenum
N terminal
Explain the mechanism of Trypsin Activation
- Eteropeptidase removes an N-terminal peptide from typsinogen
- This triggers a re arrangment in the Tertiary structure, forming active trypsin.
What is Cascade amplification?
- When active trypsin further activates other zymogens and trypsinogen moleules
