Structures of proteins Flashcards
What are the functions of LDL and LDL receptors?
LDL and LDL receptors transport cholestrol molecules and co-ordinated their uptake into cells
Give the features of cholesterol transport?
Cholesterol transport;
- Has a phospholipid monolayer shell
- Has a low-density lipoprotein and a single molecule of apolipoprotein B
- Used to transport cholesterol between cells via the circulatory system
What is the uptake of LDL particles mediated by?
The uptake of LDL particles is mediated by the LDL receptor that binds LDL and facilitates internalisation
What do patients who have a mutation in the LDL receptor gene suffer from?
Familial hypercholestrolemia - an abnormal uptake of cholesterol
What is atherosclerosis ?
Plaques can break off and cause blockages potentially becoming fatal
How are proteins used in defence?
Antibodies are made of proteins and defend against infection (they are highly specific)
What are antibodies specifically made from?
Antibodies are a glycoprotein as they have a sugar molecule attached
What are the features of the antigen recognition site?
The antigen recognition site is highly specific and tightly binds the complementary antigen allowing recognition of foreign proteins by the immune system.
The antigen recognition site is composed of two identical heavy chains and two identical light chains, both bonded by disulphide bonds.
What are the 2 types of biological catalysts and their functions ?
Enzymes - regulate all biological systems
Lysozymes;
- Catalyses the cutting of polysaccharide chains
-They bind to polysaccharide chains, catalyse the cleavage of a specific covalent bond and release the cleaved products, the lysozyme remaining unchanged at the end of the reaction.
What are the 2 types of biological catalysts and their functions ?
Enzymes - regulate all biological systems
Lysozymes;
- Catalyses the cutting of polysaccharide chains
-They bind to polysaccharide chains, catalyse the cleavage of a specific covalent bond and release the cleaved products, the lysozyme remaining unchanged at the end of the reaction.
How do proteins help control gene expression?
The Lac repressor is made of proteins which;
- helps to control the production (expression) of proteins that metabolise lactose in bacteria
- The repressor binds to DNA and prevents expression of the gene in the absence of lactose
What are proteins ?
Large complex lines polymers
- Large (usually many thousands of mass units)
- Complex (but have an underlying simplicity, chemically. they are linear polymers of amino acids)
- Linear polymers (Amino acids joined by peptide bonds)
What are proteins ?
Large complex lines polymers
- Large (usually many thousands of mass units)
- Complex (but have an underlying simplicity, chemically. they are linear polymers of amino acids)
- Linear polymers (Amino acids joined by peptide bonds)
What are proteins ?
Large complex lines polymers
- Large (usually many thousands of mass units)
- Complex (but have an underlying simplicity, chemically. they are linear polymers of amino acids)
- Linear polymers (Amino acids joined by peptide bonds)
Draw and name 3 basic hydrophilic amino acids?
Diagram
Draw and name 2 acidic hydrophilic amino acids?
Diagram
What kind of amino acid is Histidine ? Draw it
Basic amino acid
Diagram
What kind of amino acid is Aspartate? Draw it
Acidic amino acid
Diagram
What kind of amino acid is Serine? Draw it
Polar amino acid with an uncharged R group
Diagram
Draw and name the 3 special amino acids?
Cysteine, Glycine and Proline
Diagram
What is a special feature of Glycine?
Glycine is the smallest amino acid residue and this allows it to fit in tight spaces as it doesn’t have a bulky side chain
What is the special feature of proline?
The side chain of Proline bends around to form a covalent bond with the nitrogen atom of the amino group. By doing this Proline creates a kink in the protein chain.
What is an acid?
An acid is any molecule that tends to donate a hydrogen ion
What is a base?
A base is a molecule that readily accepts a hydrogen ion
How do we work out the Ka (equilibrium constant) of a reaction?
Ka = Concentration of products / Concentration of reactants
How can you work out the pKa of any acid?
The pKa of any acid is equal to the pH at which half the molecules are disassociated
How can you work out the pKa of any acid?
The pKa of any acid is equal to the pH at which half the molecules are disassociated
What causes pKa to vary?
pKa varies depending on the environment
What happens if the pH in the endosome is reduced?
A reduction in pH of the endosome causes a conformational change in the LDL - receptor due to the presence of histidine residues within the protein
This means that LDL can n
What is an endosome?
Endosomes are transporter vesicles that move things into the cell from the outside of the cell or other cells (e.g transport minerals from the cell surface, Golgi - lysosome)
What is an exosome?
Exosomes are transporter vesicles that move things out of the cell and into other cells (e.g DNA)
What is endocytosis?
Endocytosis is the absorption of molecules. The molecule binds to the Receptor on the cell and the cell engulfs the molecules to bring it inside the cell
What is familial hypercholestrolemia caused by?
Familial hypercholestrolemia is caused by a mutation in the histidine residue of the LDL receptor.
What is a polypeptide?
A polypeptide is a polymer of amino acids joined by peptide bonds
What are the features of a peptide bond?
Peptide bond is a covalent bond which is formed when a carbon from the carboxyl group shares electrons with the nitrogen atom from the amino group of another amino acid.
What kind of reaction is the joining of 2 amino acids?
A water molecules is lot when joining amino acids together so this is a condensation reaction.
Where can a peptide bond rotation occur?
The peptide bond doesn’t allow rotation however the a-carbon does allow rotation (on central carbon)
What is involved in secondary structure?
Secondary structure is about the initial folding of the polypeptide chain
What are the 3 main types of secondary structure?
The three main types of secondary structure is;
- a-helix
- B -Sheets
- Bend/loop (bonds between a-helix’s or B -sheets)
How are a-helix’s stabilised?
a-helix’s are stabilised by hydrogen bonds between amino and carboxyl groups of every 4th amino acid
What are the features of B-sheets?
B sheets;
- Are extended stretches of 5 or more amino acids called B-strands
- Are organised next to each other to make B-sheets
- Have a varying pattern of hydrogen bonding depending on the type of sheet.
What type of B-sheets are most stable?
Anti-parallel sheets are slightly more stable than parallel ones
What are the features a bend/loop?
Bend/loop;
- Has polypeptide chains which can fold upon themselves forming a bend or loop
- Usually 4 amino acids are requires to form the turn
- Proline residues are frequently found in bends/loops
What is tertiary structure and give features of it?
Tertiary structure - The 3D folding of a secondary structure
Features;
- Hydrophobic residues are buried and hydrophilic residues are exposed to the outward aqeous environment
How are proteins arranged?
Many proteins are organised into multiple ‘domains’
- Each domain contributes a specific function to the overall protein
Different proteins may share similar structures (e.g; Kinase, cysteine rich, globin domains
How do loops /bends also affect tertiary structure?
They connect regions of a-helix and B-sheets so that the polypeptide can fold into a globular domain
What types of bonds stabilise tertiary structures?
Bonds that stabilise tertiary structures;
- Disulphide bonds
- Hydrogen bonds (polar)
- Ionic interactions - Charged side chains
- Van der Waals interactions - Weak, dipolar, e.g - hydrogen bonding
- Hydrophobic interactions
What special amino acid contains disulphide bonds between its adjacent amino acids?
Cysteine residues form a covalent -S-S- bond between neighbouring residues
What is quaternary structure?
Quaternary structure - The association of more than one polypeptide
What is each polypeptide chain called?
Each polypeptide chain is referred to as being a subunit
- Subunits can be identical or different
What are many subunits joined together referred to as?
Oligomeric protein (contains highest level of organisation)
How do disulphide bonds affect the oligomeric structure?
Disulphide bonds often stabilise the Oligomeric structure - to form covalent links so the structures are permanently stuck together.
Name some structures made of subunits that are oligomeric structures, and their functions?
- Mechanosensitive conductance channel (if cell detects movement, channel opens) - 7 identical subunits
- Heterotrimeric G protein - 3 different subunits (alpha, beta and gamma)
- Stored insulin - 6 identical subunits (bound to Zn)
- 70s Ribosome - 30 different subunits
What are the 3 features of haemoglobin?
- Carries oxygen in red blood cells (erythrocytes)
- A symmetrical assembly of two different subunits (2 a-globin and 2-b globin chains)
- Each of the polypeptide chains contains a ham molecule, which binds oxygen for transport to tissues
What is Heam composed of and what does it allow?
Heam is made from a Porphyrin ring with co-ordinated Fe atom - This is what binds to oxygen for transport to tissues
What amino acid helps hold Haem in place?
Each Haem molecule is held in place by hydrogen bonds from histidine F8 and the bound oxygen molecule stabilised by Histidine E7
How is Haem changed when oxygen is bonded?
- Oxygen binding to Haem causes a change in the ring structure
- This in turn influences the structure of Haemoglobin and binding of further O2 molecules
- Haem is domed when deoxygenated. When oxygen binds it changed the orientation of Haem allowing it to become planner and undergo conformational change
What does a sigmoidal oxygen binding curve indicate?
Sigmoidal oxygen binding curve = Oxygen binding is cooperative
- The affinity of the first oxygen molecule is low but binding of subsequent molecules is the increase (4 molecules of oxygen, each one has increased affinity)
This is because the protein structure changes as the first oxygen molecule binds.
What happens when histidine binds to the Haem molecule?
The histidine that H-bonds to Haem molecule in helix F changes position causing a major structural change in the globin subunit
This subtle conformational change causes major structural realignments elsewhere in the molecule causing a dramatic increase in the binding affinity for subsequent oxygen molecules
How does relatively small changes in oxygen concentration affect the interaction of haemoglobin with oxygen and how does this affect the lungs ?
Relatively small changes in oxygen concentration results in large changes in the interaction of haemoglobin with oxygen.
This equates to tight oxygen binding in the lungs and subsequent release in tissues where oxygen concentration is lower.
Describe how the structure of proteins relates to sickle cell anaemia?
Sickles cell anaemia;
- Is caused by a single amino acid change at position 6 in the beta change of haemoglobin
- Instead of making Hydrophilic glutamic acid, hydrophobic valine is made instead
- This causes sickling of erythrocytes (RBC’s) due to aggregation (clustering) of mutated haemoglobin that forms stiff fibres (change in surface chemistry of protein)
How does pH and CO2 concentration affect haemoglobin?
Effects of pH and CO2 on haemoglobin;
- The pH of the blood influences O2 binding to haemoglobin - Bohr effect
- O2 binding occurs with higher affinity at high pH (in lung) and lower affinity at low pH tissues (peripheral tissues)
- O2 loading is therefore easier in the lung and unloading/delivery occurs much faster where O2 is needed
- CO2 (acidic) builds up during exercise, which lowers the blood pH facilitating faster oxygen delivery
How does the structure of foetal haemoglobin vary from an adults?
Foetal haemoglobin has a different quaternary structure to adult haemoglobin.
Foetal haemoglobin is composed of 2 alpha and 2 gamma subunits where as adult is made from 2 alpha and 2 beta subunits.
The gamma subunits bind oxygen at a much higher affinity than beta subunits
Low O2% by the time the blood reaches the placenta so it has to bind with a greater affinity than the maternal haemoglobin to be able to reach the foetus
Due to the absence of beta chains foetal red blood cells are unaffected by sickle cell disease.
What are the features of collagen?
Collagen;
- Is a protein that helps bind cells together to form tissues
- Assembles in long, extremely strong fibres
- Is the chief protein in bone, tendon and skin
- Constitutes 25% of the total protein mass in the body
What are the features of collagens structure and what is it made from?
Collagen structure;
- Tropocollagen is a building block of the collagen fibre and consists of 3 polypeptide chains with a left-handed twist wound together in a right handed supercoil - adding extra strength to collagen
It is also made from;
- Fiber, fibril, Microfibril and tropocollagen helix
What is the structure of Tropocollagen?
Tropocollagen structure;
- Glycine is vital for the formation of tropocollagen triple helix as it has a small side chain that allows tight. turns
- There are 3 amino acid residues per turn
- The small chain of glycine allows for close packing of subunits
- Proline is also vital for the structure of tropocollagen as it imposes left hand twist in the helix that provides main stabilising force of this unusual protein structure
- Some prolines become hydroxylated to form hydroxyproline
- Hydroxyproline forms strong hydrogen bonds that help to stabilise the triple helix
In what special pattern are collagen fibres formed in?
Collagen fibres are formed in a ‘quarter-stagger’ model - Molecules are stitched together by covalent-crosslinks
Gaps provide access sites for Lysol oxidase
What is osteogenesis imperfecta and how is it caused?
Osteogenesis imperfecta is a form of brittle bone disease
An indicator of this can be that the whites of eyes can appear as blue
Osteogenesis imperfecta is caused by a mutation in the gene that codes for one of the collagen subunits leading to a glycine being replaced by a Cysteine residue at one point in the chain
As a consequence the tropocollagen subunits cannot pack together properly and there is a. knock-on effect on collagen fibre formation
What are the symptoms and causes of Elhers-Danloss syndrome?
YVIE ODDLY
Elhers-Danloss syndrome has symptoms of loose skin and hyper mobile joints (as once ligaments are stretched they become much weaker)
The cause of Elhers-Danloss Syndrome is due to a lack of procollagen peptidase or Lysyl oxidase
What are the symptoms and causes of scurvy?
Scurvy has symptoms of loose skin and hypermobile joints
Scurvy is caused by a lack of proline hydroxylation
What is hydrogen bonding made from?
Hydroxyproline?
What is cross-linking is made from?
Cross-linking is made from Lysine-derived aldehydes
