Proteins Flashcards
What do amino acids consist of ?
- Carbon
- Amino group (H2N)
- Carboxyl group (OCOH)
- Hydrogen
- Side chain (R)
What does an atom consist of ?
Nucleus & electrons
How is a covalent bond formed between 2 atoms?
Share electrons
What is bond polarity ?
Uneven electrons share
What atoms in an amino acid are involved in polarity ?
Nδ- , Oδ- Cδ+ , Hδ+
What happens when rather than sharing electrons, atoms gain or lose them ?
- Ions: positive , lost electrons
- Ions: negative, gain electrons
Which atoms in an amino acid are often positively and which negativeley chraged?
N+ O-
They’re 5
What groups are amino acids divided in based on properties of their side chains ?
- Polar/ Non-polar
- Hydrophillic/Hydrophobic
- Acidic/Basic
- Ionisable/charged
- Special amino acids
What is the polar and non polar group about ?
Polar
* Uneven share of electrons in bond
* Electronegative stoms “pull” electrons of a bond towards them
Non-polar
* Even electroons share
What is hydrophilic / Hydrophobic?
- Polar side chains are Hyrophillic: they like water
- Nonpolar side chains are hydrophobic: they don’t like water
What is acidic and base?
- Acidic groups yield H+ to solution
- Base groups remove H+ from solution
- pH = -log H+concentration
- Higher H+, lower the pH, hence acids have low pH and bases high pH
What does ionisable and charged mean?
- Ionisation = to add or remove electrons
- charged = positive or negative
What are the chraged amino acids?
Negatively charged amino acids:
*aspartic acid
* Glutamic acid
Positively charged amino acids :
*Lysine
*Arginine
*Histidine
What are special amino acids ?
- Cysterine has sulfhydryl (SH) that can for s-s bonds
- Glycine has H (very small)
- Proline is cyclic
What type of bonds are formed between amino acids?
Peptide bonds
What type of bonds are formed between amino acids?
Peptide bonds
What are dipole-dipole interactions?
When opposite poles attract
What is hydrogen bonding?
- It’s a type of dipole-dipole interaction involving hydrogen
- Amino acids can be hydrogen bond **donors ** or acceptors
When can hydrogen bonding occur ?
It can occur between pepetide bonds in the same region chain
Secondary structure involves hydrogen bonding between atoms associated with….
- R groups
- C-termini
- N-termini
- Cysteines
- Peptide bonds (pole attraction)
What is Van der Waals interactions ? (non-covalent bonding)
non polar
* even electron share
* But temporaray dipole
* only involves non polar chains
What is hydrophibicity ?
- Polar side chains are hydrophillic (like water)
- Nonpolar side chains are hydrophobic (don’t like water)
Why are some chains hydrophillic (like water)?
Because and polar side chains can hydrogen bond , they’re attracted to each other
Why polar side chains hydrophillic (like water)?
Because side chains can hydrogen bond , they’re attracted to each other
Why are non polar side chains hydrophobic?
Because non polar side chains and water can’t hydrogen bond, non polar side don’t attrccated to water
What are hydrophobic interactions ?
- Relationship between polar water and hydrophobes (low water soluble) non polar, high hydrocrabon chain amino acids
What are ionic interaction ?
Opposites sttract strongly
What are ionic interaction ?
Opposites attract strongly
What are the levels of protein structure ?
- Primary structure
- Secondary structure
- Tertiary structure
- Quaternary structure
What does the primary structure consist of ?
sequence of amino acids linked to form chains
What does the secondary structure consist of ?
Region where chains fold and where peptide interactions occur
what does the teritiary structure consist of ?
Folded regions come together to form 3D shape, this is where R groups interactions
what does the quatenary structure consist of?
Association of several polypeptide chains (e.g. protein subunits)
what does the quatenary structure consist of?
Association of several polypeptide chains (e.g. protein subunits)
Is water polar or non polar?
Polar
What does the term polar bond mean?
Uneven electron share across the bond
What mantains tertiary structure of alpha helicases as globular protein ?
The internal hydrophobic interactions
What is the arrangements of amino acids in helicases?
- Hydrophobic amino acids face inwards
- Hydrophillic face outwards
what is a hydrophobic pocket ?
A binding site that contains mostly hydrophobic amino acids
What is a myoglobin ?
Something thst contains a heme prosthetic group that can reversibly bind to oxygen
What does oxygen binding look like with myoglobin?
- High affinity for oxygen
- Binds when very little
- Captures & stores oxygen in muscle (20-30torr)
- Exercise = reduces oxygen so myoglobin rapidly releases into the tissues as all oxygen is tranposrted in the lungs
What does oxygen binding to hemoglobin look like ?
- Low affinity for axygen
- Capture oxygen in lungs where lots
- Relese in tissue where needed
What is an ezyme ?
A biological catalyst
What is a catalyst ?
Something that speeds up chemical reactions without themselves being changed
Why do we need enzymes ?
Accelerate reactions by up to 1 million+:without them reactions are too slow !!!!
What is an active site ?
Position on protein where substrate bind and are converted to products
What is an active site ?
Position on protein where substrate bind and are converted to products
What are 3D active sites called ?
Cleft / Crevice
What are 3D active sites called ?
Cleft / Crevice
What is the lock and key mechanism of enzyme action ?
Enzyme breaks a large molecule into smaller ones. The same enzyme will aslo catalyse the reverse rection - it will join the smaller molecules together again
What is the induced fit hypothesis of enzyme action ?
When the substrate binds to the enzymes’s active site, it induces a change of shape so that the substrate and enzyme become fully complementary
What are enzymes deactivated by ?
- Heavy Metal Salts (Hg+2, Pb+2, Ag+1, Cd+2)
because they disrupt electrostatic interactions - Reducing agents
They both distrupt S-S bonds
What is added to amino acid when they’re not enough?
Add a cofactor
* Metals
* Small organics (some vitamin derivatives)
* Prosthetic group (tightly bound)
* Cosubstrate (loosely bound)
* Coenzymes
What is a competitive inhibitor ?
When an inhibitor temporarily bind to an active site so that its substrate can’t bind
What is a non-competitive inhibitors ?
Inhibitor will bind to an allosteric which changes the shape of the active site so that the substrate can’t bind.
examples on non polar amino acids
leucine
valine
phenylaline
examples of polar amino acids
aspartic acid
glutamic acids
glutamine
