protein structures Flashcards
how do you write amino acid sequence
written from amino or N terminus to carboxy or C terminus
what are 5 properties of peptide bonds
- very stable
- cleaved by proteolytic enzymes proteases or peptidases
- partial double bond
- flexibility around C atoms not involved in bond, allows multiple conformations
- usually one preferred native conformation, determined mainly by the type of side chains and their sequence in the polypeptide
what are the 2 types of ways to represent protein structure
backbone - a line following the peptide bonds
cartoon - a representation showing the fundamental secondary structures (helix/sheet)
how is the folded state of proteins stabilised
by interactions between amino acids which can be very far apart in the primary sequence
what are the 5 types of forces that hold proteins together
van der waals forces
hydrogen bonds
hydrophobic forces
ionic bonds
disulphide bonds
what are van der waals forces
weak attractive interactions between atoms due to fluctuating electrical charges
when are van der waals important
when 2 macromolecular surfaces fit closely in shape
can also be repulsive at very short distance
what are hydrogen bonds
interaction between dipoles
involving hydrogen and an oxygen/nitrogen
partial negative charges on negative atoms bound to H which has a partial positive charge
the partial charges allow weak attractive interactions between some amino acid side chains, main chain O and N and water
what are hydrophobic forces
uncharged and non polar side chains are repelled by water because they are poorly soluble
the side chains then form tightly packed cores in the interior of proteins, excluding water molecules
this attraction is the hydrophobic force
what are ionic bonds
bonds between fully or partially charged groups
they are weakened in aq systems by shielding by water molecules and other ions in solution
what are disulphide bonds
covalent bonding between side chains of cysteine residues
occurs in extracellular domains of proteins because conditions can be harsher so need extra stability
what is the primary structure of a protein
a linear sequence of amino acids linked by peptide bonds
what does the primary structure of a protein determine
it’s 3D conformation - the way in which the chain will fold to form its native structure
what are the 2 types of protein secondary structure
alpha helix
beta pleated sheet
what is the alpha helix protein structure
H bonds between each carbonyl group
H attached to the N which is 4 aa along the chain
side chains look outwards
proline breaks the helix (ring + no H)
what is the beta pleated sheet protein structure
H bonds between linear regions of polypeptide chains
chains from 2 proteins or same protein
parallel or antiparallel chains, pleated or not
if the chain is folding back, structure is usually a 4 aa turn, called hairpin loop or B-turn
what does the tertiary structure of protein mean
the overall 3D conformation of the protein
can be changed with pH and temperature
what forces are involved in protein tertiary structure
electrostatic
hydrophobicity
H bonds
covalent bonds
what are the types of conformational domains of tertiary structure (3)
barrel
bundle
saddle
what does the quarternary structure of a protein mean
3D structure of a protein composed of multiple sub units
same non covalent interactions as tertiary structures
how do we determine protein structure
X ray diffraction of protein crystals
what are enzymes
biological catalysts that bind the reactants (substrates) and convert them to products
then they release the products and return to their original form
what are benefits of enzymes (2)
speed up reactions
provide a way to regulate the rate of reactions
what occurs in mitochondria (3)
TCA cycle
fatty acid oxidation
decarboxylation of pyrvate
what occurs in cytosol (3)
glycolysis
HMP pathway
fatty acid synthesis
what occurs in nucleus
DNA & RNA synthesis
what occurs in lysosome
degradation of complex molecules
how do enzymes act as disease markers
an enzyme marker is a blood test to measure enzymes, and proteins in your blood that can indicate tissue damage or disease.
eg elevated cardiac enzymes after a heart attack are a sign of serious heart damage
what are 2 uses of enzymes
disease markers
drug targets
how do enzymes act as drug targets
they act as a target for drugs for the desired therapeutic effect, which are thereby called biological targets.
what is the porphyrin ring
the framework for the heme molecule, the pigment in haemoglobin and red blood cells.
what is the structure of the porphyrin ring
contains an iron atom which is the site of oxygen binding
what makes up a haemoglobin molecule
a chain x2
B chain x2
heme group
what factors affect haemoglobin saturation
body temperature
arterial carbon dioxide
H+ level
how is haemoglobin saturation affected
- structure gets modified
- affinity for oxygen is altered
what happens when haemoglobin saturation increases
- its affinity for oxygen decreases
- oxygen unloading from the blood is enhanced
what happens when haemoglobin saturation decreases
- its affinity for oxygen increases
- oxygen unloading from the blood is reduced
what is sickle cell anaemia
a genetic disorder characterized by the formation of hard, sticky, sickle shaped red blood cells rather than normal bioconcave shaped red blood cells
what causes sickle cell anaemia
a mutation in haemoglobin
what are immunoglobulins
antibodies
they bind to antigens which are typically toxins or proteins on the surface of microbial agents
these targets are consequently labelled for destruction by cells of the immune system or by lysis through the complement system
what is the structure of an immunoglobulin
4 polypeptide chains
two heavy (H) and two light (L) chains
Complementarity-determining regions (CDRs) are immunoglobulin hypervariable domains that determine specific antibody binding
where are the antigen binding domains on immunoglobulins
at the tip of supporting structural frameworks
