Biochem Flashcards
Heat shock proteins as chaperones
- Prevent aggregation of unfolded chain
- Assist achieving proper protein conformation
- Help transport partially folded proteins across membranes
Mislocalisation
process by which misfolded protein isn’t transported to its original location
formation of disulphide bonds between amino acids
Oxidation between cysteine residues
Which amino acid contains only 1 amino group?
Proline
TRUE/FALSE
Disulphide bonds are more common in intracellular proteins
FALSE
more common in extracellular, as they are less protected so need better support
Can peptide bonds rotate?
No - as they have double bond character due to resonance of e- between C and N
direction of residues in an alpha helix
hydrophobic residues point inward.
hydrophillic residues point outward.
β strands
polypeptide chains that are almost fully extended
β sheets
multiple β strands arranged side-side, stabilised by H bonds between C=O and N-H on adjacent strands
parallel β sheets
strands run in the same N- to C- terminal direction
antiparallel β sheets
strands run in opposite N- to C- terminal directions
screw sense
The direction in which a helical structure rotates with respect to its axis
native conformation
Polypeptide chain folds into a single stable shape, determined by sequence of amino acids & other important factors. Determines biological function
Helix-loop-helix
two helices connected by a turn
Coiled-coil
Two amphipathic α helices that interact in parallel through their hydrophobic edges
Helix bundle
Several α helices that associate in an antiparallel manner to form a bundle
β α β Unit
Two parallel β strands linked to an intervening α helix by two loops
Hairpin
Two adjacent antiparallel β strands connected by a β turn
β Meander
Antiparallel sheet composed of sequential β strands connected by loops or turns
Greek key
4 antiparallel strands (strands 1,2 in the middle, 3 and 4 on the outer edges)
β Sandwich
Stacked β strands or sheets
domain
Independently 3D folded, compact units in proteins
Proteins with very specific binding identities or catalytic functions are likely to possess
protein domains
All β
Only β sheets & connecting loop structures
α + β
Local clusters of α helices & β sheet in separate, clearly distinct regions
Mixed α /β
Motifs such as the α β α unit, where regions of α helix and β strand alternate or are interdispersed
All α
Consist almost entirely of α helices & connecting loops
Categories of protein structure
All β
All α
Mixed α /β
α + β
Aliphatic amino acids include
glycine alanine valine leucine isoleucine
Aromatic amino acids
phenylalanine
tyrosine
tryptophan
histidine
sulfure containing amino acids
cysteine
methionine
basic amino acids
lysine
histidine
arginine
acidic amino acids
aspartate
glutamate
amide versions of acidic amino acids
asparagine
glutamine
alcohol amino acids
tyrosine
serine
threonine
What is the most common structural motif in membrane proteins
spanning α-helices
Valence shell
Outer electron shell
Ligase
Enzyme which catalyses the joining of two substrates using ATP.
Competitive inhibitor on kinetic constants
Bind to enzyme active site and raises Km value for enzyme
Enzyme which cayalyses conversion of 2ADP to ATP and AMP
Adenylate Kinase
How much free energy is released in ATP hydrolysis under normal physiological conditions?
Much more negative than ΔG°
Which coenzyme is an oxidising agent used in catabolic reactions?
NAD+
Which coenzyme is a reducing agent used in anabolic reactions?
NADPH
First substance in glycolysis chain
GLucose
Enzyme which converts glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate
GAPDH
Enzyme which converts 1,3-bisphosphoglycerate to 3-phosphoglycerate
Phosphoglycerate kinase
Enzyme involved in conversion of 3-phosphoglycerate to 2-phosphoglycerate during glycolysis
Phosphoglycerate mutase
enzyme involved in conversion of 2-phosphoglycerate to Phosphoenolpyruvate during glycolysis
Enolase
Enzyme which converts Phosphoenolpyruvate to pyruvate during glycolysis
Pyruvate kinase
Other than glucose, what goes into glycolysis?
2 ADP + 2 NAD+ + 2 Pi
Other than 2 pyruvate, what is produced during glycolysis
2 ATP
2 NADH
Equation for anaerobic metabolism of pyruvate to form ethanol
Glucose (6C) + 2 ADP + 2 Pi + 2 H+ –> 2 Ethanol (2C) + 2 ATP + 2 CO2 + 2 H2O
What enzyme converts pyruvate to lactate?
Lactate dehydrogenase
what enzymes are involved in conversion of pyruvate to ethanol?
Pyruvate decarboxylase
Alcohol dehydrogenase
Intermediate in alcoholic fermentation?
Acetaldehyde
What regenerate NAD+ after use in lactic acid fermentation?
Glyceraldehyde 3-phosphate dehydrogenase in glycolysis
Activators of PFK-1
AMP and Fructose-1,6-bisPhosphate
Inhibitors of PFK-1
ATP and citrate
The main regulatory step in glycolysis is that catalysed by:
Phosphofructokinase (step 3)
Folding of polypeptide chain into secondary structure is accompanied by….
Negative free energy change
What is the main driving force for protein folding?
Increase in entropy due to reorganization of associated water molecules
During aerobic respiration, pyruvate from the glycolysis pathway enters the mitochondrial matrix via…
Co-transport with protons through a translocase
