Proteins Flashcards
(41 cards)
What are the stages of protein transcription?
RNA polymerase binds to promoter (start sequence) and Helicase unwinds DNA
Free RNA nucleotides pair up to the complementary bases on the exposed DNA strand (Thymine is replaced by Uracil)
RNA polymerase joins the nucleotides with phosphodiester bonds until the terminator (stop sequence) forming a mRNA strand
The DNA rewinds and mRNA leaves through a nuclear pore
What are the stages of protein translation and modification?
Ribosome moves along mRNA attaching tRNA molecules (3 bases/amino acids/anti-codons) (uracil is replaced by thymine)
The amino acids are linked into a peptide chain which is released into the cis-ER and packaged into a vesicle
The vesicle is sent out of the trans-ER to the Golgi where it is modified and sorted
How do Antibiotics work?
Inhibiting prokaryotic ribosomes
Preventing the formation of a cell wall
What is the general structure of an amino acid?
What is the structure of a zwitterion of an amino acid?
What is a peptide bond?
H2N - (H)C(R) - COOH
(H3N+) - (H)C(R) - COO-
a.a.1 - C(O) - N(H) - a.a.2
What type of bonds are involved and what determines the primary structure of proteins?
Covalent peptide bonds forms the linear polymer of amino acids
Determined by the sequence of nucleotides in a gene
What are the features of the primary structure of proteins?
Always:
Planar (all molecules lie in the same line)
Rigid (C-N is a partial double bond with no rotation)
Trans (R-groups can have steric clashes with cis-kinks)
What type of bonds are involved and what determines the secondary structure of proteins?
H-bonds bonds form the local spatial arrangement of polypeptide chains
Determined by the sequence of amino acids
What are the types of secondary structures of proteins possible?
Alpha-helices: Always right-handed with H-bonds between C=O and N-H 4 amino acids away
Beta-strands: Polypeptide chain with R-groups on alternate sides
Beta-sheets: H-bonds form between beta-strands (antiparallel, parallel, mixed)
What type of bonds are involved and what determines the tertiary structure of proteins?
All types of bonds/attractions form the overall 3D shape of the polypeptide
Determined by the chemical and physical properties of amino acids
What are the types of tertiary structures of proteins possible?
Fibrous:
Long strands/sheets of a single repeating secondary structure
Support, Shape, Protect
Globular:
Compact shape made of several different secondary structures
Catalysis, Regulation
What type of bonds are involved and what determines the quarternary structure of proteins?
All types of bonds/attractions form the overall multi-subunit protein
Determined by the interactions of the polypeptide chains
What are phi and psi bonds and what structure do they influence?
Influence secondary structure (able to rotate)
Phi bond: bond between (H2)N - C
Psi bond: bond between C - C(OOH)
What are disulphide bonds and what structure do they influence?
Influence the tertiary structure (interactions of amino acids)
Bonds between 2 SH (cysteine) R-groups
The R-groups are oxidised to form S-S (cystine) bond
(Found on secreted proteins as the S-S bond is unstable in the cytoplasm, can also be destroyed by reducing agents)
What is the hydrophobic effect and what structure does it influence?
Influences tertiary structure (inner hydrophobic amino acids)
Not a bond
Attraction between non-polar (hydrophobic) molecules when they are forced together by excluding H2O
How are proteins folded?
The information on the folding of a protein is contained within the primary sequence of a protein
Localised folding with maintained stable conformations allow the protein to ‘find’ its structure
How are proteins denatured?
Heat
pH
Organic solvents
What is the isoelectric point?
pH at which the amino acid has no charge (forms the zwitterion)
What happens to an amino acid when:
pKa < pH
pKa > pH
pKa < pH: deprotonated
pKa > pH: protonated
What are isoenzymes?
What are co-enzymes?
Isoenzymes: different form of the same enzyme (same function) formed from different splicing of the same gene resulting in different kinetic properties
Coenzymes: non-protein molecules that bind to the enzyme to activate it
Describe what product inhibition is
Accumulation of the product inhibits the forward reaction
Describe what the T and R states of an enzyme are and explain the action of inhibitors and activators
T-state: low affinity for substrate
R-state: high affinity for substrate
Inhibitors: Increase the proportion of T-state enzymes
Activators: Increase the proportion of R-state enzymes
Describe the action of Kinase and Phosphatase
Kinase: Transfers the phosphate group from ATP onto the hydroxy group of Serine, Threonine, Tyrosine
Phosphatase: Removes the phosphate group from the hydroxy group of Serine, Threonine, Tyrosine by hydrolysis
Describe what phosphorylation (Kinase) does to proteins and how it can be controlled
Adds a negative charge (can form H-bonds)
Increase the amount ATP, Increase the rate of phosphorylation that can occur
Explain how Chymotrypsinogen is activated in the pancreas
Enteropeptidase is released by the pancreas
Enteropeptidase cleaves trypsinogen —> trypsin
Trypsin cleaves chymotrypsinogen —> pi-chymotrypsin
Chymotrypsin cleaves pi-chymotrypsin —> alpha-chymotrypsin
