The Dawn of Proteins Flashcards
Why are proteins considered better catalysts than ribozymes?
- Smaller subunits, amino acids, rather than nucleotides
- Have hydrophobic properties unlike RNA
- Enable more diverse chemistry
What is a limitation of proteins compared to RNA?
Proteins can’t self-replicate as residues don’t pair up to act as templates.
For example: Non-ribosomal peptide synthetase and polyketide synthases can make short cyclic peptides, but they can’t replicate.
Properties of Zwitter ions
Formed by amino acids in water
Have +ve and -ve charge
Act as buffers
What are alpha amino acids? How do they differ from Beta and Gamma amino acids?
Amino acids that are incorporated into proteins
Differ from Beta and gamma amino acids can be synthesized but are not used in proteins.
Which enantiomer of amino acids is found in proteins?
Only the L-enantiomer exists in proteins
Most amino acids have chiral centres at the alpha carbon, except for glycine.
What are the two small amino acids? State their name, the single letter code, and any notable characteristics.
Glycine (G), is flexible
Proline, (P), inflexible due to bulky side chain, it bends the peptide chain
What defines non-polar/hydrophobic amino acids?
They have no O in their side chains, making them non-polar and unable to interact with water
Can be aromatic of aliphatic
Prebiotic hydrophobic amino acids.
Alanine (A)
Valine (V)
Leucine (L)
All are aliphatic
Hydrophobic amino acids with notable features
Methionine (M) has a s-methyl group
Isoleucine (I) has two chiral centres
Polar amino acid characteristics and notable examples.
Form polar bonds, so all are on the surface of the protein where H bonds affect structure
Threonine (T), prebiotic and has an extra chiral centre
Cysteine (C), thiol group
Serine (S), prebiotic
What characteristic of cysteine makes it good at its role in proteins?
Cysteine (C) has an SH thiol group that can form disulfide bonds between other C residues
This characteristic is significant for protein structure stability.
How do charged amino acids enable interactions between residues?
They can form salt bridges between oppositely charged residues
Basic amino acids accept protons, while acidic ones donate protons.
Most of these are charged only inside of cells due to pKa (except Histidine (H)) and at neutral pH
It is believed proteins were initially formed with less than 10 amino acids. State and describe these prebiotic amino acids.
- Alanine (A), aliphatic hydrophobic aa, r group is a methyl
- Aspartate (D), acidic, negatively charged aa, with a carboxyl group on its r group
- Glutamate (E), acidic, negatively charged aa, with a CH2 and carboxyl group on its r group
- Glycine (G), simple aa, H for r group
Isoleucine (I), hydrophobic with 2 chiral centres
Leucine (L), aliphatic hydrophobic aa,
Proline (P), simple aa, bulky side chain
Serine (S), polar aa, hydroxyl on side chain
Threonine (T), polar aa, hydroxyl on side chain and additional chiral centre
Valine (V), aliphatic hydrophobic aa, branched end to r group
How is a peptide bond formed? And why are partial double bonds created?
Through a condensation reaction between carboxyl and amino groups
Peptide bonds are partial double bonds, as O in the peptide is more electronegative, attracting e- from the adjacent carbon and forming a C=N bond instead leading to inflexibility.
What differentiates primary and secondary protein structures?
Primary structure is a straight polypeptide chain; secondary involves backbone interactions forming H bonds
Examples of secondary structures include alpha helices and beta pleated sheets.
What occurs during protein denaturation?
Proteins unfold due to temperature, pH, salts, or non-polar solvents
Chaperone proteins assist in refolding proteins to their lowest energy state.
What characterizes quaternary protein structures?
They contain more than one amino acid chain, like hemoglobin
Quaternary structures are important for the function of many proteins.
What is induced fit in the context of protein binding?
The conformational change in an enzyme’s active site upon substrate binding
An example is fructose binding to rhamnulose kinase.
What does allosteric regulation involve?
The binding of a molecule at a site other than the active site
An example is the binding of O2 to hemoglobin.
What is the central dogma of molecular biology?
The transfer of sequential information from DNA to RNA to proteins
This concept emphasizes that information cannot be transferred back from proteins to nucleic acids.
What does self-assembly refer to in biological systems?
The physical association of molecules into an equilibrium structure
Properties at a larger scale are determined by those of the subunits.
What is dynamic self-organization?
Non-equilibrium systems that dissipate energy to achieve a steady-state
This occurs across all scales in biology and involves spontaneous emergence of order.
What is the role of energy in measuring fitness according to Valen?
Absolute fitness could be defined as control of trophic energy level
This approach can apply to ecosystems and dynamic energy budget models.
What is the function of DNA microarrays?
To analyze gene expression patterns
Predicted genes are labeled with probes indicating upregulation or downregulation.
