1.1 Biomolecule basics Flashcards
Which stereochemical configuration is predominant in nature?
R stereochemistry / L configuration
Is glycine a chiral molecule?
No, achiral, two same side chains (H) at alpha C
What are the amino acid types?
- Hydrophobic
- Acids
- Amides
- Bases
- Aromatics
- Alcohols
- Thiol / tiolether
Selenocysteine (21st)
Explain peptide bond formation
What are Φ (phi) and Ψ (psi) bonds in a peptide? How are they different from the peptide bond?
Φ (phi) and Ψ (psi) bonds are free to rotate because they are stabilised by free e pair of N - π bond can be created
What strcutures are formed in secondary protein structure? Which atoms interact to form what bonds?
Repeated α-helices and β-sheets are formed by H-bonds between backbone atoms
How are α-helices formed?
- COOH is H-bond acceptor
- N is H-bond donor
- forms between n and n+4
Why is proline known as helix breaker?
Cyclic side chain of proline has no N to donate H-bond
How are β-sheets formed?
- COOH is H-bond acceptor
- N is H-bond donor
- forms between antiparallel β-pleats to form β-sheet (can form parallel - less stable)
How are tertiary protein structures formed?
By side chain interactions of DOMAINS:
- hydrophilic - hydrophobic
- H-bonds
- covalent (disulphide bridge)
- ionic inter.
- electrostatic inter.
How are quaternary protein structures formed?
By side chain interactions of SUBUNITS:
- hydrophilic - hydrophobic
- H-bonds
- covalent (disulphide bridge)
- ionic inter.
What are the structures of quarternary proteins? What are their characteristics?
- Globular
- Fibrous
- Molecular machines (ATP synthase)
What is the function of protein post-translational modifications (PTMs)?
PMTs are covalent processings that change the properties of a protein - makes them functional
What are heteroproteins?
Proteins which have non am. a. components (prosthetic groups) ex: nucleotides / redox active groups
Explain the structure of a nucleotide?
- Phosphate (at 5C)
- Nitrogenous base (at 1C)
- Ribose (2 OH) / deoxyribose (1 OH) sugar
What kind of nitrogenous bases are there?
PURINES: guanine and adenine [GrynAi]
PYRAMIDINES: cytosine, thymine, uracil
Why is RNA less stable than DNA?
RNA is susceptible to RNA hydrolysis because of extra OH group - RNA more functionally involved, so no need to persist - DNA for long term storage
How do nucleotides bond between each other?
How do complementary nucleotides bond?
Why do thermophilic bacteria have more C-G repeats than A-T?
Because C-G form 3 H-bonds while A-T 2 - more stable DNA
Which direction is DNA synthesised?
5’ -> 3’ end
Why is DNA acidic?
DNA is acidic because negative charge on phosphate can be protonated / deprotonated
What effect additionally stabilises DNA?
Intrastrand π stacking between aromatic ring π e stabilises DNA (Van der Waal’s interactions)
What forms of DNA are there?
- A DNA
- B DNA (most common)
- Z DNA
How are nucleotides added in DNA replication?
dNTPs are added (extra 2 phosphates) - pyrophosphate kicked out
Why are there more DNA / RNA codons than possible am. a.?
64 codons for 20 am. a. - several codons code for same proteins - to minimise mutation effects
Why do bacterial 50S and 30S ribosome subunits add up to 70S ribosome?
its total is not 80s because sedimentation rate (how quickly parts settle in a test tube after centrifugation) of a particular ribosome is not equal to the total of 50s and 30s subunits.
What are the ribosomal sites and their functions?
- Site A: tRNA with next am. a. bound
- Site P: tRNA with polypeptide chain bound
- Site E: am. a. empty tRNA exits
What is the mechanism of peptide bond formation in ribosomes?
What are the main types of lipids? What are their main characteristics?
- Fats / oils (saturated / unstaturated fatty acids)
- Phospholipids (polar - non-polar parts)
- Steroids (polycyclic molecules)
- Waxes (extremely hydrophobic)
Compare fats vs oils
FATS:
- solid at room T
- saturated - single bonds (sp3 C - rotation possible) - maximise Van der Waal’s - packing more efficient - higher melting point
OILS:
- liquid at room T
- unsaturated - double bonds (sp2 C - no rotation) - kinks - less efficient packing - lower melting point
Explain the structure of a triglyceride and its formation
Explain the structure of a phospholipid
