BCHE 7210 – Biochemistry II
Spring 2018/Exam 1
Terms and concepts to know and understand:
Standard amino acids: three letter and one-letter codes
Universal structure of the amino acid
Properties of side chains
Ionization states of amino acids; Zwitterion
PK , pK , pK and pI
Chiral center
Optical rotation; Polarimeter
Enantiomer
Absolute configuration of amino acids
Fisher’s convention: L and D amino acids
CORN law
Peptide bond v. peptide unit (group)
Dipeptide, tripeptide, …polypeptide
Amino acid classification: Hyrophobic-aliphatic/hydrophobic-aromatic/neutral-polar side
chains/acidic/basic/conformationally important
Amino acid v. imino acid
Hydrogen-bonding
Hydrophobic interactions
Polar structure of the peptide bond
Resonance hybrid structure of the peptide bond
Torsion angle/rotation angle
Ramachandran diagram
Polarity of the peptide bond
Cis v. trans conformation of the peptide bond
Formation of the peptide bond
Primary/secondary/tertiary/quaternary structure
Helix: (p) the helical pitch, (n) the number of repeating units per turn, (d) a helical rise
per repeating unit
Chirality of helices
a-helix; Right-handed v. left-handed
b-pleated sheet
N-terminus and C-terminus of a polypeptide
Parallel v. anti-parallel b-pleated sheet
Disulfide bond
Reverse turns (Type I and II)
Coil conformation
Random coil
Keratin/structure
Fibroin/structure
Motifs: Helix-turn-helix; Hairpin b motif and b-a-b motif
Protein domain
Protein secondary structure: the prediction
1
2
R
Ampholytes
Polyampholytes
Polyelectrolytes
Enzymatic activity
Assays/characteristics
Fractionation steps
Unit of enzymatic activity
Total activity v. specific activity
Protein solubility and pH
Small ions and macroion interactions
Salting in/salting out
ELISA
Equilibrium density gradient centrifugation
Chromatography:ion exchange, gel filtration, affinity chromatography
SDS polyacrylamide gel electrophoresis (SDS-PAGE)
Molecular weight and SDS-PAGE
Roles of beta-mercaptoethanol and DTT in SDS-PAGE
Isoelectric focusing
Chemical modification v. processing
Acetylation of proteins
Fatty acid acylation
Modified amino acids
Roles of Protein Phosphorylation/Glycosylation/Methylation
Proteolytic cleavage (insulin/chymotrypsin)
Protein self-splicing/intein/extein
Ubiquitination (E1/E2/E3 system)/ biological importance
Isopeptide
Proteasome: structure and function
Edman degradation
Invariant amino acids
Variable amino acids
Conservative amino acid substitution
Proteins sequences and phylogenetic relationships
Purines and pyrimidines/ structure
bases: cytosine, uracil, guanine, adenine
enol and keto forms of nucleosides
syn and anti conformations of nucleotides
Watson-Crick base-pairing; complementarity
Chargraff’s rules
Phosphodiester bond
Pucker of deoxyribose ring
Base stacking
DNA structure: B-DNA, A-DNA and Z-DNA
DNA sequencing (chemical and enzymatic)
Next-generation sequencing
Transcription in prokaryotes and eukaryotes: similarities and differences
RNA polymerase – structure and function
Sense/antisense strands (template/coding strands)
Transcription regulation in eukaryotes: ON and OFF switch
Steps of transcription
Transcription termination in prokaryotes
Operon hypothesis
Lac operon
Promoter and operator
Constitutive expression
Inducers and repressors
IPTG
Trp operon and attenuation
Catabolite repression and cAMP
Organization of split eukaryotic genes
mRNA processing
Capping of eukaryotic pre-mRNAs and cap functions
mRNA degradation
splicing of mRNA precursors
spliceosome structure and functions
Alternative splicing, breast cancer and chemotherapy