1
Section 1: Biological and Biochemical Foundations of Living Systems
1A.
Amino Acids (BC, OC)
● Description
o Absolute configuration at the α position
o Amino acids as dipolar ions
o Classifications
▪ Acidic or basic
▪ Hydrophobic or hydrophilic
● Reactions
o Sulfur linkage for cysteine and cysteine
o Peptide linkage: polypeptides and proteins
o Hydrolysis
Protein Structure (BIO, BC, OC)
● Structure
o 1° structure of proteins
o 2° structure of proteins
o 3° structure of proteins; role of proline, cystine, hydrophobic bonding
o 4° structure of proteins (BIO,BC)
● Conformational stability
o Denaturing and folding
o Hydrophobic interactions
o Solvation layer (entropy) (BC)
● Separation techniques
o Isoelectric point
o Electrophoresis
Non-Enzymatic Protein Function (BIO, BC)
● Binding (BC)
● Immune system
● Motors
, 2
Enzyme Structure and Function (BIO, BC)
● Function of enzymes in catalyzing biological reactions
● Enzyme classification by reaction type
● Reduction of activation energy
● Substrates and enzyme specificity
● Active Site Model
● Induced-fit Model
● Mechanism of catalysis
o Cofactors
o Coenzymes
o Water-soluble vitamins
● Effects of local conditions on enzyme activity
Control of Enzyme Activity (BIO, BC)
● Kinetics
o General (catalysis)
o Michaelis–Menten
o Cooperativity
● Feedback regulation
● Inhibition–types
o Competitive
o Non-competitive
o Mixed(BC)
o Uncompetitive(BC)
● Regulatory enzymes
o Allosteric enzymes
o Covalently-modified enzymes
o Zymogen
, 3
1B.
Nucleic Acid Structure and Function (BIO, BC)
● Description
● Nucleotides and nucleosides
o Sugar phosphate backbone
o Pyrimidine, purine residues
● Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure
● Base pairing specificity: A with T, G with C
● Function in transmission of genetic information (BIO)
● DNA denaturation, reannealing, hybridization
DNA Replication (BIO)
● Mechanism of replication: separation of strands, specific coupling of free nucleic acids
● Semi-conservative nature of replication
● Specific enzymes involved in replication
● Origins of replication, multiple origins in eukaryotes
● Replicating the ends of DNA molecules
Repair of DNA (BIO)
● Repair during replication
● Repair of mutations
Genetic Code (BIO)
● Central Dogma: DNA → RNA → protein
● The triplet code
● Codon–anticodon relationship
● Degenerate code, wobble pairing
● Missense, nonsense codons
● Initiation, termination codons
● Messenger RNA (mRNA)
Transcription (BIO)
● Transfer RNA (tRNA); ribosomal RNA (rRNA)
● Mechanism of transcription
● mRNA processing in eukaryotes, introns, exons
● Ribozymes, spliceosomes, small nuclear ribonucleoproteins (snRNPs), small nuclear RNAs (snRNAs)
● Functional and evolutionary importance of introns
, 4
Translation (BIO)
● Roles of mRNA, tRNA, rRNA
● Role and structure of ribosomes
● Initiation, termination co-factors
● Post-translational modification of proteins
Eukaryotic Chromosome Organization (BIO)
● Chromosomal proteins
● Single copy vs. repetitive DNA
● Supercoiling
● Heterochromatin vs. euchromatin
● Telomeres, centromeres
Control of Gene Expression in Prokaryotes (BIO)
● Operon Concept, Jacob–Monod Model
● Gene repression in bacteria
● Positive control in bacteria
Control of Gene Expression in Eukaryotes (BIO)
● Transcriptional regulation
● DNA binding proteins, transcription factors
● Gene amplification and duplication
● Post-transcriptional control, basic concept of splicing (introns, exons)
● Cancer as a failure of normal cellular controls, oncogenes, tumor suppressor genes
● Regulation of chromatin structure
● DNA methylation
● Role of non-coding RNAs
Section 1: Biological and Biochemical Foundations of Living Systems
1A.
Amino Acids (BC, OC)
● Description
o Absolute configuration at the α position
o Amino acids as dipolar ions
o Classifications
▪ Acidic or basic
▪ Hydrophobic or hydrophilic
● Reactions
o Sulfur linkage for cysteine and cysteine
o Peptide linkage: polypeptides and proteins
o Hydrolysis
Protein Structure (BIO, BC, OC)
● Structure
o 1° structure of proteins
o 2° structure of proteins
o 3° structure of proteins; role of proline, cystine, hydrophobic bonding
o 4° structure of proteins (BIO,BC)
● Conformational stability
o Denaturing and folding
o Hydrophobic interactions
o Solvation layer (entropy) (BC)
● Separation techniques
o Isoelectric point
o Electrophoresis
Non-Enzymatic Protein Function (BIO, BC)
● Binding (BC)
● Immune system
● Motors
, 2
Enzyme Structure and Function (BIO, BC)
● Function of enzymes in catalyzing biological reactions
● Enzyme classification by reaction type
● Reduction of activation energy
● Substrates and enzyme specificity
● Active Site Model
● Induced-fit Model
● Mechanism of catalysis
o Cofactors
o Coenzymes
o Water-soluble vitamins
● Effects of local conditions on enzyme activity
Control of Enzyme Activity (BIO, BC)
● Kinetics
o General (catalysis)
o Michaelis–Menten
o Cooperativity
● Feedback regulation
● Inhibition–types
o Competitive
o Non-competitive
o Mixed(BC)
o Uncompetitive(BC)
● Regulatory enzymes
o Allosteric enzymes
o Covalently-modified enzymes
o Zymogen
, 3
1B.
Nucleic Acid Structure and Function (BIO, BC)
● Description
● Nucleotides and nucleosides
o Sugar phosphate backbone
o Pyrimidine, purine residues
● Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure
● Base pairing specificity: A with T, G with C
● Function in transmission of genetic information (BIO)
● DNA denaturation, reannealing, hybridization
DNA Replication (BIO)
● Mechanism of replication: separation of strands, specific coupling of free nucleic acids
● Semi-conservative nature of replication
● Specific enzymes involved in replication
● Origins of replication, multiple origins in eukaryotes
● Replicating the ends of DNA molecules
Repair of DNA (BIO)
● Repair during replication
● Repair of mutations
Genetic Code (BIO)
● Central Dogma: DNA → RNA → protein
● The triplet code
● Codon–anticodon relationship
● Degenerate code, wobble pairing
● Missense, nonsense codons
● Initiation, termination codons
● Messenger RNA (mRNA)
Transcription (BIO)
● Transfer RNA (tRNA); ribosomal RNA (rRNA)
● Mechanism of transcription
● mRNA processing in eukaryotes, introns, exons
● Ribozymes, spliceosomes, small nuclear ribonucleoproteins (snRNPs), small nuclear RNAs (snRNAs)
● Functional and evolutionary importance of introns
, 4
Translation (BIO)
● Roles of mRNA, tRNA, rRNA
● Role and structure of ribosomes
● Initiation, termination co-factors
● Post-translational modification of proteins
Eukaryotic Chromosome Organization (BIO)
● Chromosomal proteins
● Single copy vs. repetitive DNA
● Supercoiling
● Heterochromatin vs. euchromatin
● Telomeres, centromeres
Control of Gene Expression in Prokaryotes (BIO)
● Operon Concept, Jacob–Monod Model
● Gene repression in bacteria
● Positive control in bacteria
Control of Gene Expression in Eukaryotes (BIO)
● Transcriptional regulation
● DNA binding proteins, transcription factors
● Gene amplification and duplication
● Post-transcriptional control, basic concept of splicing (introns, exons)
● Cancer as a failure of normal cellular controls, oncogenes, tumor suppressor genes
● Regulation of chromatin structure
● DNA methylation
● Role of non-coding RNAs
