CHEM/BIOL 3520 Exam III Study Guide 2017

To help focus your studying, here is an outline of topics covered in lecture and/or the textbook that I
recommend you understand. This study guide should not be deemed as a guarantee for what will
or will not be covered on the exam.

Chapter 18 (Sections 18.1 and 18.3)

Know the three circumstances under which amino acid oxidation is initiated
Roles of stomach, pancrease and intestines in enzymatic hydrolysis of dietary proteins
Process of amino group removal in liver for amino acids broken down from dietary proteins
and ammonia release
- Mechanism for PLP mediated enzymatic transamination reactions
Formation of Enz-PLP complex (internal aldimine)
1st step: Deamination of amino acid to -keto acid; formation of PMP from
PLP
2nd step: Amination of -ketogluterate to Glu; formation of Enz-PLP inernal
aldimine from PMP
- Role and mechanism for L-Glu Dehydrogenase in liver mitochondria
- Definition of transdeamination
Mechanisms for PLP mediated racemization and decarboxylation reactions
Role of Gln Synthetase in ammonia transport
- Two step mechanism for Glu to Gln conversion
Role of Glutaminase in ammonia release within liver mitochondria
Role of Glucose-Ala cycle in ammonia transport
Know the 6 amino acid degradation products that the 20 amino acids are broken down into,
and which amino acids are associated with each degradation product
Know the names (full and abbreviated) and functions of the three cofactors involved in one-C
transfer reactions
Understand the activated methyl-cycle and the relationship between SAM and N5-
methyltetrahydrofolate
Be able to describe what makes the Phe and Trp degradation pathways of particular interest
- Know what causes PKU
Understand branched amino acid degradation

Chapter 22 (Sections 22.1, 22.2 and 22.4)

Nitrogen Cycle primary and secondary sources for reduced N
Importance, properties and mechanism of Gln Synthetase
Gln Synthetase Regulation
- Direct feedback regulation
- Regulation through covalent modification
General mechanism for NH3 transfer from Gln (Gln Amidotransferases)
- Mechanisms for NH3 release from Gln (Chamber 1)
- Mechansims for NH3 incorporation through either direct displacement or imine
formation (Chamber 2)
Know Three Major Pathways that Contribute C Sources for Amino Acid Biosynthesis
Mechanism for Glu Synthase (from -ketogluterate to Glu)
Mechanism for Pro Biosynthesis
Mechanism for Ser Biosynthesis
 - Know reverse of NADPH reduction reaction
Mechanism for Gly Biosynthesis
- PLP mediated conversion of Ser to Gly
- THF mediated sequestration of formaldehyde
Mechanism for Thr Biosynthesis
Know Various functions of Nucleotides in the Cell
De novo Purine Biosynthesis
- Mechanisms for all steps starting from PRPP to IMP (you do not need to memorize
all the enzyme names) you only need to know the detailed electron pushing
mechanisms for the steps that we went over in class OR for the steps where we saw
the mechanisms previously in 22a (for example, we did not go over a detailed
mechanism for SAICAR lyase, so I do not expect you to know this).
- Know difference for the carboxylation of AIR between prok. and higher order euk.
- Mechanisms for IMP conversion to AMP and GMP
- Three major feedback mechanisms for regulating purine biosynthesis
Pyrimidine Biosynthesis
- Mechanisms for all steps starting from Asp to UTP and CTP (you do not need to
memorize all the enzyme names) - you only need to know the detailed electron
pushing mechanisms for the steps that we went over in class, OR that I told you to
go over (e.g. the formation of carbamoyl phosphate) OR for the steps where we saw
the mechanisms previously in 22a.
- Feedback mechanisms for regulating pyrimidine biosynthesis
Know enzymatic processes for getting NTPs from NMPs
Structure, Properties and Mechanism for Ribonucleotide Reductase
Mechanism for dTMP formation from dUMP
- Know two pathways for cellular generation of dUMP
- Coupled pathway between THF oxidation and dUMP conversion to dTMP
- Mechanism for Thymidylate Synthase inhibition