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[BIOCHEM 3G03] - Final Exam Guide - Ultimate 34 pages long Study Guide!
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Department
Biochemistry
Course Code
BIOCHEM 3G03
Professor
Daniel Yang

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McMaster
BIOCHEM 3G03
FINAL EXAM
STUDY GUIDE
Chapter 1: The Chemical Basis of Life
1.1 What is Biochemistry?
- Biochemistry: study of chemical processes and chemical transformations in living organisms
o Scientific discipline that seeks to explain life at the molecular level using tools and
terminology of chemistry
o Science of reductionism
o Focuses on structures and functions of molecules that make up structures, eventually
leading to the entire organism
- Bioinformatics is important in this field
1. What are living organisms made of? Structure of a molecule is intimately linked to function
2. How do organisms acquire and use energy?
3. How does an organism maintain its identity across generations?
1.2 Biological Molecules
- Only a small subset of known elements are
found in living systems
o Most abundant: C, N, O, and H; then
Ca, P, K, Cl, Na, and Mg
o Trace elements are also present in
small quantities
- Biological molecules are constructed from H, N, O, P, and S
- Chemical reactivity of biomolecules is limited, relative to the reactivity of all chemical
compounds
Cells contain 4 major types of biomolecules
1. Amino Acids
o Amino (-NH2) and carboxylic acid (-COOH) groups
o Ionized to NH3+ and COOH- under physiological conditions
o Common aa: alanine (H, methyl)
o Can also contain N, O, or S
2. Carbohydrates
o Simple carbohydrates (CH2O)n where n >= 3
o Ring structure and multiple OH groups
o OH groups can be replaced by other groups
3. Nucleotides
o 5C sugar + nitrogen containing ring + 1 or more phosphate groups
Ex. ATP
o Nitrogenous groups: adenine, cytosine, guanine, thymine or uracil
4. Lipids
o No single structural similarity, diverse collection of molecules
o All poorly soluble in water bulky structure
- Cells also have few other small molecules that do not fit into the 4 groups, or are constructed
from molecules belonging to more than one group
find more resources at oneclass.com
find more resources at oneclass.com
- Few kinds of building blocks can be combined in different ways to produce a wide variety of
larger structures
o Cells can get by with a limited array of raw materials
o Also a way to encode information in a stable form
o Monomers = residues after they have been incorporated into a polymer
o Lipids do not form polymers but they do aggregate to form larger structures
Three major kinds of biological polymers
1. Proteins (polypeptides): polymer of amino acids
o 20 different aa serve as building blocks
o Linked together by peptide bonds
o Conformation (3D shape) of the protein depends on its aa composition and sequence
o Aa can be combined in almost any order, all polypeptides have unique 3D shapes
2. Nucleic Acids (polynucleotides): polymer of nucleotides
o Phosphate and sugar groups link together through phosphodiester bonds
o Tend to have a more regular structure than proteins
o Information encoded into sequence, not 3D shape
o However, some still fold into unique shapes
3. Polysaccharides
o Tend to contain only one or a few different types of monosaccharides
Most homogenous polymers limited potential for carrying genetic info.
Also limits variety of shapes for mediating chemical reactions
o Function as fuel-storage, and providing structural support
o Linked by glycosidic bonds
- Exceptions to these generalizations
o Small polysaccharides: encode information to allow cells to recognize each other
o Nucleic acids: can perform structural roles (scaffolding in ribosomes)
o Proteins: fuel-storage molecules, in some situations
1.3 Energy and Metabolism
- First law of thermodynamics: energy cannot be created or destroyed (can be transformed)
Enthalpy and Entropy are Components of Free Energy
- Gibbs free energy or just free energy (G), units: J mol-1
o Two components: Enthalpy (H; J mol-1) is the heat of the system, and entropy (S; J K-1
mol-1) is a measure of how the energy is dispersed within the system (disorder/random)
o More ways a system can be arranged = more disordered
find more resources at oneclass.com
find more resources at oneclass.com

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McMaster BIOCHEM 3G03 FINAL EXAM STUDY GUIDE find more resources at oneclass.com Chapter 1: The Chemical Basis of Life 1.1 What is Biochemistry? Biochemistry: study of chemical processes and chemical transformations in living organisms o Scientific discipline that seeks to explain life at the molecular level using tools and terminology of chemistry o Science of reductionism o Focuses on structures and functions of molecules that make up structures, eventually leading to the entire organism Bioinformatics is important in this field 1. What are living organisms made of? Structure of a molecule is intimately linked to function 2. How do organisms acquire and use energy? 3. How does an organism maintain its identity across generations? 1.2 Biological Molecules Only a small subset of known elements are found in living systems o Most abundant: C, N, O, and H; then Ca, P, K, Cl, Na, and Mg o Trace elements are also present in small quantities Biological molecules are constructed from H, N, O, P, and S Chemical reactivity of biomolecules is limited, relative to the reactivity of all chemical compounds Cells contain 4 major types of biomolecules 1. Amino Acids o Amino (NH 2 and carboxylic acid (COOH) groups o Ionized to NH3and COOH under physiological conditions o Common aa: alanine (H, methyl) o Can also contain N, O, or S 2. Carbohydrates o Simple carbohydrates (CH O) where n >= 3 2 n o Ring structure and multiple OH groups o OH groups can be replaced by other groups 3. Nucleotides o 5C sugar + nitrogen containing ring + 1 or more phosphate groups Ex. ATP o Nitrogenous groups: adenine, cytosine, guanine, thymine or uracil 4. Lipids o No single structural similarity, diverse collection of molecules o All poorly soluble in water bulky structure Cells also have few other small molecules that do not fit into the 4 groups, or are constructed from molecules belonging to more than one group find more resources at oneclass.com
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