BS1005 / CM1051: Biochemistry I
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Course Syllabus
Contacts
FAQs
1
Chemical Basis of Biochemistry
1.1
Biochemistry as a Chemical Science
1.2
Biochemistry as a Biological Science
1.2.1
Types of polymers
1.2.2
Lipids
1.2.3
Water in Biology
1.3
Informational Biochemistry
1.4
Intermolecular Interactions
1.4.1
Hydrophobic interactions
1.4.2
Ionic interactions
1.4.3
Dipole-dipole movements
1.4.4
Induced dipoles and van der Waals interactions
1.5
Energetics of Life
1.5.1
Gibbs’ free energy
1.5.2
Free energy in Biological systems
2
Amino Acids and Peptides
2.1
Structures and Properties of Amino Acids
2.1.1
Structure of amino acids
2.1.2
20 common amino acids and their pK
a
values
2.1.3
Modifications of amino acids
2.2
Amino Acid Stereochemistry
2.3
Acid-Base Properties of Amino Acids
2.3.1
Isoelectric point
2.4
Spectroscopic Properties of Amino Acids
2.5
Amino Acids as Building Blocks
2.5.1
Peptide bonds
2.6
Analysis of Amino Acids in Proteins
3
Protein Structure
3.1
Determining the Primary Structures of Proteins
3.1.1
Enzymatic cleavage
3.1.2
Short peptide sequencing
3.1.3
Mass spectrometry
3.2
Secondary Structures
3.2.1
Ways of folding the polypeptide chain
3.2.2
Types of secondary structures
3.2.3
Steric constraints on
\(\phi\)
and
\(\psi\)
3.2.4
Circular dichroism spectroscopy
3.3
Fibrous Proteins
3.3.1
\(\alpha\)
-keratin
3.3.2
Collagen
3.3.3
Fibroin and
\(\beta\)
-keratin
3.4
Globular Proteins
4
Protein Folding
4.1
Determining the 3D Structure of Proteins
4.1.1
X-ray crystallography
4.1.2
Nuclear magnetic resonance spectroscopy
4.1.3
CATH system
4.2
Functional Domains and Symmetry
4.2.1
Symmetry
4.3
Folding of Polypeptides to Globular Structures
4.3.1
Critical concepts in protein folding
4.4
Protein Denaturation
4.5
Mechanisms of Protein Folding
4.5.1
Generalizations
4.5.2
Protein misfolding
5
Protein Functions
5.1
Protein-Protein Interactions
5.2
Myoglobin and Hemoglobin
5.2.1
O
2
binding in the globins
5.2.2
O
2
storage and transport problem
5.2.3
T / R state transitions
5.2.4
2,3-Biphosphoglycerate (i.e., BPG)
5.3
Bohr Effect
5.3.1
Stabilization of the T state
5.3.2
CO
2
transport by hemoglobin
5.4
Fetal Hemoglobin
5.5
Sickle Cell Anemia
6
DNA I
6.1
Components of Nucleotides
6.1.1
Chemical Properties of Nucleotides
6.1.2
Stability and Formation of the Phosphodiester Linkage
6.2
Primary Structure of Nucleic Acids
6.2.1
DNA as a genetic substance
6.3
Secondary and Tertiary Structure of DNA
6.3.1
Chargaff’s rule
6.3.2
Base pairing
6.3.3
Base pair stacking
6.3.4
Base pair rotation
6.3.5
Base pair distance
6.3.6
Major and minor grooves of DNA
6.4
Double Helix Structure of DNA
6.4.1
Semi-conservative nature of DNA replication
6.5
A and B Forms of DNA
6.5.1
Structural differences between A form and B form DNA
6.5.2
Miscellaneous information to note
7
DNA II
7.1
Modifications of DNA
7.1.1
Non-enzymatic modifications
7.1.2
Enzymatic Modifications of DNA
7.2
Alternative Secondary Structures of DNA
7.2.1
Left-handed (i.e., “Z”) DNA
7.2.2
Hairpins
7.2.3
Triple helices and Hoogsteen pairs
7.2.4
Quadruplex DNA
7.2.5
Circular DNA and supercoiling
7.3
Stability of Secondary and Tertiary DNA Sttructures
7.3.1
Disassociation and Reassociation of double-stranded DNA
7.3.2
Denaturation
7.3.3
Melting and melting temperature of DNA
7.3.4
Hyperchromic effect
7.4
Polymerase Chain Reaction
7.4.1
Human genome project
8
RNA I
8.1
Primary Structure of RNA
8.1.1
Poly(A) tail of mRNA
8.2
Secondary Structures of RNA
8.2.1
A-form double helix
8.2.2
Bulges
8.2.3
Internal loops
8.3
More Complex RNA Secondary Structures
8.3.1
Psuedoknots
8.3.2
Kissing hairpins
8.3.3
Hairpin loop bulge contact
8.4
tRNA Structure
8.4.1
Primary structure of tRNAs
8.4.2
Common secondary structural features of tRNA
8.4.3
Tertiary structures of tRNAs
8.5
Biological Functions of RNA
8.5.1
RNA viruses
8.5.2
Protein synthesis
8.5.3
Ribozymes
8.5.4
RNA splicing (group I intron mechanism)
8.5.5
Ribonuclease P
8.5.6
Hammerhead ribozymes
8.5.7
Small non-coding RNAs
9
Carbohydrates
9.1
Basics of Carbohydrates and their Stereochemistry
9.1.1
Cyclic structures in solution
9.1.2
Anomeric forms of monosaccharides
9.1.3
Pyranose and furanoses
9.1.4
Oxidation and reduction reactions
9.1.5
Monosaccharides as reducing agents
9.1.6
Monosaccharide derivatives
9.2
Chiral and Achiral Molecules
9.2.1
Chiral centers of glucose
9.2.2
Aldose and ketose stereoisomers
9.2.3
Epimers
9.2.4
In summary…
9.3
Disaccharides
9.3.1
Lactose intolerance
9.4
Polysaccharides
9.4.1
Amylose and amylopectin
9.4.2
Plant starch and animal glycogen
9.4.3
Cellulose
9.4.4
Chitin
9.4.5
Bacterial cell wall
9.4.6
Glycoconjugates
9.4.7
Glycosaminoglycans
9.4.8
Proteoglycans
9.4.9
Glycoproteins
9.4.10
Glycolipids and lipopolysaccharides
10
Lipids I
10.1
Characteristics of Fatty Acids
10.1.1
Saturated and unsaturated fatty acids
10.1.2
Naming conventions of fatty acids
10.1.3
Omega fatty acids
10.2
Triacylglycerols
10.2.1
Insulation and energy from triacylglycerols
10.2.2
Brown and whtie adipose tissue
10.3
Fatty Acid Rancidity
10.3.1
Types of rancidity
10.3.2
Hydrolysis
10.3.3
In summary…
10.4
Waxes and Other Complex Lipids
10.4.1
Glycerophospholipids
10.4.2
Sphingolipids and glycosphingolipids
10.4.3
Glycoglycerolipids
10.4.4
Sterols and steroids
11
Lipids II
11.1
The Cell Membrane
11.1.1
History of the cell membrane
11.1.2
Lipid asymmetry
11.1.3
Components of cell membranes
11.1.4
Interior protein networks
11.2
Membrane Dynamics
11.2.1
Flippases and floppases
11.2.2
Functions of membrane proteins
11.3
Passive and Active Transport
11.3.1
Passive transport
11.3.2
Active transport
11.4
Bulk Transport
11.4.1
Exocytosis
12
Vitamins
12.1
Basics of Vitamins
12.1.1
Cofactors
12.2
Vitamins as Electron Carriers
12.2.1
Vitamin C
12.2.2
Vitamin B
3
(niacin)
12.2.3
Vitamin B
2
12.3
Other Water Soluble Vitamins
12.3.1
Vitamin B
6
12.3.2
Vitamin B
12
12.3.3
Vitamin H
12.3.4
Vitamin B
9
12.3.5
Vitamin B
1
12.3.6
Vitamin B
5
12.3.7
Other metabolic pathways involving vitamin Bs
12.4
Fat-Soluble Vitamins
12.4.1
Vitamin A
12.4.2
Vitamin D
12.4.3
Vitamin E
12.4.4
Vitamin K
Bonus for BS1005 Students
A
The Dry Lab
A.1
DISCLAIMER
A.2
FAQs About the Lab
A.3
Introduction
A.4
Lab #1: .pdb Files
A.4.1
Task #1: examining a .pdb file
A.4.2
Task #2: editing a .pdb file
A.4.3
Task #3: creating a .pdb file
A.5
Lab #2: PyMOL Visualizations
A.5.1
Task #1: identifying secondary structures using PyMOL
A.5.2
Task #2: visualizing neuraminidase
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BS1005 / CM1051: Biochemistry I
1.3
Informational Biochemistry
Information biochemistry
includes molecular genetics and describes the…
molecular processes in heredity.
expression of genetic information.
processes that communicate molecular signals to regulate cellular activity.