BIOC 212 Study Guide - Winter 2018, Comprehensive Midterm Notes - Protein, Phosphorylation, Root Mean Square
12 Oct 2018
School
Department
Course
Professor
BIOC 212
MIDTERM EXAM
STUDY GUIDE
Fall 2018
LECTURE 1 08/01/2018
Protein Folding in the Cell I
Professor Young
Course Details
- Midterm, February 21 worth 46% covering lectures 1-18
- Non-cumulative, worth 54% covering lectures 18-36
- Suggested Reading:
o Molecular Biology of the Cell, Alberts et al. 4th/5th/6th editions
o Molecular Cell Biology, Lodish et al. 5th edition
- Exam questions exclusively from lecture content
What is Biochemistry?
- Biochemistry is the study of the structure composition and chemical reactions of substances in
living systems
- Study of chemical processes relating to living organisms
- Concepts: information flow through biochemical signaling and energy flow through chemical
reactions, which combine to give us human biology
- How biological molecules give rise to the processes that occur within living cells (which make up
tissues, which make up organisms)
Foundational Concepts
- Evolution
- Matter and energy transformation (metabolism)
- Homeostasis (balance/dynamic constancy)
- Macromolecular structure and function (working parts of cell biology)
- Storage/transmission/transformation of biological information
The Cell
- Inside and outside of the cell are separated by a plasma membrane
- Various organelles with differing functions
- Cytosol is the interior of the cell which is packed mostly with proteins
Cellular Proteins
- Proteins are the main functional components in cells (how are they made, put together, transported)
- Central Dogma:
o Genes are encoded in DNA and transcribed into mRNA and both are linear
o Translated proteins are made as linear polypeptides by cytosolic ribosomes
o Proteins are folded into three dimensional confirmations to accomplish cell functions
- Folding provides physical stability (forming an interior and exterior with defined structure) and
functional surfaces
- The sequence of a protein determines its structure, function and localization
Amino Acids
- 20 different amino acids and you need to know the names, chemical structures, category and (three
and one letter) abbreviations will be examined not expected to draw them
- Side chains have different chemical characteristics:
o Hydrophobic, polar or charged (acidic or basic)
o Small or large
o Covalently linked into polypeptides
find more resources at oneclass.com
find more resources at oneclass.com
- These categories are too convenient and the amino acids are more nuance in function
Polypeptides
- Polypeptides are made up of amino acids
linked together in chains
- Each amino acid has a charged C terminus
and a charged N terminus
- However, peptide bonds in the backbone are
uncharged but polar (charges at the terminals
of chain)
- Charge and hydrophobicity of a polypeptide
is determined by the side chains
- Both side chains and back bone can form non-covalent contacts with other amino acids
Polypeptide Backbone
- The peptide bond is planar and cannot rotate
o The image shows a resonance structure between the
C=O double bond C–N and N–H single bonds →
giving a transient C=N double bond
o Thus, there is no rotation around the C–N bond
- Only rotation is around the bonds to the central, alpha
carbon (C) where the sidechains are attached
- Therefore, the polypeptide backbone has limited freedom
of rotation
- Some rotation angles between amino acids depending on the characteristics of the side chains
(residues in a polypeptide are preferred)
Non-Covalent Bonds
- Most of the bonds that support protein structure and function are non-covalent bonds
- Interactions between residues of a polypeptide stabilize protein structure
o Hydrophobic interactions – exclusion of water
o Hydrogen bonds – hydrogen shared between two partially polar atoms
o Ionic charged atoms – strong charge-charge interactions, for instance the salt bridge
o Van der Waals interactions – any atom can form due to transient dipoles carrying a partial
charge (weak interaction)
Disulfide Bond
- Secretory proteins often have covalent disulfide bonds
between cysteine side chains
o The terminal S can be oxidized in order to form the bond
o Extracellular proteins and inside secretory organelles
o Disulfide reinforce structure (important as some proteins
need to circulate in the blood for days and not degrade –
ex. antibodies)
- Cytosolic proteins normally do not have disulfide bonds as it
is a milder environment
o Rare in cytosol, nucleus, mitochondria
Units of Protein Structure
- Primary structure – amino acid sequence
- Secondary structure – local conformation patterns
find more resources at oneclass.com
find more resources at oneclass.com
