BIOC 212 Study Guide - Winter 2018, Comprehensive Midterm Notes - Protein, Adenosine Triphosphate, Cytosol
12 Oct 2018
School
Department
Course
Professor
BIOC 212
MIDTERM EXAM
STUDY GUIDE
Fall 2018
Protein Folding in the Cell
Biochemistry
• Study of structure, composition and chemical reactions of substances in living
systems
• Foundational concepts:
o Evolution
o Matter & Energy transformation
o Homeostasis
o Macromolecular structure & function
o Biological information
The Cell
• Plasma membrane & organelles
• Cytosol is the interior of the cell (gray); packed with proteins and other components
Cellular Proteins
• Proteins are the main functional components in cells
o Genes (DNA) and mRNA are linear --central dogma
• Proteins are made as linear polypeptides by cytosolic ribosomes, but fold into 3-
dimensional conformations
o Need to fold in order to accomplish function in the cell
o Not trivial process
• Folding provides physical stability and functional surfaces
o Have interior and exterior, with defined shape and surface
o Surface determines function, interaction with other molecules in the cell
o The sequence of a protein determines its:
• Structure
• Function
• Localization
Amino Acids
• 20 different amino acids
o Need to know names, abbreviations, and molecular structures
• Side chains have different chemical characteristics that contribute to function
o Hydrophobic (non-polar), polar, or charged (acidic or basic)
o Small or large
o Covalently linked into polypeptides
• Broken down into categories, but not perfect --simplification, convenient
o Much more nuance in what amino acids can do
• Basic = + charged
• Acidic = - charged
find more resources at oneclass.com
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• Lysine and arginine are both positively charged, but have different chemical groups
and thus different chemical reactive properties
• Aromatic chain behaves differently than straight chain
Polypeptides
• Peptide bonds in backbone are uncharged but polar
• Charge and hydrophobicity of a polypeptide is determined by the side chains
• Both side chains and backbone can form non-covalent contacts with other amino
acids
o Amino acids linked together into polypeptide chains
o Gives protein structure and interactions between proteins
• N (amino) and C (carboxyl) terminus
o In polypeptide, form peptide bond so not charged anymore except at the ends
• Peptide bonds between the amino acids; between C terminus of first amino acid
and N of second
o Most charge in polypeptide are thus coming from side chains
o Lose 2Hs from NH3 and O from COO-, release water and from C-N bond
Polypeptide Backbone
• Peptide bond is planar and cannot rotate
o Between O=C & N
• Rotation around the bonds of\ the central carbon (Cα) is possible
o Thus, the polypeptide backbone has limited freedom of rotation
o Some rotation angles between amino acids (residues) in a polypeptide are
preferred
• Depends on size and characteristics of side chains
o Resonance structure --Double bond C=O can flip so have transient double
bond between C and N (pink)
• But since transient, would not have rotation around C-N bond
o Only have rotation at the alpha carbon where side chains attach
Non-Covalent Bonds
• Most bonds that support protein structure are non-covalent
• Interactions between residues of a polypeptide stabilize structure
o Hydrophobic interactions (exclusion of water, carbon groups)
o Hydrogen bonds
• Very strong, H bonded to F, O or N
• Hydrogen shared between two partially polar atoms
o Van der Waals interactions (transient dipoles between all atoms)
• Transient dipoles can carry partial charge and interact weakly with
surrounding atoms
• For all molecules
find more resources at oneclass.com
find more resources at oneclass.com
