BCEM 393 Study Guide - Summer 2018, Comprehensive Midterm Notes - Carboxylic Acid, Protein, Covalent Bond
12 Oct 2018
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BCEM 393
MIDTERM EXAM
STUDY GUIDE
Fall 2018
Introduction to Biochemistry and Buffers
UNIFYING THEMES IN BIOCHEMISTRY
- Millions of biological macromolecules (often polymers) of four types (proteins, lipids,
carbohydrates, and nucleic acids) are each formed from only a few monomers
- Amides link together to make proteins
- Each type of polymer usually has one particular type of linkage (proteins — amides, lipids
— ester, carbohydrates — glycosidic, nucleic acids — phosphodiester)
- The properties of the monomers change in some unique ways when they are linked
together to form a macromolecule
- Biopolymers fold up in 3 dimensions to form their active structures
- The order of the monomers in a polymer is important for native folding and properties
- Noncovalent interactions (hydrogen bonds, hydrophobic interactions, Van der Waals
interactions, ionic interactions) are very important in holding together the native folded
structures of biomolecules and in the binding to other molecules
- Native folding is important for function
- Non covalent interactions present between monomers
- In biochemistry, the default solvent is water
- Living cells use many accessory molecules in addition to the 4 types of macromolecules
- Organic and inorganic
- Examples: electron carriers, high energy molecules, signalling molecules, inorganic ions
(H, O, K, Na, P, S, N, Cu, NI, Zn, Fe)
- The central dogma describes biological information transfer: DNA —> RNA —> protein
- DNA —> RNA is done through the process of transcription
- RNA —> protein is done through the process of translation
- Eukaryotic cells are compartmentalized
- Membranes define the cell and the compartments
- Membranes are a fluid mosaic of lipids/glycolipids and proteins/glycoproteins
- Membrane proteins function in transport, energy processing, and recognition
- Question: List 3 more things you know about the structure of biological membranes
- Hydrophobic interior, hydrophilic exterior
- Fatty acid conformations
- Compromised of integral membrane proteins
- Fluid mosaic membrane
- Enzymes are required for (almost) every reaction which occurs in a living organism
- Every reaction goes downhill in free energy (delta G°)
- Enzymes decrease the activation energy of reactions
- The metabolic pathways found in different organisms are similar
- All use ATP for energy storage and transfer
- Homologous enzymes with similar mechanisms
- Metabolic pathways and intermediates (eg. pyruvate) are the same (or similar)
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- Similar phosphorylation reactions
- Similar redox reactions
NONCOVALENT INTERACTIONS
- Hydrogen Bonds (4 - 40 kJ/mol) partial charges on H-bond donor and H-bond acceptor and a
small amount of covalent character
- H-bond acceptor is an atom with lone pairs
- H-bond donor is a hydrogen atom on an electronegative atom. For example, —OH or —NH
- The lone pair on the N of an amide in not and H-bond acceptor because H is partially
positive
- Example: H-bonds are found between groups in the side chains and/or backbone parts of
proteins
- Hydrophobic interactions (2 - 10 kJ/mol) from favourable entropy of releasing water from non
polar surfaces
- Hydropathy measures water character, and it includes the ideas of degree of
hydrophobicity and hydrophilicity
- Hydropathy scales are positive for hydrophobic molecules and negative for hydrophilic
molecules
- Electrostatic interactions (5 - 200 kJ/mol) from attraction between charges (aka, salt bridge,
ionic interaction, ionic bond)
- Charges depend on the pKa and the pH
- Interactions are much weaker than ionic bonds because of water and ion exchange
- Question: Where are the ionic interactions in lipid bilayers? In the head group region,
because some lipids have charges thus, there is a possibility of having ionic interactions
there
- Van der Waals’ Interactions (2 - 4 kJ/mol) from permanent dipoles and/or induced dipoles on
any molecules
- Three types of Van der Waals Interactions
- Dipole-Dipole
- Dipole-Induced dipole: a permanent dipole induces a weaker dipole in the opposite
direction (temporarily) to form a favourable Van der Waals interaction
- Induced dipole-induced dipole
- Even for two non-polar surfaces next to each other
WATER FORMS HYDROGEN BONDS
- Water has polar covalent bonds because the sharing of electrons is unequal. As a result,
water molecules are polar and form hydrogen bonds which cause water molecules to stick
together
- Water has a partial positive on the hydrogen atoms
- Water has a partial negative charge on the oxygen atom
- Hydrogen bonds are not chemical bonds. They should be called hydrogen interactions, but
normally are called H-bonds
find more resources at oneclass.com
find more resources at oneclass.com
