MCDB 310 Study Guide - Fall 2018, Comprehensive Midterm Notes - Protein, Hydrogen Bond, Covalent Bond

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Published on 12 Oct 2018
School
U of M
Department
Molec, Cell & Develop Biology
Course
MCDB 310
MCDB 310
MIDTERM EXAM
STUDY GUIDE
Fall 2018
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Biochemistry Lecture #1
Biochemistry is the study of the molecules that function in very specific ways to sustain life;
explores how chemistry relates to the biology of keeping cells alive
C, H, O, N four most abundant elements in cells because they are versatile and can
react/associate i R groups
Functional groups are transferred within or between molecules to regulate cellular activity
Factors that control and affect cellular activity in biological systems
pH
Temperature
Barometric pressure
Concentration of chemicals and reactants/products
Available energy
Biomolecules are major molecular groups (lipids/proteins/nucleic acids/carbohydrates) [high
energy compounds] that are abundant and essential for life
All amino acids can be charged @ some point, all have a carboxyl and amino groups
-i.e. 2 cysteines can make a disulfide bond!
Non-polar molecules act totally differently from polar molecules in cells and need to be treated
differently
Stereoisomers are 2 molecules with the same bond order but with different spatial
arrangements
-Stereochemical fit of biomolecules underlies most biochemical interactions
Configuration is hard to change because it requires the breaking and remaking of covalent
bonds; defined as the fixed spatial orientation of organic molecules
- Sometimes rapid changes in cis/trans configurations of retinal isomerization is the basis of our
vision (breaking and flipping double bond)
Conformation is rotation without breaking bonds; atoms are free to rotate about single bonds,
but they are sometimes hindered by neighboring functional groups
Conformation and configuration dictate a lot in biochemical interactions
-use NMR and X-ray crystallography to study the precise arrangement of atoms in binding sites
METHODS- Need to know
1) What is the purpose of the method?
i.e. the purpose of x-ray crystallography is to determine the structure of molecules
2) How do you perform the method?
3) What kind of data do you get and how do you analyze it?
Chiral center: a carbon with four different substituents
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-Asymmetric
-Arrangement matters, can move around to change form
-Rotates plane of polarized light
2 different configurations for a chiral center are called enantiomers and they are mirror images
and not superimposable.
Enantiomers have similar chemical, but different physical properties
i.e. rotation of polarized light is different depending on form
Number of stereoisomers is calculated by doing 2n, where n is the number of chiral centers;
stereoisomers are distinguishable by small differences in chemistry (i.e. spearmint and caraway
are enantiomers)
How do we determine conformation and configuration?
1) X-ray crystallography/diffraction
a. Purpose: determine structural elements
b. Method: requires a crystal, which can be hard to make
c. You get a good resolution ~1-3Å (a C-C is 1.54Å)
d. Structure of crystal turns out to be similar to its biological form
e. Can use large molecules, i.e. DNA, protein, ribosome
2) Nuclear Magnetic Resonance Spectroscopy (NMR)
a. Purpose: structural determination of molecules in solution
b. Can identify specific functional groups in a 3D relationship
c. Shows conformational changes of molecules in solution
d. Usually small molecules (<30,000 Daltons)
e. Requires a large sample (milligrams)
Common Chemical Reactions and Mechanisms
1) Reactions that make or break a bond
2) Group transfer reactions
3) Oxidation and reduction reactions
4) Elimination, isomerization, and rearrangement reactions
Reactions that make or break a bond
Depends on the strengths of bonds involved in reaction
Bond strength depends on electronegativity of atoms involved
How strong of a nucleophile is important
o Stronger nucleophile break bond more easily
Distance of bonding electrons from each nucleus
Nuclear charge of each atom
Number of electrons shared (double bond is stronger than single bond)
1A: Breaking Covalent Interactions
Hemolytic cleavage: one electron remains with each atom and often results in the
formation of free radicals
o Least common cleavage type
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Document Summary

Biochemistry is the study of the molecules that function in very specific ways to sustain life; explores how chemistry relates to the biology of keeping cells alive. C, h, o, n four most abundant elements in cells because they are versatile and can react/associate i(cid:374) (cid:862)r(cid:863) groups. Functional groups are transferred within or between molecules to regulate cellular activity. Factors that control and affect cellular activity in biological systems: ph, temperature, barometric pressure, concentration of chemicals and reactants/products, available energy. Biomolecules are major molecular groups (lipids/proteins/nucleic acids/carbohydrates) [high energy compounds] that are abundant and essential for life. All amino acids can be charged @ some point, all have a carboxyl and amino groups. I. e. 2 cysteines can make a disulfide bond! Non-polar molecules act totally differently from polar molecules in cells and need to be treated differently. Stereoisomers are 2 molecules with the same bond order but with different spatial arrangements. Stereochemical fit of biomolecules underlies most biochemical interactions.

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