01:694:301 Study Guide - Comprehensive Final Exam Guide - Enzyme, Protein, Adenosine Triphosphate

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Intro to Biochemistry and Molecular Biology
(001:694:301) - Section H1
Study Guide
Chapter 1‘Biochemistry: An Evolving Science
The most power lesson of Biochemistry is the great similarity between all life forms on Earth.
o Only logical explanation common ancestry; all life forms are related (far back in time)
Analogy: one ‘operating system’ + one kind of ‘software’ (genetic code) used by every organism on
the plant
There are three domains of life: Eukarya, Bacteria (prokaryotes), and
Archaea (also prokaryotic)
o Figure 1.3
All multicellular organisms are Eukarya and their cells have
nuclei and other structures inside
Bacteria have no nucleus and no real subcellular compart-
ments
Archaea are single celled organism with no nucleus which
tend to be found in extreme environments (hot, acidic, salty)
‘extremophiles’
o Figure 1.2 Note the following timeline: *2.25 bya O2 came into at-
mosphere
Earth was more than 2 billion years old, ferrous chloride ubiquitous; in presence of O2 fer-
rous chloride ferrous oxide;
~2.25 bya O2 caused depletion of iron salts in ocean; deposits of iron banded iron for-
mations (BIFs) (red beds);
Banded iron is made of iron which could only be dissolved in water under anaerobic condi-
tions; provides evidence that the Earth used to be anaerobic with no free O2
Stromatolites are photosynthesized colonies (cyanobacteria) which puts oxygen into the air
How did O2 affected BIFs and stromatolites?
KNOW the structure of DNA as described on pg. 4 5
o DNA illustrates how form and function interplay
o DNA is constructed of 4 building blocks (monomers)
Each monomer of DNA consists of sugar phosphate unit + one the following 4 bases:
Thymine (T), Adenine (A), Cytosine (C), Guanine (G)
**Uracil (U) is only found in RNA, not DNA (if found in DNA it is a mistake); when C is
oxidized (deamination) U
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2
o Note the difference between U and T; T contains a methyl group which acts as a
‘sticker’ and indicates ‘belonging’ (to DNA);
Mnemonics to Remember
o All Tigers Can Growl
o PUre As Gold & CUt The PYe
Nomenclature
o Note the following suffixes:
Base Ex: adenine
Base + sugar Ex: adenosine
Base + sugar + phosphate Ex: adenylate
o
KNOW how to draw these bases and show *where sugars attach
KNOW how to draw AT or GC base pairs
o GC bonds are harder to break (50% stronger) due to 3 H-bonds
o AT bonds only have 2 H-bonds
Be able to recognize and draw a right-handed helix
DNA Structure
o Base pairs are held together by H-bonds
o Two stands of DNA are anti-parallel; always read 5’ 3’
o 5’-end contains phosphate; 3’-end contains sugar
KNOW how to convert b/w stick model and line-angle model
Strong vs. Weak Forces in structure and stability of biological molecules
o Molecules are held together by covalent bonds (a strong force ~75kcals)
o Note that molecules with more resonance structures have greater stability
o A few weak noncovalent forces determine how proteins fold and how enzymes bind to their sub-
strates
o Electrostatic interactions A charged group on one molecule can attract an oppositely charged
group on another molecules (dielectric constant is important)
Coulomb’s Law E = kq1q2/Dr
o Hydrogen bonds – A bond partially shared between H atom and electronegative atom such as N,
O, S (not carbon); weaker than covalent bonds (~5 kcal); more linear (180°) the stronger H-bond
o Van der Waals forces induced dipoles (regardless of polarity all molecules have this force); fluc-
tuation of charge distribution; weaker than H-bonds
Figure 1.10 Repulsion caused by overlapping electron cloud as two atoms get too close
o Hydrophobic interactions (‘Clathrate Cage’)
Occurs in presence of water; nonpolar molecules can’t participate in H-bonds/ionic interac-
tion
Water forms ‘cage’ around nonpolar molecules becoming more well ordered; not energet-
ically favored
When two nonpolar molecules come together; some water molecules are freed to interact
with surrounding water molecules (favorable disorder increased)
Thus nonpolar molecules have increased tendency to interact w/each other in water vs.
other less polar solvents
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