01:694:301 Study Guide - Comprehensive Final Exam Guide - Enzyme, Protein, Adenosine Triphosphate
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20 Nov 2018
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01:694:301
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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