Chem 365 - FA17 Midterm 1 Study Guide

Objectives Answers

Lecture 1
1. List four elements C, N, O, H
that occur in
virtually all
biological molecules

2. Summarize the 1) Small chemical units combine to make larger polymers

major stages of
chemical evolution 2) Complementary molecules associate

Separate macromolecules with complementary arrangements of

functional groups can associate with each other, giving rise to more
complex molecular assemblies with an even greater range of functional
possibilities.

3) Intramolecular complementarity & replication

Complementarity makes it possible for a macromolecule to replicate, or

copy itself, by directing the assembly of a new molecule from smaller
complementary units, hence transition to systems in which molecules
were organized and specifically replicated.

3. Explain why It allows the assembly of new molecules from smaller , more readily
complementarity available, complementary units
was necessary for
the development of
self-replicating
molecules

4 List the differences Prokaryotes: 1-10 microns; 3,000-6,000 compounds; helical, rod like,
between prokaryotes or spheroids; the simplest cells/unicellular; nucleoid region contains
and eukaryotes circular DNA structure; asexual; anaerobic

Eukaryotes: membrane-bound organelles with nucleus; 10-100

microns; 100,000 compounds; multicellular; sexual reproduction;
aerobic
5. Draw a schematic
of a eukaryotic cell
showing at least 5
major organelles and
their functions

6. Plot the tree of life

with its three
domains

7. Explain how Natural selection acts on randomly occurring variations among

individual variations individuals
allow evolution to
occur

Origin of Life Life is 3.5 Billion years-old (fossil evidence).

Before that was 1 billion years of prebiotic era.
How did life on 1) Organic gases in primordial atmosphere and thunder (Miller-Urey
Earth begin? Two experiment).
theories. Formation of amino acids from organic gases
using an electric discharge

2) Primordial ocean water and heat (under-ocean volcanic vents)

Hydrothermal vents in the ocean floor
which emit solutions of metal sulfides at
temperatures as high as 400C

***both could form biomolecules.

Major Biological Polymer Monomer

Polymers Protein Amino Acid
Nucleic Acid Nucleotide
Polysaccharide Monosaccharide

How did Cellular Compartmentalization --> protection & concentration.

Life Start?
Metal catalysis -->making of new compounds.
Metabolic pathways evolved to synthesize molecules and generate
energy.

Making oxygen --> aerobic metabolism -->

propagation into new habitats --> adaptation/speciation
--> diversity.

Lecture 2
Thermodynamic the part of the universe that is of interest, e.g. a reaction vessel, a cell.
system:

Surroundings of a everything else in the universe.

system:

Total energy U: the sum of all energies harbored within the system (potential energy
stored in chemical bonds, kinetic energy due to motions, electrical
energy due to electric charges).
Heat reflection of random molecular motions within the system.

Work work exerted by the system on its surroundings to cause an organized

motion.

8. State the first & 1st law: total energy U of a system is conserved (cannot be created
second laws of nor destroyed; this means that there must be interactions from
thermodynamics and surroundings if a change in total energy U occurs
explain how they
enhance our 2nd law: energy spontaneously disperses from being localized to
understanding of become spread out and random if it is not hindered from doing so
biochemical (entropy increases)
processes

The change in total the heat absorbed by the system from its surroundings minus the work
energy of a system exerted by the system on its surroundings.

Enthalpy "H" We define enthalpy H of a system: the sum of its own total energy U
plus the energy resulting from its interactions with its surroundings.

For a biochemical 1) The process is occurring at constant pressure.

system undergoing a
process: 2) The change in enthalpy H of the system is equivalent to the heat it
absorbs.

3) The change in total energy U of the system is equivalent to the

change in its
enthalpy H.

Entropy "S" measure of the degree of randomness within the system. It reflects the
number of ways of arranging the components of the system.

9. Explain what when an exergonic process occurs without input of additional

determines the energy from outside the system
spontaneity of a Decrease in Gibbs free energy (G is negative)
chemical process This has nothing to do with the rate at which the process occurs
(i.e. how fast or slow it is).

Types of Isolated system: does not exchange matter nor energy.

thermodynamic Closed system: exchanges only energy.
systems Open system: exchanges both matter and energy.
10. Describe the An open system (exchanges both matter and energy) in steady state
thermodynamic
cycle within the
biosphere

Lecture 3
11. Illustrate the
structure of a water
molecule

Water molecules Water molecules are polar and can form hydrogen bonds with each
are____________ other and with other molecules.
Each water molecule interacts tetrahedrally with four other water
molecules.

Liquid Water rapidly fluctuating 3D network of H-bonds.

consists of:

Transfer of nonpolar entropically driven

substance (e.g.
hydrocarbons)
from water to
nonpolar solvents is
____________

What happens when Water forms a cage around nonpolar

we mix water with a (hydrophobic) solutes to maximize H-bonds.
nonpolar substance? To release the nonpolar solute:
1) water H-bonds must be broken (energy cost).
2) water molecules must be dispersed (entropic benefit).

12. Identify -OH, =O, -NH , -O

3
+ -

functional groups in
a compound that can
function as hydrogen
bond donors and
acceptors

13. Order by relative Covalent > Ionic > Hydrogen

strength covalent
bonds, ionic
interactions, &
hydrogen bonds

14. Compare Hydrophobic: water forms cage around nonpolar (hydrophobic) solute
interaction with to maximize H-bonds
water of Hydrophilic: polar molecules that form ionic bonds with water
hydrophobic, molecules
hydrophilic, and Amphiphilic: both hydrophobic (nonpolar) and hydrophilic (polar)
amphiphilic parts; form bilayers with hydrophobic parts hidden
molecules

15. Define an acid Acid: compound that can donate a proton

and a base Base: compound that can accept a proton

16. What makes a Buffers are substances that resist changes in pH when in solution.
substance a buffer?
What are buffers Used to prepare biological molecules which may contain ionizable
used for in groups that are sensitive to changes in pH in their environment.
biochemistry?

17. What is the The external pressure that needs to be applied to prevent changes in
osmotic pressure of solution volume
a solution?

18. What is dialysis Method that relies on diffusion of solutes in water to remove
& what is it used substances from solutions
for?

Lecture 4
What makes The central dogma of life: the two-step process,
biological life what transcription and translation, by which the information in genes flows
it is? into proteins

19. Write full name A - Adenine

& one letter name of G - Guanine
each of th2e five C - Cytosine
U - Uracil
nucleobases found in T - Thymine
DNA & RNA

20. Classify the 5 Purines: A, G (2 rings)

nucleobases Pyrimidines: C, U, T (1 ring)
commonly found in
DNA & RNA into
purines and
pyrimidines

21. List the DNA nucleobases A, T, C, G

nucleobases found in RNA nucleobases A, U, C, G
DNA (A, T, C, G)
versus the
nucleobases found in
RNA (A, U, C, G)

22. Determine Nucleoside: nucleobase linked to sugar; the sugar is pentose

whether a compound Nucleotide: nucleoside w/ phosphate at C5 or C3
is a nucleobase,
nucleotide,
nucleoside, or none
of the above from its
overall structure

23. Identify a
nucleoside
monophosphate, a
nucleoside
diphosphate, & a
nucleoside
triphosphate from a
drawing of their
structures

24. Distinguish a DNA lacks 2-OH, RNA has it

DNA chain from an
RNA chain based on
the absence or
presence of the
ribose 2-OH
25. Circle the
individual
nucleotides in a
DNA or RNA chain
when presented with
its structure (i.e.
identify the
phosphodiester
bridges)

Nomenclature of Nucleosides
Nucleosides If the nucleoside contains a purine (two rings), the name of the
structure will end with "----osine." (Adenosine, Guanosine).
If the nitrogenous base is a pyrimidine (one ring), the name will end
with "----idine." (Cytidine, Thymidine, Uridine).
Odd one: cytosine (nucleobase) vs. cytidine (nucleoside).

Nucleotides may be C5' and C3'

built by
phosphorylation of
the ribose
at__________

What is the best ATP!!!

known nucleotide?
ATP is the energy carrier used by all life. Cleavage of the third
phosphate releases energy used
in motion and in facilitating chemical reactions in the cell.

Ribose vs ribose (in RNA). This sugar has a 2'-OH.

Deoxyribose 2'-deoxyribose (in DNA). Has 2'-H. This sugar lacks a 2'-OH.
The difference: 2'-OH in RNA vs 2'-H in DNA.
This difference affects secondary structure and stability of DNA and
RNA. DNA lives longer than RNA because DNA lacks the 2'-OH
which makes RNA degradable by nucleases,
 enzymes used by organisms to defend themselves against foreign RNA
(e.g. viruses).

What are nucleic THEY ARE DNA AND RNA

acids? a chain of nucleotides covalently linked 5' to 3'.
It is made of polynucleotides linked 5' to 3' by phosphodiester bridges
to form a chain.
DNA and RNA sequence is always read from the 5' end to the 3' end.

Lecture 5
26. Describe the 3D DNA is an antiparallel double helix. Has a sugar phosphate backbone
structure of DNA, that minimizes electrostatic repulsion.
detailing its fain Base pairing between polynucleotide chains is responsible for the
features (major double-stranded nature of DNA.
groove, helix pitch,
number of base pairs Major Groove: where the backbones are far apart. Wide and shallow.
per turn) Minor Groove: where the backbones are close together. Narrow and
deep.
Base pairs per turn:10.5
Helical pitch: 35.5 = one helical turn

How did Watson and 1) They learned about Chargaff's rule.

Crick arrive at an 2) They knew the structures of the four nucleobases of DNA.
accurate model for 3) Rosalind Franklin's X-ray Photograph 51.
the structure of Knowing the structure of the nucleobases allowed
DNA? Watson & Crick to propose hydrogen bonding pattern of
complementary base pairs in DNA

Photo 51: Meaning - Helix, zig zag shape

of the photo - the helix repeats continuously
- there are two strands going in opposite directions
-missing peaks indicates where the two strands cross each other
-Spacing between the stacked bases is 3.4 A
- Full turn of the helix is 34

27. Explain why the Each DNA strand can act as a template for the synthesis of its
double-stranded complementary strand. Therefore, hereditary information is encoded in
nature of DNA is the sequence of bases on either strand.
relevant for copying
and transmitting
genetic information
when a cell divides
28. Explain the Chargaffs rule tells us that the nucleobases come in 1:1 proportions.
structural basis of That is, the number of purines equals its paired pyrimidine.
Chargaffs rules amount of C= amount of G in DNA
amount of A= amount of T in DNA
Base pairing is set by Chargaffs rules: G pairs with C, and A pairs
with T.

29. List the The nature of DNA

structural differences DNA is double stranded, large 25-250,000 kilo base pairs.
between DNA and DNA is a stiff molecule, but can bend with the help of
RNA proteins, e.g. packaged in chromosomes.
Diploid organisms have two equivalent sets of
chromosomes, each is a tightly wound large DNA molecule.
Haploid DNA is the unique DNA of an organism.

RNA
It forms a single strand sugar-phosphate chain.
The sugar in its nucleotides is ribose (DNA is deoxyribose).
The base thymine is replaced by the base uracil.

30. Draw the

schematic
differences between
DNA & RNA

31. List the 3 major
large RNAs in
biology & their roles
in the central dogma
Messenger RNA (mRNA): is a transcript (copy) of DNA and
carries its genetic message out of the nucleus. It is the RNA of
the central dogma of life.
Ribosomal RNA (rRNA): is the structural scaffold of the
ribosome, the organelle that conducts protein translation.
Transfer RNA (tRNA): carries the building blocks of proteins,
the amino acids, to the ribosome and defines the genetic code.
Transfer-RNAs do not carry any message. They are L-shaped
molecules. They define and carry the genetic code.
32. Describe the Translation
overall process of First, each tRNA gets loaded or charged or
translation, and the aminoacylated with its cognate amino acid by a
role of tRNA in it specific aminoacyl-tRNA synthetase
Then, the charged tRNA is used by the ribosome to read the
mRNA message and translate it

33. Summarize the

steps of the central
dogma

Transcription and DNA directs the synthesis of messenger RNA (mRNA).

Translation The sequence of the resulting mRNA is complementary to that of the
DNA strand.
The message is translated when transferRNA (tRNA) molecules align
with mRNA by complementary base pairing between codon and anti-
codon. This happens at the ribosome.
Each tRNA carries a covalently attached, specific amino acid that is
cognate to that codon.

Lecture 6
What do newer Rely on Enzyme that cleave DNA at specific sites
methods of Restriction enzymes were discovered in bacteria where they are used to
sequencing rely on? kill bacteriophage.
They are endonucleases and exonucleases. Most useful in sequencing
are Type II restriction enzymes.
There are currently > 11,000 known restriction endonucleases with
over 270 recognition sites.
What do most type II Most Type II restriction endonucleases recognize and cleave
restriction palindromic DNA sequences (sequence with 2-fold symmetry).
endonuclease
recognize?

Cloning production of multiple identical organisms derived from a single

ancestor

Clone a copy of the DNA/gene of interest, or the collection of cells that

contain the vector carrying that DNA

Vector any carrier DNA molecule that contains sequences necessary to direct
DNA replication. It carries foreign DNA.

Plasmid circular DNA molecules 1-200 kb long, found in bacteria or yeast, re-
engineered to be used as vectors for cloning in bacterial or yeast
cultures

34. Explain how Sticky ends: The end on a fragment of ds DNA generated by cutting
restriction enzymes the DNA with restriction endonuclease. Have overlap that allows the
generate either ends to base pair and join together with another strand of DNA.
sticky ends or blunt Blunt ends: Also created by restriction endonucleases but the ends are
ends of DNA cut evenly with no overlap

35. Describe the Gel electrophoresis is used to separate DNA fragments

components & Gel material is agarose or polyacrylamide.
explain their purpose Separates DNA fragments by molecular mass.
in the reaction Detection by stain, fluorescence, or radioactivity.
mixture used for the Nanogram sensitivity
dideoxy DNA
sequencing method

36. Summarize what The human genome contains ~23,000 genes, corresponding to about
is known about the 1.2% of its 3 billion nucleotides.
size and gene
content of the human
genome

Lecture 7
37. Summarize the Initialization: Heat activate DNA polymerase
steps required to Denaturing: Breaking down the hydrogen bonds between
amplify a given complementary bases, yielding 2 single stranded DNA molecules
segment of DNA Annealing: Polymerase binds to the primer template hybrids to begin
DNA formation
using the polymerase Extension/Elongation: DNA polymerase synthesizes a new DNA
chain reaction (PCR) strand complementary to the DNA template strand by adding free
dNTPs from the reaction mixture

38. Summarize the Properties of a good plasmid used in the lab for cloning:
procedure for Small
cloning Replicates easily
(reproducing) a gene Carries genes encoding selection markers.
in a cloning plasmid. Contains a number of restriction endonuclease sites needed to
insert foreign DNA.
Plasmids can be used to clone foreign DNA fragments no more than
10 kilobases.

39. Describe the -DNA recombinants technology:made it possible to purify specific

activities of the DNA sequences and to prepare them in quantities sufficient for study.
enzymes required to Also called molecular cloning or genetic engineering, makes it possible
construct a to isolate, amplify, and modify specific DNA sequences.
recombinant DNA .
molecule (i.e.
endonuclease and
DNA ligase).

What are the two 1) Antibiotics (e.g. Ampicillin)

types of selection 2) Colored substances (e.g. X-gal)
markers?

Cloning with a A restriction fragment can be inserted into a cut made in a cloning
plasmid vector by the same restriction enzyme

What is the result of Chimeric DNA containing a portion of the foreign DNA inserted into
cloning with a the vector
plasmid?

What are the sticky DNA ligase

ends of the vector
and the DNA
fragments covalently
joined by?

How to produce transformation followed by selection

large quantities of
the
constructed plasmid?

40. Explain why a Selectable Marker: a gene introduced to a cell that has a trait suitable
cloning vector for artificial selection
usually contains a Vectors have selectable markers to determine which recombinant has
selectable marker. the insert DNA of interest

41. What is a DNA 2 types of DNA libraries are Complementary(cDNA) and Genometric
library and what are (gDNA)
the two types of DNA libraries are screened for a particular gene by In Situ
DNA libraries? how Hybridization (colony hybridization)
can it be screened
for a particular
gene?

How the Polymerase To amplify a gene = to reproduce it many times over

Chain Reaction
(PCR) is Used to
Amplify a Gene?