Biochem 3510

Unit 1 Study Guide

Here’s a list of things I think you should have learned from your reading and personal
study.

Disclaimer: This is not an exhaustive list of exact topics/question types that you will see
on the exam. I think these kinds of lists can be a crutch to some students (some students
assume that once they’ve answered everything on this list that they’re done studying and
they will dominate the exam). This study guide should be an indicator of how much
detail I expect you to know, not exactly what you will need to know.

Remember to get clever and active in your study. Make lists, draw pictures, recite out
loud concepts and pathways etc., find a chalkboard and write things out from memory,
make up acronyms to remember lists/pathways/etc. Often the stupider the memory link,
the stronger the memory will be (ex: Kings Play Chess on Fat Girl’s Stomachs =
Kingdom, Phylum, Class, Order, Family, Genus, Species).

Chapter 1:

Draw a water molecule. Label the partial charges. Which atom(s) are the most and least
electronegative? Why is the water molecule polar (Hint: why are molecules like CO2 not
polar?)? Draw another water molecule in the correct orientation adjacent to the first one
you drew. Why will the two molecules assume these orientations when close to each
other? What kind of bonds hold these 2 water molecules together? Which atoms are the
H-bond donors and acceptors?

Water has a lot of unique characteristics that result from water molecule polarity and
hydrogen bonding. Name and describe some of these properties and explain the
implications of these characteristics in living organisms.

For the equation Δ G = Δ H - TΔ S, define each term. What does it mean if the Δ G for
an event (like the folding of a protein into its 3-D structure) is negative? The second law
of thermodynamics says that the total entropy (disorder) of a system plus that of its
surroundings always increases. Why then do proteins and other complex highly
structured molecules spontaneously form? This appears to violate the 2nd law of
thermodynamics, but it doesn’t; why?

In terms of thermodynamics, why do two strands of complementary DNA spontaneously

come together to form a double helix when placed in water? Again, this appears to
violate the 2nd law of thermodynamics, but it doesn’t.

What does the equation Ka=[H+][A-]/[HA] tell you? If I tell you that Ka for HCl in a
solution is 20, would you expect there to be more H+ or HA in the solution? What does
this tell you about how acidic HCl is?
The pKa of an acid or base can be used to deduce whether an acid/base will be protonated
or not. When the pH of a solution is equal to the pKa then the concentration of acid [HA]
is equal to the concentration of base [A-] (see pages 15 and 16 for the derivation if you’re
interested). When the pH of the solution is above the pKa, do you expect there to be an
increase or decrease in [HA], what about for [A-]? What does this have to do with
proteins and DNA? Why do the two strands of a DNA double helix separate when you
increase the pH of the solution the DNA is in? Why do proteins denature (unfold) when
you increase or decrease the pH dramatically?

Describe the structure and function of a DNA double helix. Compare and contrast DNA
and RNA.

Describe the structure and function of proteins.

Describe as many types of bonds you can think of. Compare and contrast these bond
types. Which types of bonds bind together 2 amino acids in a protein? What about
nucleotides in a single strand of DNA? What about the two strands of a DNA double
helix? What about the bonds important for holding a protein in it 3-D/tertiary structure?

Individual hydrogen bonds are relatively weak. Why then are these bond types seen so
often in biological structures? For example, why is it good that two DNA strands are
held together by hydrogen bonds rather than the much stronger covalent bonds?

Why does a DNA double helix separate into individual strands if there’s no positive ions
(like Na+) in the surrounding solution? Why do most proteins in an aqueous (water is the
solvent) solution have their hydrophobic residues buried in the interior of the protein and
their hydrophilic residues on the surface?

Chapter 2:

Draw an alanine amino acid in a solution at pH 7 (hint: the amino and carboxyl group
protonation states will vary depending on the pH because each of these groups has a
specific pKa: see table on pg 33). Label the α-carbon, the α-amino group, the α-carboxyl
group, and the side group. What’s the overall charge of this amino acid?

Now perform the function of a ribosome by covalently attaching an aspartic acid amino
acid to the alanine. Draw the correct structure for ala bonded to asp (hint: the ribosome
always builds a protein in amino to carboxyl direction: so, would the asp be bonded to the
amino or carboxyl group of the ala?). What’s the charge on the asp side group (we’re
still at pH = 7)? What’s the overall charge of this dipeptide? Now do the ribosome’s job
and covalently attach a cysteine residue. Draw the structure of this tripeptide. What’s
the charge on the cysteine side chain? What’s the overall charge of the tripeptide? If you
were to write out this peptide how would you do it using the correct 1 letter abbreviations
in the correct order (hint: is A-D-C the same as C-D-A?)? What will happen to the
charges on each individual group and the net peptide charge if you put this peptide into a
solution with a pH of 1?
Describe the 4 levels of protein structure. Which bonds hold together the primary
structure? Which types of bonds are really important for forming secondary structures
like α-helices and β-sheets? How does a protein achieve its tertiary structure? What role
does thermodynamics play? Why do some proteins have a quaternary structure while
others don’t (for example, why does hemoglobin have a quaternary structure but
glycogen synthase does not)?

Why are glu and asp considered “acidic amino acids?” Why are K, H, and R considered
“basic amino acids?”

Chapter 3:

You’re interested in studying glycogen synthase which is a protein (enzyme) in cells that
functions to store extra glucose as glycogen. Describe a strategy (there’s no single
correct strategy) using a number of the lab techniques described in chapter 3 to
isolate/purify glycogen synthase (hints: glycogen synthase is found in the cytoplasm of
the cell. It is negatively charged due to modification with a number of phosphates which
are negatively charged. There are antibodies available for purchase that specifically
recognize glycogen synthase. There are available assays for measuring glycogen
synthase activity. Glycogen synthase has a mass/size of 87 kDa).

What if you wanted to compare two samples of cells that were treated differently to see if
these treatments result in changes in protein levels of glycogen synthase. What
techniques would you use to quantify glycogen synthase levels?

What techniques might you use to confirm that glycogen synthase really is located in the
cytoplasm of cells?

You’re interested in finding out how many different proteins are found in the nucleus of a
cell. How might you do this?

You determine that there are 10 proteins (there are obviously way more than that, but
work with me) in the nucleus, but you don’t know the identity of these proteins. How
might you go about identifying these proteins?

You determine that nine of the ten are proteins that have been described and
characterized before, but one of them we don’t know anything about. The first thing to
do is to determine the amino acid sequence of this unknown protein. How will you do
that? What can you do with the amino acid sequence information (besides go publish it
in Science and accept your nobel prize)?

In order to help you figure out how this protein functions you would like to determine its
3-D/tertiary structure. How will you do this? How will determining its structure help you
figure out its function?
Chapter 4:

Draw deoxyadenosine monophosphate (an adenine nucleotide). Label the 3’-OH and the
5’ phosphate and the 2’-H of the sugar. Which numbered carbon is the adenine base
bonded to? Label the H-bond donors and acceptors on the adenine base.

Now perform the job of DNA polymerase and covalently attach a deoxycytosine
monophosphate (a cytosine nucleotide) to the deoxyadenosine monophosphate. Does it
matter whether you bond it to the top or bottom of the deoxyadenosine monophosphate
(hint: DNA polymerase only synthesizes DNA in a 5’ to 3’ direction because in order to
do the chemical reaction of adding a nucleotide, this enzyme requires the 3’-OH)?
Which end of this dinucleotide strand is the 5’ end and which is the 3’ end?

Draw the complementary DNA strand and correctly depict the hydrogen bonds between
base pairs on the two strands? Don’t forget that the 2 DNA strands are anti-parallel.
What does this mean in terms of the 5’ and 3’ ends of the strands?

How does RNA differ from DNA? If the DNA sequence 5’-AGCTCCG-3’ were
transcribed, what would the RNA strand sequence be (use the correct 5’ and 3’
designations on the RNA strand: remember, RNA polymerase, like DNA polymerase
only adds bases in a 5’ to 3’ direction)?

What’s a codon? What’s an anticodon? If there was a mutation in a gene that resulted in
a change of the codon sequence from AUGCUC……UAG to AUGCUG……UAG,
would you expect there to be any change in the structure or function of the translated
protein? Why or why not?

Describe the events and important players in DNA replication. Where in the cell does
this happen? What is the result of DNA replication. Why/When does a cell replicate its
DNA? What function does DNA polymerase play? Why can DNA polymerase only
work in a 5’to 3’ direction?

What is “gene expression?” What is transcription? Translation? Where does each of

these processes happen in the cell? What is the result of transcription? Translation?
Why/When does a cell transcribe/translate sections of its DNA? How are RNA
polymerase and DNA polymerase similar and different? What’s the function of mRNA,
rRNA, tRNA? There are important sequences on the DNA strand that signal the start and
end sites for transcription. What are these called?

How do prokaryotic and eukaryotic transcripts differ?

In Eukaryotes the RNA strand that’s produced by transcription needs to be processed

before it can be translated by the ribosome. What processing events take place?
For the following mRNA sequence: CCUAUGCGGACGGGGCUCUAGAAA. How
does the ribosome know where to start and stop translating this mRNA strand? Why
does it matter that it starts there? What would happen if the ribosome skipped one
nucleotide to the right and started translating with the first codon as UGC? Would this
change the sequence of amino acids in the resulting protein? Would you expect this to
affect the protein structure/function?