1.

Biochemistry Supplement, Northwestern Medical Review, 2007

Supplemental Plates and Notes For Biochemistry Review Course

Hemochromatosis
Iron induces formation
of free radicals (due to
Fenton reaction.)
H
2
O
2
and free radicals
cause lipid
peroxidation of cell
membranes
Necrosis of Cells
Iron
accumulates as
hemosiderin in
hepatocytes
Hepatocellular
Carcinoma
Iron alters DNA
Iron stimulates
collage formation
Cirrhosis
Excessive GI Iron
Absorption


How to Get Pyruvate Back to The Cytoplasm?
Malate
Pyruvate
PEP
Aspartate Aspartate
Pyruvate
Carboxylase
Oxaloacetate
PEP Carboxylase
Malate
Oxaloacetate
NADH
NADH
NAD
NAD
C
y
t
o
p
la
s
m

How to Get Fatty Acids Into Mitochondria
CO
2
Acetyl CoA Carboxylase
Fatty Acid Synthetase
Triacylglycerol
Fatty Acyl CoA
-oxidation
C
y
t
o
p
la
s
m
Mitochondria
Citrate
ACETYL CoA
Carnitine
Carnitine Acyl-transferase
Fatty Acyl CoA
Acetyl CoA
Citrate
Fatty Acid
MALONYL CoA
Crossing!
Long Chain
Short & Medium Chain



4 Must-Know Fatty Acid-Related Enzymes
Acetyl CoA Carboxylase
Methyl Malonyl CoA Mutase
Carnitine Acyl Transferase
Medium-Chain Fatty-acyl CoA Dehydrogenase

Note on Fatty Acyl CoA Dehydrogenases
Fatty acyl-
CoA
Long Chain Fatty Acyl-CoA
Carnitine Acyl Transferase
Medium Chain Fatty Acyl-CoA
Short Chain Fatty Acyl-CoA
LCAD
MCAD
SCAD
Acetyl CoA
LCAD=Long Chain Fatty Acyl CoA Dehydrogenase
MCAD=Medium Chain Fatty Acyl CoA Dehydrogenase
SCAD= Short Chain Fatty Acyl CoA Dehydrogenase
MCAD is the most common deficiency. It increases medium chain fatty
acids and decreases their degradation, low acetyl CoA and low ATP
formation; and decreases overall synthetic activities due to low ATP.
M
i
t
o
c
h
o
n
d
r
i
a


Note On Vitamin B12
Methionine
Tetrahydrofdolate (TH4)
Methylene-tetrahydrofdolate
B12
B12 CH3
Methionine Synthase
S-adenosyl homocysteine
S-adenosyl methionine (SAM)
CH3
Homocysteine
Propionyl CoA
Cystathionine
TCA
B12



2. Biochemistry Supplement, Northwestern Medical Review, 2007
Supplemental Note on Purine and Pyrimidines
Glutamine
CO2
Glutamate
Aspartate
Carbamoyl
Aspartate
PRPP
A
s
p
a
r
t
a
t
e
T
r
a
n
s
c
a
r
b
o
m
o
y
l
a
s
e
Carbamoyl
Synthetase
(OMP) Orotidine-
Monophosphate
Orotate
OMP Decarboxylase
Pyrimidine Synthesis
Orotate Phosphoribosyl
Transferase
Carbamoyl Phosphate
2ATP
Uridine-Mono
Phosphate (UMP)
UTP CTP
RNA


More on Purine Degradation and Salvage
De novo pathway makes 10-15% of bodily purines in 24 hours. Purine salvage pathway recycles hypoxanthine and
guanine and accounts for 80 to 85% of daily purines.
Slow or inhibition of salvage pathway, too much PRPP production and excess degradation of DNA (anticancer
treatment) promote uric acid production.
Note that HGPRTase deficiency promotes GMP and IMP loss (and inhibition) over guanylate PRPP Amidotransferase.
Hence, there is an exaggerated formation of uric acid.

Uric Acid
HGPRtase
Adenine
Adenosine
A
d
e
n
o
s
i
n
e

D
e
a
m
i
n
a
s
e
Xanthine Oxidase
Adenine Phosphoribosyl Transferase
Purine Nucleoside
Phosphorylase
Purine Nucleoside Phosphorylase
PRPP
Guanine
Guanosine
Xanthine
Hypoxanthine
Inosine
IMP
Guanylate PRPP Amidotransferase
De novo
Salvage
Degradation Degradation
GMP
AMP
3. Biochemistry Supplement, Northwestern Medical Review, 2007
Biochemistry Review: DNA, RNA and Protein Synthesis Supplement

1. Which of the following RNA segments is formed
by RNA polymerase from a DNA chain with the
sequence of CTATGC?

A. GATACG
B. GCATAG
C. GUAUGC
D. GCAUAG
E. CGTATC

2. A polynucleotide sample has the following base
ratio: cytosine 20; guanine 20; thymine 25; and
adenine, 50. Which of the following conclusions
can be made about the sample?

A. It is a linear DNA duplex
B. It is a circular DNA duplex
C. It is a single-stranded DNA
D. It is a linear RNA duplex
E. It is a single-stranded RNA

3. Ultraviolet-induced dimers of thymine cannot be
corrected in patients with xeroderma
pigmentosum due to defect in which of the
following enzymes?

A. Endonuclease
B. Exonuclease
C. DNA polymerase I
D. DNA polymerase II
E. DNA ligase

4. DNA polymerase I among other things has
editing function and catalyzes the hydrolytic
removal of incorrectly paired terminal nucleotides.
Which of the following options would better
describe this function?

A. Ligase activity
B. 3 to 5 exonuclease activity
C. 3 to 5 endonuclease activity
D. 5 to 3 exonuclease activity
E. 5 to 3 endonuclease activity


5. DNA polymerase I functions in the hydrolytic
removal of RNA primers in DNA replication.
Which of the following options would better
describes this function?

A. Primase activity
B. 3 to 5 exonuclease activity
C. 3 to 5 endonuclease activity
D. 5 to 3 exonuclease activity
E. 5 to 3 endonuclease activity

6. DNA polymerase I performs the so called nick
translation. Which of the following options better
describes this function?

A. Acting both as a polymerase and exonuclease
B. Acting both as a polymerase and endonuclease
C. Acting both as a polymerase and ligase
D. Acting both as a primase
E. Cutting a base pair

7. DNA polymerase III has polymerase activity plus
which of the following functions?

A. Primase activity
B. 3 to 5 exonuclease activity
C. 3 to 5 endonuclease activity
D. 5 to 3 exonuclease activity
E. 5 to 3 endonuclease activity

8. What would be the RNA produced from a DNA
segment with 5-TACGATA-3 sequence?

A. 5-ATAGCAT-3
B. 5-AUGCUAU-3
C. 5-UAUCGUA-3
D. 3-ATAGCAT-5
E. 3-ATGCTAT-5

4. Biochemistry Supplement, Northwestern Medical Review, 2007
9. Most eukaryotic mRNAs have a chain of 40 to
200 adenine nucleotide, poly (A) tail, at their 3
end. Which of the following statements more
correctly is applicable to poly (A) tail?

A. It is transcribed from the DNA
B. It is added to mRNA in the cytoplasm
C. It is added to mRNA after transcription in the
nucleus
D. It is required for termination codon function
E. It is chopped off before the mRNA enters
cytoplasm

10. Which of the following options is NOT correct
regarding hnRNA (heterogeneous nuclear RNA)?

A. It may not have a poly (A) if it codes for histone
proteins
B. It includes introns that code for protein
C. 5 capping catalyzed by guanylyl transferase is
the first processing reaction of hnRNA
D. It is extensively modified after transcription
E. It is the primary transcript synthesized by RNA
polymerase

11. What would be the consequence of inability of
endonuclease to identify the AAUAAA sequence
in the 3N end of hnRNA?

12. Given the numbered mRNA codons shown above;
insertion of cytidine molecule between codon
number 40 and 41, the resultant protein will have
how many amino acids?


Note: The initiation codon is AUG and termination
codons are UAG, UAA and UGA.

A. 41
B. 42
C. 43
D. 44
E. 45

13. Type II restriction endonucleases bind to DNA at
any position and then travel along the strand of
DNA until they reach a recognition sequence.
Tight binding of the enzyme at the recognition
site cuts the DNA molecule into two fragments.
The nucleotide pattern that is recognized by
different restriction enzymes, including EcoRI is
frequently palindromic. Given the following base
pairing, what would be the most likely pair of DNA
segments produced by the application EcoRI?



A. GTCGGG AATTCC
B. GTAGGG CATCCT
C. GAATTC CTTAAG
D. TCAAGA AGTTCT
E. CCGGTT GGCCAA


14. In the following diagram synthesis of A begins
simultaneously with which other segment?


A. A
B. B
C. C
D. D
E. E

15. What is the most accurate description of
repressors effect on gene function among the
following options?

A. Removal of the introns
B. Affecting the promoter region
C. Affecting the operator region
D. Modification of structure of DNA polymerase
E. Modification of structure of RNA polymerase


5. Biochemistry Supplement, Northwestern Medical Review, 2007
16. The fact that operon for lactose (lac-operon) is
inducible is compatible with which of the following
pieces of information?

A. Lactose attaches to and inhibits operator of
lactose operon
B. Lactose attaches to and inhibits promoter of
lactose operon
C. Lactose attaches to and inhibits lactose operon
D. Lactose activates repressor protein for lactose
operon
E. Lactose inactivates repressor protein for lactose
operon

17. The fact that operon for tryptophan (tryp-operon)
is repressible is compatible with which of the
following pieces of information?

A. Tryptophan acts as the repressor
B. Tryptophan acts as a co-repressor
C. Tryptophan attaches to and inhibits tryptophan
operon
D. Tryptophan attaches to and inhibits tryptophan
promoter
E. Presence of tryptophan in the medium is required
for synthesis of tryptophan

8. Cysteine that is placed on tRNA-Cys (Cys-
tRNACys) is chemically modified to the amino
acid alanine (Ala-tRNACys), and then used in a
biochemical system for protein synthesis. Which
of the following statements would better describe
the result of this chemical maneuver?

A. Protein synthesis would cease
B. There will be a no amino acid on polypeptide
chain at the positions that were destined for
cysteine
C. The polypeptide will cease to have both alanine
and cysteine
D. Cysteine will be placed in the protein at positions
that was occupied by alanine
E. Alanine will be placed in the protein at positions
that was occupied by cysteine

19. All of the following statements correctly
distinguish eukaryotic and prokaryotic cells with
the exception of:

A. Transcription and translation in prokaryotes
happen simultaneously.
B. The DNA of prokaryotes as opposed to
eukaryotes does not complexes with histones.
C. The genes of prokaryotes as opposed to
eukaryotes do not have introns
D. Several bacterial genes are controlled by one
promoter, while each eukaryotic gene has its own
promoter.
E. In eukaryotes as opposed to prokaryotes
histones facilitate gene transcription

20. Resistance of the patients to methotrexate, a
folate analogue, is due to what major
mechanism?

21. The hybridization technique that uses DNA
probes would be described by which of the
following options?

A. Labeled DNA that identifies complementary DNA
or RNA sequences
B. Labeled DNA that identifies complementary DNA
sequences
C. Labeled DNA that identifies complementary RNA
sequences
D. Use of specific sequences of DNA to obtain DNA
fragments
E. Technique for fast production of large amounts of
DNA

22. Make a match using the following options?
1. Gel electrophoresis
2. Southern blot
3. Northern Blot
4. Western Blot
5. Hybridization
6. Restriction Endonuclease

A. Proteins probed with antibodies binding specific
proteins
B. Radioactive DNA probe hybridizing with RNA on
nitrocellulose gel blot
C. Radioactive DNA probe hybridizing with DNA on
nitrocellulose gel blot
D. Separating DNA chains with variable length
E. Identifying a single DNA strand with
complimentary sequence
F. Recognition of short sequences in DNA and
cleaving both strands within that segment
G. Radioactive DNA probe hybridizing with dextrans
on nitrocellulose gel blot
6. Biochemistry Supplement, Northwestern Medical Review, 2007
23. In DNA sequencing process dideoxynucleotides
are added to media wherein the DNA polymerase
is already in the process of polymerization of a
DNA chain. Upon addition dideoxynucleotides
(ddNTP) polymerization is terminated. Result
would be DNA fragments with variable length that
are visualized by electrophoresis. Which of the
following characteristic of ddNTP is crucial in
DNA sequencing?

A. The fact that ddNTP does not have a 3 hydroxyl
group
B. The fact that ddNTP does not have a 5 hydroxyl
group
C. ddNTP acts like a DNA polymerase
D. ddNTP acts like an RNA polymerase
E. ddNTP acts like a ligase

24. In an attempt to produce a recombinant DNA the
following two DNA strands (A and B) are
subjected to EcoRI, that is, a restriction
endonuclease. The resultant recombinant DNA
would have which of the following structures?


A. 5- T C C C G A A C A C G G - 3
3- A G G G C T T G T G C C - 5

B. 5- T C C C G A A T C C C T - 3
3- A G G G C T T A G G G A - 5

C. 5- T C C C G T T T T C C C - 3
3- A G G G C A A A A G G G - 5

D. 5- T C C C G A A T T C G G - 3
3- A G G G C T T A A G C C - 5

E. 5- T C C C G A A T T C C C - 3
3- A G G G C T T A A G G G - 5

Question #1:
Uracil in RNA replaces thymine. The complimentary
RNA strand is GAUACG in 3 to 5 direction. Written in
5 to 3 direction it would yield GCAUAG.
Question #3:


Question #4:
DNA polymerase I can copy long stretches of primed
single DNA. It has several functions including 3 to 5
exonuclease activity for removal of incorrectly paired
nucleotides.

Question #6:
At a single-stranded DNA break or nick, DNA
polymerase can act both as an exonuclease
(removing 5 nucleotide) and replacing it with another
by polymerase activity.

Note: Endonuclease cuts a base pair.



Question #8:

Question #9:
Poly A tail is not transcribed from the DNA
7. Biochemistry Supplement, Northwestern Medical Review, 2007
It is added after transcription by nuclear enzyme
poly (A) polymerase.
It stabilizes the mRNA and promotes its entry into
the cytoplasm
Within the cytoplasm the tail is gradually
shortened

Question #10:
Maturation of eukaryotic mRNA requires removal
of introns that do NOT code for proteins.
hnRNA the code for histones usually do not have
poly A
The cap is a 7-methyl-guanosine added to
hnRNA in the nucleus by guanylyl transferase
and stabilizes the molecule

Question #11:
The sequence of AAUAA in hnRNA (heterogeneous
nuclear RNA) serves as a signal for cleavage of the
hnRNA and addition of poly (A) tail by poly (A)
polymerase.

Question #12:

Question #13:



EcoRI recognizes a pattern that reads GAATTC from
the 5 to the 3 end of the DNA molecule. The
complement of this sequence (on opposite DNA
strand) also reads GAATTC when read from 5 to 3.

About Restriction Enzymes
EcoRI of Escherichia coli is a restriction
enzyme (AKA. restriction nucleases). It acts
on the DNA strand at the target point , that is
the sequences of GAATTC in the cited
example. EcorRI cuts strand of the DNA
double helix at one point and the second
strand at the complementary point; resulting in
two segments of single stranded DNA with
sticky-ends. The sticky ends are combined
together and ligated by DNA ligase.

Question #15:
An operon (operator gene) is a set of genes adjacent to each other that transcribe a
mRNA that produces several structural proteins.
Operons are either On or Off
Transcription of the operator genes begin upstream at the promoter region.
Operator region is a short segment next to a promoter sequence.
Binding of repressors protein to the operator region inhibits transcription by inhibiting
binding of RNA polymerase to the promoter region.

Question #16:
Lactose acts as an inducer and binds to repressor
Attachment of lactose inactivates the repressor and it cannot bind to the
operator
Hence, RNA polymerase can bind to the promoter and transcribe proteins
and enzymes that are responsible for lactose metabolism.
Note: Lactose operon requires absence of glucose for induction.

8. Biochemistry Supplement, Northwestern Medical Review, 2007
Question #17:
Co-repressor bind to the repressor
Binding of the co-repressor activates the repressors, and the repressor represses the
operons function.
Tryptophan is a co-repressor and activates the repressor
Hence, in the presence of tryptophan no new tryptophan will be synthesized

Question #19:
Histones are only found in eukaryotes and act as non-
specific repressors of transcription.

Question #20:
Methotrexate causes genes amplification and
formation of numerous copies of dihydrofolate
reductase enzyme formation.

Question #21:
The hybridization technique takes advantage of
the ability of DNA to make complimentary stands
with DNA and RNA sequences.
Labeled DNA or RNA is used as probes to
identify homologous sequences of DNA or RNA

Question # 22:
Make a match using the following options?
1. Gel electrophoresis [D]
2. Southern blot [C]
3. Northern Blot [B]
4. Western Blot [A]
5. Hybridization [E]
6. Restriction Endonuclease [F]
A. Proteins probed with antibodies binding specific proteins
B. Radioactive DNA probe hybridizing with RNA on nitrocellulose gel blot
C. Radioactive DNA probe hybridizing with DNA on nitrocellulose gel blot
D. Separating DNA chains with variable length
E. Identifying a single DNA strand with complimentary sequence
F. Recognition of short sequences in DNA and cleaving both strands within
that segment
G. Radioactive DNA probe hybridizing with dextrans on nitrocellulose gel blot
G is nonsense!


Question #23:
ddNTP (i.e. ddATP, ddGTP, ddCTP, ddTTP)
molecules differ from deoxynucleotides by the
having a hydrogen atom attached to the 3' carbon
rather than an OH group. Hence, ddNTPs do not
have a 3 hydroxyl group.
3'-OH (hydroxyl) group is necessary for continued
5'-to-3' DNA synthesis. Their incorporation into
the growing chain terminates polymerization
process.
Dideoxynucleotides are used in molecular biology
for Sanger-type DNA sequencing, and also as
anti-retroviral drugs for the treatment of HIV
infection (e.g. AZT)

Question # 24: