Session 4 Packet - Wednesday, 06-05-2019 - Main - Carlos Ortiz

MCAT PREPARATION – FALL 2018 The road to success is dotted
Course: MCAT PREPARATION Delivered: Wednesday, June 5, 2019 with many tempting parking
Instructor: Mr. Carlos Ortiz TBCB: Next Session spaces.
Student: CARLOS ORTIZ/VIC POPP ETC: 120-180 Will Rogers
# of Elements: 137
Topics: BIOLOGY and CHEMISTRY
Time: Will vary: Anywhere from 120-180 minutes
TBCB: NEXT SESSION
Notes/Instructions: PrePacket 4.1 Review
Check these off as we
complete them. BIOLOGICAL AND BIOCHEMICAL FOUNDATIONS OF
LIVING SYSTEMS: Biochemistry of Nucleic Acids
M4
MCAT PREPARATION – BIOLOGY & BIOCHEMISTRY | CHEMISTRY

Mr. Carlos Ortiz | VICTORIA POPP PLEASE CONTINUE ON THE NEXT PAGE
Copyright © 2019 Carlos Ortiz | 305.785.5005 | www.mrcarlosortiz.com | carlos@mrcarlosortiz.com page 1 of 13
WORD BANK a “multiplier” indicates the word is used THAT MANY TIMES throughout the page.
nitrogenous tensile active pentose five enhances
polymerization polar (x2) dehydration Condensation nitrogenous phosphate
BIOLOGICAL AND BIOCHEMICAL 2 Nucleic Acids vs. Proteins

FOUNDATIONS OF LIVING
Unlike proteins, nucleic acids contain no
SYSTEMS: Biochemistry of
Nucleic Acids A. H
Biological Molecules: Nucleotides B. O
Every nucleotide is made up of THREE BASIC C. S

PARTS:
D. N
1) A five-carbon sugar; also known as a E. C
pentose.
3 Dehydration Synthesis
2) A base that is replete with nitrogen;
hence, it is called a nitrogenous base.
3) A charged (and therefore polar) group
containing P and O → a phosphate
group.
RIBOSE DEOXYRIBOSE
In the reaction shown above, what is the
specific product formed?
A. a 2’ nucleotide
B. a 5’ nucleoside
C. a 2’ nucleoside
Figure 1: The nucleic acid pentoses
D. a 2 nucleotide
NB: Vic, take note that the carbon atoms are E. a 2 nucleoside
numbered with “prime” notation: 1’ = 1 prime.
This is to distinguish these C atoms from those Condensation polymers form more slowly
on the nitrogenous base of a nucleotide. The than addition polymers, often requiring heat,
pentoses differ at the 2’ location. and they are generally lower in molecular
weight. The terminal functional groups on a
1 Nucleotides chain remain active, so that groups of
shorter chains combine into longer chains in
a In the context of nucleic acids, the late stages of polymerization.
A. amino acids are comparable in MW The presence of polar functional groups on
` B. ribose and pentose are the sole sugar
the chains often enhances chain-chain
components of any nucleotide monomer attractions – particularly if these involve
hydrogen bonding – and thereby crystallinity
C. all nucleic acid strands can serve as
and tensile strength.
templates for mRNA synthesis
D. ribose and deoxyribose constitute the sole NB: Victoria, condensation polymerization is
sugar components of all nucleotides also commonly referred to as dehydration
synthesis because WATER IS LOST as the
E. all of the above POLYMER is MADE or SYNTHESIZED (or even
ELONGATED) in the process.

carbon ribose pentose (x2) 2’
nucleoside nitrogenous deoxyribose phosphoric
RIBOSE DEOXYRIBOSE 6 Naming a Product

In the reaction shown above, a generic
NB: Ms. Popp, take note that the carbon atoms nitrogenous base is being combined with a
are numbered with “prime” notation: 1’ = 1 pentose (specifically deoxyribose) to create
prime. This is to distinguish these C atoms from a nucleoside which is LATER joined with
those on the nitrogenous base of a nucleotide. phosphoric acid.
The pentoses differ at the 2’ location.
If the nitrogenous base is adenine (shown
below in two forms), what is the name of the
4 Nucleic Acid Sugars resulting product (without the phosphoric
a acid)?
ADENINE
What is the most appropriate name for the

pentose shown above? →
A. 2’-hydrose
` B. 2-deoxyribose
Figure 2: One of three purines: adenine
C. 2’-ribose
D. 2’-deoxyribose A. 2’-deoxyadenosine
E. any of the above is appropriate B. 2’-adenine

C. 2-adenosine
Vic, recall that the C atoms of the pentose
(either ribose or deoxyribose) are labeled D. 2’-deoxyadenine
with the prime notation to distinguish them E. 6’-deoxyadenosine
from the C atoms of the nitrogenous base.
7 Nucleotides
5 Nucleic Acid Pentoses
Ribose is a 5-carbon sugar (a.k.a. as a
pentose) that
A. is exclusively found in DNA nucleotides

B. generates acidic aqueous solutions
C. is exclusively found in RNA nucleotides What are the two pieces of evidence that the
molecule above is a ribonucleotide?
D. generates basic aqueous solutions
The presence of the OH group at the 2’ C atom
E. none of the above
of the pentose and the attachment of the three
phosphate groups to the 5’ C atom.

carbonyl ester OH
H oxoacid nucleophilic
RIBOSE DEOXYRIBOSE 11 The Acyl Group

The acyl group results from the removal of
the OH group of an oxoacid with a
central C atom. The acyl group, then, is
represented by
A. R-C-OH
8 What’s needed? ` B. R-C-R’
a Nucleosides are solely comprised of C. R-C(OH)=O
A. a sugar (a hexose) bonded to a nitrogenous D. R-C=O

base
E. any of the above is appropriate
` B. a sugar (a pentose) bonded to a
nitrogenous base ACYL GROUP
C. a nitrogenous base bonded to a phosphoric
acid group
D. a nitrogenous base bonded to another
nitrogenous base
E. a sugar (a pentose) bonded to a Figure 3: The acyl group
nitrogenous base and also to a phosphoric
acid group The acyl group just above contains a C atom
double bonded to an O atom (this C=O is the
9 Nucleotides familiar functional group known as the
In nucleotides, one or more phosphate groups
carbonyl) as well to some R group.
are bonded to
12 Nucleotide Bond Types
A. the 9-C atom of the nitrogenous base
B. the 3-C atom of the pentose
C. the 5’-C atom of the ribose or the 3’-C

atom of the deoxyribose The figure just above shows an acyl group
D. the 5’-C atom of the deoxyribose or the 3’- (R2-C(O)=O) attached to another R group (R1)
C atom of the ribose via an O atom. This is called a(n)
E. the 5-C atom of the ribose or the 3-C atom
A. phosphodiester
of the deoxyribose
B. thioester
10 Naming a Product
C. ester
The DNA nucleotide containing cytosine is
D. carboester
A. 2’-deoxycytidine-5’-monophosphate E. none of the above
B. 2’-deoxycytidine-3’-monophosphate NB: Vic, if a carboxylic acid ionizes (by losing
C. 2’-cytidine-5’-monophosphate its acidic H atom), the resulting conjugate base
possesses a very nucleophilic O atom. If this
D. 2’-cytidine-3’-monophosphate nucleophilic O atom attacks and bonds to
E. 2’-deoxycytosine-5’-monophosphate another C atom of some R group, an ester is
formed.
nucleotides 5’ polarity phosphate phosphodiester nucleoside
ribose heterocyclic polymer backbone phosphorylation nucleotide
13 Nucleotide Bond Types Here we see a ribose

sugar with a single
phosphate group
located at the 5’-C.
The sugar ring is
The figure just above shows an acyl group heterocyclic because
(R2-C(O)=O) attached to another R group (R1) it contains different
via an S atom. This is called a(n) atoms. Once all three
components come
A. phosphodiester together (ribose +
B. thioester base → that’s our
nucleoside … and
C. ester Figure 4: A sugar- then the phosphate
phosphate and its
D. carboester group, we have a full
“brother” nucleotide
nucleotide.
E. none of the above
14 The Phosphoryl Group 15 The Nitrogenous Base “Connection”

When a phosphate group is added to a The nitrogenous base bonds to the
molecule, the step is called a ___-C atom via a(n) ____________ bond.
phosphorylation. The resulting ADDED
group is a phosphoryl group and it is A. 1’, N-glycosidic
necessarily bonded to the new molecule B. 2’, N-glycosidic
via an O atom. Here’s the result of a
phosphorylation of R1: C. 2’, C-glycosidic
D. 1’, C-glycosidic
E. 1, N-glycosidic
16 Linkages
Which of the following is most accurate
regarding phosphodiester bonds?
The bond in this result is called a(n)
A. They link the 4’-C atom of one pentose to
A. ester the 3’-C atom of another pentose
` B. thioester B. They always exist in DNA and sometimes
exist in RNA
C. phosphoryl bond
C. They link the 3’-C atom of one pentose to
D. phosphoester the 5’-C atom of another pentose
E. phosphodiester D. They are specialized examples of hydrogen
bonds
NB: Victoria, the phosphoDIester bonds are E. They link P to three other atoms via an O
the primary LINKS between adjacent “bridge”
nucleotides on one nucleic acid strand. This
network of “support” links in a nucleic acid strand Vic, at its most basic, a nucleic acid is simply a
is often called the “sugar-phosphate backbone” polymer of nucleotides held together by
of the strand and it gives the strand polarity. phosphodiester bonds.

Figure 5: A generic nucleotide structure and the nitrogenous bases.
17 Some Differences 19 Chemical differences

Which of the following purines is found in DNA? Describe the chemical differences between
a ribonucleoside triphosphate (e.g. ATP)
A. I and a deoxyribonucleoside monophosphate
(dTMP).
B. G
C. T The ribonucleoside triphosphate has an

-OH group at the 2’-C atom which is
D. C missing in the deoxyribonucleoside
E. both A and B monophosphate. The absence of the -OH
group in the deoxyribonucleoside
monophosphate makes it resistant to
18 Drawing
HYDROLYSIS compared to the
Draw adenosine (with the ribose pentose) ribonucleoside.
and then show where a single PHOSPHATE
group would bond (also name the BONDS Also, the ribonucleoside triphosphate
that connect the BASE and PHOSPHATE has THREE PHOSPHATE GROUPS (at either
GROUPS to the ribose) the 3’- or 5’-C atom) whereas the
deoxyribonucleoside monophosphate
only has ONE PHOSPHATE GROUP (at
either the 3’- or 5’-C atom).

20 Some Nucleotide Roles
Consider each of the following NUCLEOTIDE STRUCTURES. Fill in the blanks for each
description.
ATP (or adenosine triphosphate): a high energy molecule that
serves as the cell’s PRIMARY energy currency. It is responsible for
mediating practically ALL metabolic processes hosted by the cell.
GTP (or guanosine triphosphate): another high energy

molecule that serves as the PRIMARY source of energy for
nucleotide synthesis as well as protein synthesis.
CTP (or cytidine triphosphate): another high energy molecule

that serves as the PRIMARY source of energy for lipid synthesis.
UTP (or uridine triphosphate): another high energy molecule

that serves as the PRIMARY source of energy for carbohydrate
metabolism → one key product is an activated sugar such as
UDP-glucose.
UDP-glucose (or uridine diphosphate glucose):

this is an activated sugar that donates a
glucosyl unit to a growing chain of glycogen. This
molecule is most likely found I what type of cell? A
hepatocyte.
NAD (or nicotinamide adenine dinucleotide):

this is a famous co-factor or cosubstrate; as
we’ve seen, it is involved in several key redox
reactions AS AN ELECTRON-CARRIER.

within endonucleases (x2)
palindromic bacteria
21 Manipulating Nucleic Acids

Which of the following is useful in
“cleaving” nucleic acids at specific
sequences?
A. phosphodiester hydrolases
B. restriction enzymes from bacteria
C. Okazaki fragments
D. agarose gel electrophoresis (AGE)
E. restriction enzymes from humans
Figure 6: Some restriction enzyme digestions
and the resulting “digested” DNA products.
22 DNA “Digestion”
Nonspecific digestion of DNA leads to 24 Specificity of Site Cut & Product Formed
fragments with Restriction enzymes (or endonucleases)
predictably cleave DNA at palindromic
A. defined length sequences (reads the same FORWARD
` B. high symmetry and BACKWARD). In the top 2 “digestions”
shown above in Figure 5, the cuts result
C. at least 30,000 base bairs
in staggered ds DNA fragments with either
D. both indeterminate length and symmetry 5’ or 3’ protruding ends. These are called
E. none of the above is accurate A. underhangs
B. smooth ends
NB: Restriction enzymes are DNA-cutting
enzymes found in bacteria (and harvested from C. sticky ends
them for use). Because they cut within the
molecule, they are often called restriction D. blunt ends
endonucleases.
E. cut ends
23 Sequencing DNA 25 Specificity of Site Cut & Product Formed
To sequence DNA, it is first necessary to
In the third “digestions” shown above in
Figure 6, the cut results in blunt ends. In this
A. label its nucleotides with radionuclides case, the cut shows that the endonuclease
` B. replicate it via “replication”
A. always cuts to create staggered ends
C. transcribe it via “transcription”
B. only cuts between A and T on a strand
D. cut it into smaller fragments
C. can cut straight through a double strand
E. separate it into Okazaki fragments
D. always cuts to create sticky ends
True or False E. is not specific where it cuts

T The pancreas contains DNA-digesting
True or False
enzymes that cut DNA at random
locations producing a heterogeneous F The idea behind the use of
collection of fragments of varying sizes. endonucleases is that the smaller
fragments created are easier to copy.
After treatment with a restriction endonuclease, DNA fragments can be separated on an
agarose gel via electrophoresis. The advantage of this method is that it separates
molecules on the basis of
A. their size in the presence of sodium dodecyl sulphate (SDS)
B. their size without the need for SDS
C. their charge
D. their polarity
E. their degree of hydrogen bonding

Why is AGE electrophoresis the preferred SEPARATION method for dsDNA fragments?
Because since it separates without the use of SDS (which denatures the DNA), the dsDNA structure is
preserved.
Figure 7: The replication of DNA
Above we see DNA polymerase in action:

➔ Firstly, its primary function is to convert ssDNA into dsDNA.
Where does the ssDNA originate? It can actually be generated by heating dsDNA samples
to break up the hydrogen-bonding that holds the strands together.
➔ The DNA polymerase SPECIFICALLY elongates the new strand by first adding a short, 20-40
base-pair nucleotide sequence that is complementary to the 3’ end of the strand to be
copied. This short “starting” sequence is the primer and the nascent (or new) chain does
require priming of its synthesis.
➔ Each new deoxyribonucleotide comes in with THREE phosphates but loses 2 of them as PPi
which is inorganic phosphate. The phosphate that remains forms phosphodiester
bonds between adjacent nucleotides on the growing strand.

To the left in Figure 8 we see a modified
nucleotide called a dideoxy nucleotide. The
base can be any of those found in DNA: A, G,
C, or T.
Why is the absence of an -OH group at the 3’-

C atom of any importance?
Because with replication would HALT if such
a dideoxy nucleotide were added to a
Figure 8: A dideoxy nucleotide growing strand.
28 A Method
If DNA is incubated with DNA polymerase, a complementary primer, deoxynucleoside triphosphates
(dNTPs) and dideoxynucleoside triphosphates (ddNTPs), chain growth is terminated the moment a
ddNTP is incorporated into a growing complementary strand. This is called the
A. Salk method
B. Sanger method
C. Watson-Crick method
D. Franklin-Wilkinson method
E. Frederick method
Victoria, the Sanger method consistently generates DNA fragment of predictable size that can
then be separated using the non-denaturing AGE setup. These truncated DNA fragments that
differ by ONE NUCLEOTIDE
29 The Sanger Method

Why is chain growth halted when a ddNTP is incorporated into a growing strand?
A. The presence of an -OH group at the 3’-C prevents further nucleotide additions
B. The absence of an -OH group at the 3’-C prevents further nucleotide additions
C. The absence of an -OH group at the 2’-C prevents further nucleotide additions
D. The absence of an -OH group at the 5’-C prevents further nucleotide additions
E. none of the above correctly explains why chain growth is halted.
30 Chain Terminator Method

The Sanger method is a type of chain-terminator method. In a more modern version of chain-
termination, electrophoresis is conducted in a capillary tube (called capillary electrophoresis or
simply CE). As the negatively charged DNA fragments are “sifted” through the electrolyte gel – it is
hydroxyethyl cellulose instead of agarose used in AGE – used in CE, they exit the tube where a LASER
detects the ddNTP that was last attached. A series of colored peaks are generated to create a
chromatogram. Check out this piece of a chromatogram on the left – use it to determine the
sequence of DNA indicated by the piece on the right:
GCTCCAGCT

Phosphoanhydride heating Inorganic Phosphoester Hydrogen phosphoryl
phosphodiester biphosphate phosphate Phosphodiester annealing nucleotides
31 DNA Double Helix

The DNA double-helix can adopt all of the following conformations except:
A. A-DNA
B. C-DNA
C. Z-DNA
D. B-DNA
E. none of these is actually possible.
32 DNA and SOME IMPORTANT GROUPS and BONDS

DNA can be denatured by heating and renatured by annealing. DNA consists of two strands; each
strand is a biopolymer of nucleotides held together by phosphodiester bonds.
Here we see four different species containing phosphorus. From top to

bottom we have the:
(i) Inorganic phosphate group: PO43-
(ii) Hydrogen phosphate group: HPO42- (also known as

biphosphate)
(iii) The phosphoryl group: R-O-PO32-
(iv) The phosphate group: R-PO42-
These are important to know so that you can identify OTHER BONDS
in which they appear:
Phosphoester Bond Phosphodiester Bond
Phosphoanhydride Bond ATP Bonds

PRACTICE TEST QUESTION 1
PRACTICE TEST QUESTION 2

Figure 9: A schematic representation of RNA
Figure 10: A partial rendition of the Pentose Phosphate Pathway

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MCAT PREPARATION – FALL 2018 The road to success is dotted

MCAT PREPARATION – BIOLOGY & BIOCHEMISTRY | CHEMISTRY

BIOLOGICAL AND BIOCHEMICAL 2 Nucleic Acids vs. Proteins

Biological Molecules: Nucleotides B. O

Every nucleotide is made up of THREE BASIC C. S

MCAT PREPARATION – BIOLOGY & BIOCHEMISTRY | CHEMISTRY

RIBOSE DEOXYRIBOSE 6 Naming a Product

Figure 1: The nucleic acid pentoses

What is the most appropriate name for the

E. any of the above is appropriate B. 2’-adenine

A. is exclusively found in DNA nucleotides

MCAT PREPARATION – BIOLOGY & BIOCHEMISTRY | CHEMISTRY

RIBOSE DEOXYRIBOSE 11 The Acyl Group

A. a sugar (a hexose) bonded to a nitrogenous D. R-C=O

C. the 5’-C atom of the ribose or the 3’-C

13 Nucleotide Bond Types Here we see a ribose

14 The Phosphoryl Group 15 The Nitrogenous Base “Connection”

MCAT PREPARATION – BIOLOGY & BIOCHEMISTRY | CHEMISTRY

17 Some Differences 19 Chemical differences

C. T The ribonucleoside triphosphate has an

MCAT PREPARATION – BIOLOGY & BIOCHEMISTRY | CHEMISTRY

GTP (or guanosine triphosphate): another high energy

CTP (or cytidine triphosphate): another high energy molecule

UTP (or uridine triphosphate): another high energy molecule

UDP-glucose (or uridine diphosphate glucose):

NAD (or nicotinamide adenine dinucleotide):

MCAT PREPARATION – BIOLOGY & BIOCHEMISTRY | CHEMISTRY

21 Manipulating Nucleic Acids

B. restriction enzymes from bacteria

True or False E. is not specific where it cuts

A. their size in the presence of sodium dodecyl sulphate (SDS)

B. their size without the need for SDS

27 Manipulating Nucleic Acids

Figure 7: The replication of DNA

Above we see DNA polymerase in action:

MCAT PREPARATION – BIOLOGY & BIOCHEMISTRY | CHEMISTRY

Why is the absence of an -OH group at the 3’-

29 The Sanger Method

30 Chain Terminator Method

MCAT PREPARATION – BIOLOGY & BIOCHEMISTRY | CHEMISTRY

31 DNA Double Helix

32 DNA and SOME IMPORTANT GROUPS and BONDS

Here we see four different species containing phosphorus. From top to

(i) Inorganic phosphate group: PO43-

(ii) Hydrogen phosphate group: HPO42- (also known as

(iii) The phosphoryl group: R-O-PO32-

(iv) The phosphate group: R-PO42-

Phosphoester Bond Phosphodiester Bond

Phosphoanhydride Bond ATP Bonds

MCAT PREPARATION – BIOLOGY & BIOCHEMISTRY | CHEMISTRY

PRACTICE TEST QUESTION 2

MCAT PREPARATION – BIOLOGY & BIOCHEMISTRY | CHEMISTRY

Figure 10: A partial rendition of the Pentose Phosphate Pathway

MCAT PREPARATION – BIOLOGY & BIOCHEMISTRY | CHEMISTRY

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