Campbell, Farrell - 7th edition - Biochemistry

Review 1: Nucleic Acids

CONCEPT: NUCLEIC ACIDS

●Nucleic acids are one of the four major biological macromolecules that compose all cells.
●One of the major functions of nucleic acids is to store/encode hereditary information.
□ __________,
DNA __________,
RNA & __________ are examples of nucleic acids.
●Nucleic acids are polymers of nucleotide monomers & have directionality (5’ end & a 3’ end).
EXAMPLE:
5’ 3’

Nucleotide Monomers Nucleic Acid Polymer

The Nucleotide
●Nucleotide monomer consists of at least one phosphate
_________ group, a _______
5C sugar & a _______________
nitrogenous _____.
base
EXAMPLE: Comparing DNA/RNA Nucleotides Nitrogenous
Base
Nitrogenous
Phosphate group Phosphate group
Base

Nucleotide _________
____________________ RNA Nucleotide _________
____________________ DNA
Deoxyribose Sugar
Ribose Sugar

Nitrogenous Bases & Base-Pairing

●DNA & RNA differ in several ways, including the nucleotides they consist of.
●________
5 different nitrogenous bases are grouped as pyrimidines or purines.
●The nitrogenous bases of a nucleic acid pair via __________
hydrogen bonds according to Watson & Crick base-pairing rules.

EXAMPLE:

Pie
Cytosine (C) Thymine (T) Uracil (U) Adenine (A) Guanine (G)

Pyrimidines Purines
DNA Comparing DNA & RNA vs.
Base-Pairing
5' 3' Strands Usually Double-Stranded Usually ________-Stranded
Single

A T Usual Structure/Shape _________-Helix

Double Varies greatly

________________
Desoxyribose Ribose
Pentose Sugar
G C (Lacks Oxygen)
Strands Oriented in A, ___,
U C, G
A, T, C, G
Opposite Directions: Nitrogenous Bases (Uses U’s instead of T’s)
______-__________
Anti paralleles -Encode Hereditary Info
Function -Encode Hereditary Info
-Catalytic function: Ribozymes
5’ → 3’
Directionality of Strand (______
Anti -_________
Paraleles Strands)

# of Nucleotides ______________
3 billion
Hundreds to Thousands
3' 5' in a Typical Molecule (Depends on Organism) Page 7
Campbell, Farrell - 7th edition - Biochemistry
Review 1: Nucleic Acids

CONCEPT: NUCLEIC ACIDS

PRACTICE: A) What is the assumed directionality of the nucleotide sequence below? Label the ends of the molecule.
A C G T C T A A A C G G C T A
5' 3'

B) Is the sequence above from a DNA or RNA molecule? How do you know?
From a DNA molecule, because it has a nitrogenous base named Thymine, wich only exists on DNA molecules

C) Write the complementary sequence to the strand below (include the directionality).
5'
A C G T C T A A A C G G C T A 3'
5' 3'
T A G C C G T T T A G A C G T

PRACTICE: Which of the following nitrogenous bases is a purine?

a) Cytosine
b) Uracil
c) Thymine
d) Guanine

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Campbell, Farrell - 7th edition - Biochemistry Clutch
Review 1: Nucleic Acids

CONCEPT: NUCLEIC ACIDS

● Nucleic acids are made of three components:

□ Phosphate group

□
Ribose
Desoxyribose

Nitrogenous bases
A G C U T
● Nucleic acids are polymers of _____________________________
nucleotides

□ Nucleosides lack a phosphate groups, nucleotides have one

□ Nucleotide triphosphates are used to synthesize nucleic acids because they provide the energy for the reaction

□ Nucleotides use a unique carbon numbering system

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Campbell, Farrell - 7th edition - Biochemistry Clutch
Review 1: Nucleic Acids

CONCEPT: NUCLEIC ACIDS

PHOSPHODIESTHER
● Nucleotides are connected by ___________________________________ bonds.
● The individual strands of DNA are _________________________________
antiparaleles to each other.
● RNA is less stable than DNA at high pH because of it’s 2’ hydroxyl group
● Nucleotides, and nucleic acids, have a maximum light absorption at 260 nm (proteins at 280 nm)

● The two strands of DNA are complementary due to the specificity of base pairing.
□ Strands of DNA with a higher GC composition are harder to separate, and have a higher melting temperature

PRACTICE: What percentage of DNA is made of purines? Pyrimadines?

50 - 50

PRACTICE: If a piece of double-stranded DNA is made of 35% A and 15% C, what percent of its composition is T and G?

35 T and 15 G

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Campbell, Farrell - 7th edition - Biochemistry Clutch
Review 1: Nucleic Acids

CONCEPT: NUCLEIC ACIDS

● Chargaff’s rules – a series a rules about the composition of DNA, used by Watson and Crick to determine DNA structure
□ In a double stranded molecule of DNA, %A=%T and %G=%C, likewise %A+%G=%T+%C
● Watson and Crick also used the X-ray crystallography image from Rosalind Franklin
□ This image showed the structure to be simple, and have substituents 3.4 Å apart

double helice
● The structure of DNA is called a ______________________________.
□ It contains a major and minor groove, allowing degrees of access to the nucelobases
□ Proteins bind DNA via H-bonds with their R groups, and generally use either the major groove

● The structural bonds of DNA are all single bonds, so the molecule is quite flexible
□ Nucleotides can have two conformations, but most DNA is in the anti conformation

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Campbell, Farrell - 7th edition - Biochemistry Clutch
Review 1: Nucleic Acids

CONCEPT: NUCLEIC ACIDS

● The double helix of nucleic acids can appear in three forms: A, B, and Z form
□ A and B forms are both right-handed helices, but A is more squished that B
- Double stranded RNA takes the A form
- Most DNA is found in the B form
□ Z form is a left-handed helix
- Z form is found near regulatory sequences
□ There is a hole through the A form, but B and Z are filled in
● B-Z junctions – areas where the helix switched between the B and Z forms
□ The nucleotides flip out from the strands, switching helix direction
- This shape makes regulatory sequences easy for the cell to identify

● Single strands of DNA are held together as double-stranded DNA(dsDNA) by H-bonds and hydrophobic stacking forces
□ The stacking forces result from the fact that the relatively hydrophobic bases are stacked within the B form helix

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