Chapter 4 objectives Flashcards
nucleotide
Monomers that consist of a sugar, phosphate group and nitrogenous base to form a nucleic acid.
nitrogenous bases
The nitrogenous base is a nitrogen containing base. The bases in ribonucleotides are:
Cystosine
Guanine
Adenine
Thymine (DNA only)
Uracil (RNA only)
They are grouped in two categories - pyrimidine and purine.
pyrimidine
A structural group of a nitrogenous base. Includes the following molecules:
Cystosine
Thymine (DNA)
Uracil (RNA)
They are the smaller of the two structural groups.
purine
A structural group of the nitrogenous base. Includes the following molecules:
Guanine
Adenine
Purines are larger than pyramidines
Nucleoside
In a nucleic acid - a purine or pyrimidine base covalently linked to a ribose or deoxyribose sugar molecule
What are the three components of a nucleotide?
- A phosphate group
- A sugar
- A nitrogenous base
What is a sugar?
An organic compound with a carbonyl group (>C=O) and several hydroxyl groups (>C=O)
What are the two 5-carbon sugars that contribute to the structure of a nucleotide?
ribose, deoxyribose
Where does the phosphate group attach to the sugar?
The phosphate group in a nucleotide attaches to the 5’ (5 prime) carbon of the sugar.
Ribose
The sugar in the ribonucleotide. Ribose has an Hydroxyl (–OH) group on the 2’ carbon.
(5')
---- CH2 O (N)
I / \ I
(4') C / \ C (1')
I \ H H /
H C\ \_\_\_\_\_\_/C
(3') I I (2')
OH OH
Deoxyribose
The sugar in the deoxyribonucleotide. Deoxyribose has a Hydrogen (H) instead of Hydroxyl (–OH) bonded to the 2’ Carbon. Hint: Deoxy means lacking oxygen.
The sugar in the ribonucleotide. Ribose has an -OH (Hydroxyl) group on the 2’ carbon.
The sugar in the ribonucleotide. Ribose has an Hydroxyl (–OH) group on the 2’ carbon.
(5')
---- CH2 O (N)
I / \ I
(4') C / \ C (1')
I \ H H /
H C\ \_\_\_\_\_\_/C
(3') I I (2')
OH H
What is the 2’ deoxyribose?
Hydrogen
How do nucleotides form nucleic acids?
Through polymerization that involves the formation of a bond between the phosphate group of one nucleotide and the hydroxyl group at the 3’ of the sugar in another nucleotide. This is a condensation reaction that is called phosphodiester linkage.
What is the backbone of a nucleic acid?
Sugar-phosphate form the backbone that is directional in the 5’ –> 3’ direction. One strand of DNA will have an unlinked 5’ carbon (top) and an unlinked 3’ carbon (bottom)
Is polymerization endergonic or exergonic? Why?
The process is endergonic (Nonsponstaneous) due the attached phosphate groups that make the molecules phosphorylated. The phosphates groups raise the potential energy of substrate molecules to make an otherwise energonic reaction possible. These phosphorylated nucleotides are called “activated”
What are antiparallel strands?
Two strands of DNA that run in opposite directions, with one running in a 5’ –> 3’ direction and the other oriented 3’–>5’. They are twisted together to form a double helix with the sugar-phosphate backbone forming an outer coil. The nitrogenous bases are on the inside and form purine-pyrimidine pairs.
What is complementary base pairing?
The nitrogenous bases form purine-pyrimidine pairs.
Adenine - Thymine (A-T) - 2 hydrogen bonds
Guanine - Cystocine (G-C) - 3 hydrogen bonds
This is called complementary because these pairs form hydrogen bonds that form a tightly packed, hydrophobic interior. This is also called the Watson-Crick pairing.
Secondary Structure of DNA
DNA has only two structres. Its secondary structure is the two antiparallel strands that twist into a double helix that is stabilized by hydrogen bonding between complementary bases (A-T and G-C) and by hydrophobic interactions.
Template Strand
The original strand of DNA
Complementary Strand
The newly synthesized strand of DNA (or RNA) that has a base sequence complementary to that of the template strand
How does the DNA make a copy of itself by complementary base pairing?
- The double helix strands separate due to heating or enzyme-catalyze reactions that break the hydrogen bonds.
2 a. The free deoxyribonucleotides form hydrogen bonds with complementary bases on the original strand of DNA (template strand) on the 3’ end. - b The sugar phosphate groups form phosphodiester linkages to create a complementary strand. (5’–>3’ directionality)
- Complementary base paring allows each strand of a DNA double helix to be copied exactly, producing two daugther molecules
What are the two key functions of a self-replicating molecule?
- Carry information
2. Perform Catalysis
How many structures does RNA have?
Four!
What is the primary structure of RNA?
same for DNA
The sugar-phosphate backbone formed by phosphodiester linkages and a sequence of four types of nitrogenous bases (AUGC)
What are the four nitrogenous bases in RNA?
Adenine - Uracil
Cystosine - Guanine
What sugar molecule is in RNA? What is different about it?
Ribose
It is much more reactive due to the hydroxyl group (–OH) on the 2’ carbon. This group can participate in reactions that tear the polymer apart, making RNA much less stable than DNA.
What is the secondary structure of RNA?
The purine and pyrimidine bases in RNA undergo hydrogen bonding with complementary bases on the SAME strand.
This forms a hair pin when a single strand folds back on itself to form a double helix stem and loop.
Tertiary structure of RNA
Folds that form distinctive three dimensional face
Quartenary Structure
Associations between several RNA molecules.
Ribozymes
Any RNA molecule that can act as a catalyst to speed up a chemical reaction
Transcription
The nucleotide sequence in on strand of DNA is used to construct a complementary RNA sequence.
Translation
The synthesis of proteins under the direction of mRNA (messenger RNA).
What is the central dogma?
DNA -> RNA -> Protein
What does ATP become?
ATP -> AMP + PP
NMP
Nucleoside mono phosphate
NDP
nucleoside diphosphate
NTP
Nucleoside triphosphate
What powers nucleic acid polymerization?
Through the condensation of phosphates
2 NTP –> dimer + H2O + PPi
Phosphodiester reaction
Endergonic and less entropy
