Nucleic Acids
- The genetic code in cells is made up of DNA.
- DNA specifies the construction of proteins and the generation of RNA.
- DNA and RNA are nucleotide polymers.
Structure of nucleic acids
- Nucleic acids are information molecules in cells.
- Deoxyribonucleic acid is the most famous nucleic acid.
- Ribonucleic acid is less known and very important in cells.
- Nucleic acid polymers are made up of repeating nucleotide monomers.
- The structure of nucleic acid is complex because of the following reasons:
- The nucleic acid monomers are nucleotides. Nucleotides contain 3 components which makes them complicated before the formation of chains.
- Nucleic acids can be double-stranded or single-stranded. Joining nucleotides together leads to the formation of polynucleotide chains.
- RNA has a single polynucleotide chain while DNA has two double -helix polynucleotide chains.
Nucleotides
- Nucleotides are built from 3 components;
- Pentose sugar (5 carbon) – DNA has deoxyribose sugar while RNA has a ribose sugar
- Nitrogenous base – It is a double ring structure or a single ring structure containing many nitrogen atoms
- Phosphate group – Contains a phosphorus atom that is surrounded by atoms of oxygen. They have a negative charge which makes nucleic acids negative in charge.
Navigating nucleotides
- Carbon atoms on nucleotides are numbered using the following system:
- The sugar carbon atoms are numbered in a sequence from one to five.
- The numbered carbon atoms are awarded a prime designation resulting in 1′, 2′, 3′,4′ and 5′.
- Oneprime carbon is the first carbon.
- All other carbon atoms are numbered consecutively.
The naming of nucleotide bases
- There are five nitrogenous bases found on nucleotides. This includes the following:
- Adenine (A)
- Guanine (G)
- Cytosine (C)
- Thymine (T)
- Uracil(U)
- Nucleotides vary depending on the nitrogenous base attached to it.
- Nitrogenous bases fall into two categories:
- Pyrimidine- Contain a single ring structure and two nitrogen atoms.
- Purines- contain 2 fused rings with each ring containing two nitrogen atoms.
DNA and RNA synthesis
- Nucleotides are joined together by a condensation reaction.
- Repeating the process leads to the formation of a polynucleotide.
- A primary structure is formed by the type and number of nucleotides.
Differences between RNA and DNA
- DNA has thymine nitrogenous base while RNA has uracil base.
- DNA nucleotides have a deoxyribose sugar while RNA nucleotides have a ribose sugar.
- RNA is single-stranded while DNA is double-stranded.
The DNA double helix
- The DNA secondary structure is a double helix.
- Two chains of polynucleotides join to form a molecule with a twisted ladder-like shape.
- The sides of the ladder represent the Sugar phosphate backbones.
- Nitrogenous bases project from the sugar backbone.
- The two double helix chains are antiparallel.
- The antiparallel strands are joined by hydrogen bonds between bases.
- Adenine (A) joins to Thymine (T) by hydrogen bonds.
- Cytosine (C) joins Guanine (G) by hydrogen bonds.
The function of DNA and RNA
- Protein structure; the structure of proteins is determined by the DNA nucleotide sequence. Protein is generated from the process of transcription and translation.
- RNA structure; the structure of RNA id determined by the DNA nucleotide sequence. The process of transcription generates nucleotides required to build RNA.
- DNA regulation; it happens through the interaction of DNA binding proteins with special DNA regulatory sequences.
Types of RNA and their function
- Messenger RNA (mRNA) carries a protein structure code from DNA to ribosomes where proteins are generated.
- Transfer RNA (tRNA) decodes the mRNA message by allocating an amino acid that matches to the mRNA code.
- Ribosomal RNA (rRNA) is part of the structure of the ribosome.
Revision
What does RNA stand for?
ribonucleic acid
Central Dogma
DNA➞mRNA➞Protein
What is the structure of RNA?
Single strand of nucleotides, ribose sugar, uricil (instead of thymine)
Adenine pairs with…
Uracil
Uracil pairs with…
Adenine
Guanine pairs with…
Cytosine
Cytosine pairs with…
Guanine
Function of mRNA
carries genetic information from DNA in the nucleus to the cytosol in eukaryotic cells
Structure of mRNA
single uncoiled chain
Function of tRNA
amino acids bind to it and it carries the amino acid to the ribosome for protein synthesis
Shape of tRNA
single chain (about 80 nucleotides) in hairpin shape
How many varieties of tRNA are there?
45 varieties
What does mRNA stand for?
messenger RNA
What does tRNA stand for?
transfer RNA
What is the most abundant form of RNA?
rRNA
Function of rRNA
site of protein synthesis
Structure of rRNA
globular shape composed of rRNA and proteins
Transcription
transfer of genetic information from DNA to RNA
Where does transcription occur?
in the nucleus
Where does DNA separate?
at the beginning of the gene
What is the only enzyme used in transcription?
RNA Polymerase
What is RNA Polymerase’s role in transcription?
binds to promoter region and causes the DNA to seperate
Promoter Region
a nucleotide sequence that is at the beginning of a gene. it shows the RNA Polymerase where to bind
TATA Box
a series of only Thymine and Adenine on the DNA template
How many strands of DNA are used as a template?
One
Termination Signal
specific sequence of nucleotides on the DNA template that signals the end of transcription. it is marked by a series of Cytosine and Guanine followed by a series of Adenine
When does transcription stop?
when RNA Polymerase hits the termination signal
What does RNA Polymerase do when it reaches the termination signal?
it breaks off the DNA template and the mRNA
Can the DNA template be reused to make more mRNA?
yes
What is the product of transcription?
mRNA (called transcribes)
Where does mRNA go after transcription?
out of the nucleus (through nuclear pores) and into the cytosol where it will bind to a ribosome
Every 3 mRNA nucleotides is called a…
codon
Each codon codes for…
a particular amino acid
What determines the sequence of amino acids in the protein?
mRNA
How many codons are there?
64
AUG
the codon that signals the ribosome to start translation of mRNA
What does AUG code for?
methionine
What codons signal the ribosome to stop translation (stop codons)?
UAA, UAG, and UGA
Definition of Translation
the process of assembling polypeptides from the coded message of mRNA
What is needed for translation?
a ribosome and tRNA
What is the ribosome’s role in transcription?
holds mRNA in place
What is the tRNA’s role in transcription?
transports amino acids to mRNA
What is a ribosome composed of?
rRNA and proteins
How many binding sites are on a ribosome?
three
What is the function of the first binding site?
holds mRNA transcript in place
What is the function of the second and third binding sites?
allow tRNA to bind to them
What is tRNA composed of?
a region where the amino acid binds and the opposite side contains an anticodon
Anticodon
the complement of a codon triplet on mRNA
The assembly of the polypeptide chain begins when…
the ribosome attaches to the start codon (AUG)
As the ribosome moves along mRNA, each codon is paired with what?
an anticodon (which causes a specific sequence of amino acids)
What bond holds the amino acids together?
peptide bond
When does translation stop?
when the ribosome hits the stop codon (UGA, UAG, or UAA)
What happens when translation stops?
the ribosome releases the mRNA strand, and the polypeptide chain is released and sent to the golgi or used by the cell
Why does the polypeptide chain go to the golgi?
to become functional
What are 3 differences between DNA and RNA?
DNA is double helix shaped, has thymine, and has deoxyribose sugar. RNA is a single strand, has uracil, and has ribose sugar.
How many carbon are in ribose sugar?
five
In what direction does RNA polymerase work?
5′ to 3′
How is it possible that an error in transcription may not make a difference in the polypeptide chain?
it could code for the same amino acid
What happens to a protein made in a free ribosome?
it is used by the cell
What happens to a protein made in an attached ribosome?
it is transported out of the cell
Replication Fork / Replication Bubble
point on DNA where two chains separate
Helicase
separates strands of DNA by breaking hydrogen bonds between complimentary nitrogen bonds
DNA Polymerase
binds to each open chain at the RNA primer and adds complementary nucleotides to the template
Where is DNA polymerase found?
floating in nucleoplasm
What happens to DNA polymerase when it is done adding complementary nucleotides?
it falls off
RNA Polymerase
synthesizes a short “RNA primer” that marks the origin of replication
How long is the RNA Primer?
about 10 nucleotides long
Which way does DNA polymerase read DNA?
3′ to 5′
Which way does replication occur in DNA?
5′ to 3′
Leading Strand
DNA polymerase makes a new 5′ to 3′ strand moving towards replication fork (continuous)
Lagging Strand
DNA polymerase moves away from the replication fork adding new nucleotides in short segments
Okazaki Fragments
short segments of nucleotides that provide a building block for DNA synthesis of the lagging strand
DNA Ligase
joins Okazaki Fragments together in one long strand
Overhang
stretch of unpaired nucleotides in the end of a DNA molecule
Why is DNA Replication semiconservative?
each resulting DNA double helix retains one strand of the original DNA
DNA Proofreading
enzymes run down the new DNA and detect any abnormal shapes in the DNA due to non-complemantary base paring
How many errors are detected in DNA proofreading?
one error every 1 billion to 10 billion nucleotides
Adenine pairs with…
Thymine
Thymine pairs with…
adenine
Guanine pairs with…
cytosine
Cytosine pairs with…
guanine
A purine-purine bond creates a…
bulge in DNA strand
A pyrimidine-pyrimidine bond creates a…
pinch in DNA strand
Where is DNA located?
the nucleus
Watson and Crick
developers of a model for the structure of DNA (double helix)
Why is the double helix DNA shape accepted as correct?
- explained how DNA was replicated
- explained how it was stored in the nucleus
- functional shape/structure
What makes up the backbone of DNA?
phosphate and sugar
Rosilane Franklin
used x-ray diffraction to find the backbone of DNA
Purine
nitrogen base with two carbon rings
Pyrimidine
nitrogen base with one carbon ring
DNA Nucleotides
the repeating subunits of DNA
What are the parts of a nucleotide?
phosphate group, deoxyribose sugar, nitrogen bases
C5H10O4
chemical formula for deoxyribose sugar
What does DNA stand for?
Deoxyribonucleic Acid
The backbone of DNA is held together by…
covalent bonds
Base pairs are held together by…
hydrogen bonds
How many bonds are between adenine and thymine?
two hydrogen bonds
How many bonds are between guanine and cytosine?
three hydrogen bonds
Chargaff’s Rule
in a molecule of DNA, the % of adenine always equals the % of thymine and the % of guanine always equals the % of cytosine
When is DNA replicated in the cell cycle?
S phase of interphase
Template
the original strand of DNA that the new strand uses as a guide for replication
Chemical Formula for Ribose
C5H10O5
