CHAPTER 7: DNA and RNA: Instructions for Life summary

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?

1. explained how DNA was replicated
2. explained how it was stored in the nucleus
3. 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