DNA: The Blueprint of Life

● DNA is made up of repeated subunits of nucleotides. Each nucleotide has a

five-carbon sugar, a phosphate, and a nitrogenous base.
● The name of the pentagon-shaped sugar in DNA is deoxyribose. Hence, the name
deoxyribonucleic acid. Notice that the sugar is linked to two things: a phosphate
and a nitrogenous base. A nucleotide can have one of four different nitrogenous
bases:
○ adenine—a purine (double-ringed )
○ guanine—a purine (double-ringed )
○ cytosine—a pyrimidine (single-ringed )
○ thymine—a pyrimidine (single-ringed )
● Prokaryotes and eukaryotes can also contain plasmids, which are small
double-stranded, circular DNA molecules. The nucleotides can link up in a long
chain to form a single strand of DNA
● The nucleotides themselves are linked together by phosphate bonds between the
sugars and the phosphates. This is called the sugar-phosphate backbone of DNA
and it serves as a scaffold for the bases.

Two DNA Strands

● Each DNA molecule consists of two strands that wrap around each other to form a
long, twisted ladder called a double helix. The structure of DNA was brilliantly
deduced in 1953 by three scientists: Watson, Crick, and Franklin.
○ Adenine pairs up with thymine (A–T ) by forming two hydrogen bonds.
○ Cytosine pairs up with guanine (G–C ) by forming three hydrogen bonds.
● This predictable matching is is known as base pairing. The two strands are said to
be complementary.
○ The 5′ end has a phosphate group, and the 3′ end has an OH, or “hydroxyl,”
group.
○ The 5′ end of one strand is always opposite to the 3′ end of the other
strand. The strands are therefore said to be antiparallel.
● The DNA strands are linked by hydrogen bonds.

Genome Structure

● All of the DNA for a species is called its genome.

● Each separate chunk of DNA in a genome is called a chromosome.
● DNA is wrapped around proteins called histones, and then the histones are
bunched together in groups called a nucleosome.
● When the genetic material is in a loose form in the nucleus, it is called
euchromatin, and its genes are active, or available for transcription.
● When the genetic material is fully condensed into coils, it is called
heterochromatin, and its genes are generally inactive.
DNA Replication

● This copying of DNA is known as DNA replication.

○ The first step in replication is to unwind the double helix by breaking the
hydrogen bonds. This is accomplished by an enzyme called helicase.
○ The exposed DNA strands now form a y-shaped replication fork.
○ Each strand can serve as a template for the synthesis of another strand.
○ DNA replication begins at specific sites called origins of replication.
○ DNA helix twists and rotates during DNA replication, another class of
enzymes, called DNA topoisomerases, cuts, and rejoins the helix to prevent
tangling.
○ The enzyme that performs the actual addition of nucleotides to the freshly
built strand is DNA polymerase. But DNA polymerase can add nucleotides
only to the 3′ end of an existing strand.
○ To start off replication, an enzyme called RNA primase adds a short strand
of RNA nucleotides called an RNA primer.
○ After replication, the primer is degraded by enzymes and replaced with
DNA so that the final strand contains only DNA.
○ During DNA replication, one DNA strand is called the leading strand, and it
is made continuously. The nucleotides are steadily added one after the
other by DNA polymerase.
○ The other strand—the lagging strand—is made discontinuously. Unlike the
leading strand, the lagging strand is made in pieces of nucleotides known
as Okazaki fragments.
○ Nucleotides are added only in the 5′ to 3′ direction since nucleotides can be
added only to the 3′ end of the growing chain.
○ However, when the double-helix is “unzipped,” one of the two strands is
oriented in the opposite direction—3′ to 5′.
○ Because DNA polymerase doesn’t work in this direction, the strand needs
to be built in pieces.
○ The lagging strand is built in the opposite direction of the way the helix is
opening, so it can build only until it hits a previously built stretch. Once the
helix unwinds a bit more, it can build another Okazaki fragment.
○ These fragments are eventually linked together by the enzyme DNA ligase
to produce a continuous strand.
○ Finally, hydrogen bonds form between the new base pairs, leaving two
identical copies of the original DNA molecule.
○ When DNA is replicated, we don’t end up with two entirely new molecules.
○ Each new molecule has half of the original molecule. Because DNA
replicates in a way that conserves half of the original molecule in each of
the two new ones, it is said to be semiconservative.
○ The bits of unimportant DNA are at the ends of a molecule. These ends are
called telomeres.
○ Many enzymes and proteins are involved in DNA replication.
The ones you’ll need to know for the AP Biology Exam are DNA helicase, DNA
polymerase, DNA ligase, topoisomerase, and RNA primase:

● Helicase unwinds our double helix into two strands.

● DNA Polymerase adds nucleotides to an existing strand.
● Ligase brings together the Okazaki fragments.
● Topoisomerase cuts and rejoins the helix.
● RNA primase catalyzes the synthesis of RNA primers.

Central Dogma

● The first step of DNA expression is to turn it into RNA. The RNA is then sent out
into the cell and often gets turned into a protein.
● These proteins, in turn, regulate almost everything that occurs in the cell.
● The process of making an RNA from DNA is called transcription, and the process
of making a protein from an RNA is called translation.

DNA - mRNA via transcription - protein via translation

RNA

1.RNA is single-stranded.

2. The 5-carbon sugar in RNA is ribose instead of deoxyribose.

3. Uracil replaces thymine as adenine’s partner.

● Messenger RNA (mRNA) is a temporary RNA version of a DNA recipe that gets
sent to the ribosome.
● Ribosomal RNA (rRNA), makes up part of the ribosomes.
● Transfer RNA (tRNA) brings amino acids to the ribosomes. It brings the brings a
specific amino acid into place at the appropriate time by matching anticodons to
codons. It does by reading the message carried by the mRNA.

Transcription

● Transcription involves making an RNA copy of a bit of DNA code.

● In replication we end up with a complete copy of the cell’s DNA, in transcription
we end up with only a tiny specific section copied into an mRNA.
● Transcription begins at special sequences of the DNA strand called promoters.
● The official starting point is called the start site.
● We copy only one of the two DNA strands.
● The strand that serves as the template is known as the antisense strand.
● The other strand that lies dormant is the sense strand, or the coding strand.
● RNA polymerase builds RNA by adding nucleotides only to the 3′ side, therefore
building a new molecule from 5′ to 3′
RNA Processing

● The regions that express the code are exons.

● The noncoding regions in the mRNA are introns.
● Prokaryotes will transcribe a recipe that can be used to make several proteins.
This is called a polycistronic transcript.
● Eukaryotes tend to have one gene that gets transcribed to one mRNA and
translated into one protein. Our transcripts are monocistronic.
● The introns must be removed before the mRNA leaves the nucleus. This process,
called splicing, is accomplished by an RNA-protein complex called a spliceosome.
● In addition, a poly(A) tail is added to the 3′ end
● And, a 5′ GTP cap is added to the 5′ end.

Translation

● mRNA —> protein

● Process occurs on ribosomes in cytoplasm and on the rough endoplasmic
reticulum
● 3 nucleotides is called a codon. Each codon corresponds to a particular amino
acid.
● One end of the tRNA carries an amino acid. The other end, called an anticodon,
has three nitrogenous bases that can complementarily base pair with the codon in
the mRNA.
● The third position is said to experience wobble pairing. Things that don’t normally
bind will pair up, like guanine and uracil.
● Translation also involves three phases: initiation, elongation, and termination.

Initiation

● It begins when a ribosome attaches to the mRNA.

● Ribosomes contain three binding sites: an A site, a P site, and an E site. The
mRNA will shuffle through from A to P to E. As the mRNA codons are read, the
polypeptide will be built.
● The start codon is A–U–G, which codes for the amino acid methionine.
● The tRNA with the complementary anticodon, U– A–C, is methionine’s personal
shuttle; when the AUG is read on the mRNA, methionine is delivered to the
ribosome.

Elongation

● Addition of amino acids is called elongation and when many amino acids link up,
a polypeptide is formed.

Termination
The synthesis of a polypeptide is ended by stop codons. There are three that serve as a
stop codon. Termination occurs when the ribosome runs into one of these three stop
codons.