Unit 6: Gene Expression and Regulation

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.

Regulation of Zene Expression and Cell Specialization

• Regulation of gene expression can occur at different times. The largest point is before transcription, or pre-transcriptional regulation.
• Transcription factors can encourage or inhibit this from happening.
• Sometimes changes to the packaging of DNA will alter the ability of the transcription machinery to access a gene, this is called epigenetic changes.
• In bacteria, a cluster of genes can be under the control of a single promoter; these functioning units of DNA are called operons.
• The operon consists of four major parts:

structural genes, promoter genes, the operator, and the regulatory gene:

• Structural genes code for enzymes needed in a chemical reaction. These genes will be transcribed at the same time to produce particular enzymes.
• The promoter gene is the region where the RNA polymerase binds to begin transcription.
• The operator is a region that controls whether transcription will occur; this is where the repressor binds.
• The regulatory gene codes for a specific regulatory protein called the repressor. The repressor is capable of attaching to the operator and blocking transcription.
• Post-transcriptional regulation occurs when the cell creates an RNA, but then decides that it should not be translated into a protein. This is where RNAi comes into play.
• RNAi molecules can bind to an RNA via complementary base pairing. This creates a double-stranded RNA
• Post-translational regulation can also occur if a cell has already made a protein, but doesn’t yet need to use it.

Gene Regulation in Embryonic Development

• The cell changes shape and organization many times by going through a succession of stages. This process is called morphogenesis.
• Fertilization triggers the zygote to go through a series of cell divisions.
• The early genes that turn certain cells in the early embryo into future-this or future-that are called homeotic genes. A subset of homeotic genes are called Hox genes.

Mutations

• A mutation is an error in the genetic code.
• Mutations can occur because DNA is damaged caused by chemicals or radiation and cannot be repaired or because DNA damage is repaired incorrectly.

Base Substitution

• Base substitution (point) mutations result when a single nucleotide base is substituted for another. There are three different types of point mutations:
• Nonsense mutations cause the original codon to become a stop codon, which results in early termination of protein synthesis.
• Missense mutations cause the original codon to be altered and produce a different amino acid.
• Silent mutations happen when a codon that codes for the same amino acid is created and therefore does not change the corresponding protein sequence.

Gene Rearrangements

1. Insertions and deletions result in the gain or loss, respectively, of DNA or a gene. Introduction or deletion of bases often results in a change in the sequence of codons used by the ribosome (called a frameshift mutation) to synthesize a polyprotein.
2. Duplications can result in an extra copy of genes and are usually caused by unequal crossing-over during meiosis or chromosome rearrangements. This may cause a new trait
3. Inversions can result when changes occur in the orientation of chromosomal regions
4. Translocations occur when two different chromosomes break and rejoin in a way that causes the DNA sequence or gene to be lost, repeated, or interrupted.
5. Transposons are gene segments that can cut/paste themselves throughout the genome. Its presence can interrupt a gene and cause errors in gene expression.

• Bacteria are prokaryotes that come in many shapes and sizes.

• Bacteria divide by fission; however, this does not increase their genetic diversity. Instead, they can perform conjugation with other bacterial cells and swap some of their DNA.

• Viruses are nonliving agents capable of infecting cells since they require a host cell’s machinery in order to replicate.

• A virus has two main components:

  • a protein shell (the capsid)
  • genetic material made of DNA or RNA.

  The thing infected by a virus is called a host.

• Bacteriophages undergo two different types of replication cycles, the lytic cycle and the lysogenic cycle.

• In the lytic cycle, the virus immediately starts using the host cell’s machinery to replicate the genetic material and create more capsid proteins.

• The transfer of DNA between bacterial cells using a lysogenic virus is called transduction.

• Viruses with a lipid envelope are called enveloped viruses.

• Retroviruses like HIV are RNA viruses that use an enzyme called reverse transcriptase to convert their RNA genomes into DNA so that they can be inserted into a host genome.

Biotechnology

• Recombinant DNA is generated by combining DNA from multiple sources to create a unique DNA molecule that is not found in nature.
• A common application of recombinant DNA technology is the introduction of a eukaryotic gene of interest into a bacterium for production for research and to cure diseases
• This technology that produces new organisms or products by transferring genes between cells is called genetic engineering.

Polymerase Chain Reaction (PCR)

• PCR is a laboratory technique that is used to create billions of identical copies of genes within hours.
• The process of creating many copies of genes is known as amplification.
• The process of giving bacteria foreign DNA is called transformation.
• A technique that is alike, is transfection, which is putting a plasmid into a eukaryotic cell, rather than a bacteria cell.
• DNA fragments can be separated according to their molecular weight and charge with gel electrophoresis. Since DNA and RNA are negatively charged, they go through a gel toward the positive pole of the electrical field.
• When restriction fragments between individuals of the same species are compared, the fragments differ in length because of polymorphisms, which are differences in DNA sequences.
• These fragments are called restriction fragment length polymorphisms, or RFLPs.
• DNA sequencing allows scientists to determine the order of nucleotides in a DNA molecule. Scientists could design their own DNA plasmid and use it to study a gene of interest.