Unit 5: Molecular Genetics
Contrast the structures of a section of DNA with the mRNA formed from it
3′ - AAAAAAA - 5′ 5' - UUUUUUU - 3' mRNA is made up of the complementary base pairs to the DNA—e.g. U instead of T. mRNA is single-stranded, with a ribose-phosphate backbone as opposed to the DNA's double-stranded deoxyribose-phosphate backbone.
Explain how mutations in gametes may result in phenotypic changes in offspring
A mutation in one of the gametes moves into the fertilized egg cell. (For the types of mutations, see two questions below and three questions below.) The fertilized egg cell divides, forming an embryo of embryonic stem cells, all of which carry the mutation. The stem cells divide and differentiate, and the embryo develops into a full organism. The mutation remains in all of the cells and can manifest in the phenotype.
Explain some practical applications of recombinant DNA technology:
A sheep with better-quality wool. Leaner-meat pig. Herbicide resistance. Delayed ripening. Spoilage and disease resistance. Improved nutrition. Produce a useful biological substance—e.g. use bacteria to produce human insulin instead of harvesting a similar, but not identical insulin from animals. Production of vaccines—e.g. proteins in hepatitis B viruses have been cloned in yeast cells, allowing for production and distribution of viral proteins that can be used to immunize the body against them. Not limited by species; a gene from a plant could be inserted into a bacterial cell
Relate the concept of DNA being the "universal code" to the possibility of making transgenic organisms
Because DNA is found in every living organism, and similar sections of DNA correspond between organisms, it is logical that genes can be substituted between organisms. Every organism 'reads' DNA in the same way. This process forms transgenic organisms.
Single Base Substitution (Point Mutation):
Can be okay; at most it changes one amino acid, and sometimes it even produces the same one, because multiple codons code for the same amino acid (this could lead to a silent mutation). Plus, the new amino acid may have similar enough properties to still let the protein work.
Inserting/deleting (frame shift):
Can have a huge impact because the triple-nucleotides align into different codons all the way down the gene and thus produce entirely different amino acids, breaking the final protein.
Explain how DNA/chromosomes become altered and the effects these alterations have on protein formation
DNA can be altered through silent mutation (substitution and the amino acid may not change due to more than one way for an amino acid to be coded), point mutation (substitution only a few nucleotides in the DNA sequence), or frameshift mutation (deletion or insertion, changing all codons after the deletion/insertion) Causes of mutations include: Environmental factors (e.g. radiation), A mistake in DNA replication
Describe how DNA fingerprinting works. Explain how gel electrophoresis can be used in the process.
DNA fingerprint—the particular banding pattern of restriction enzymes cutting up your DNA, unique from anyone else's (unless you have a twin) and revealed through gel electrophoresis. Of course, your entire fingerprint looks really similar to everyone else's, but... Genetic markers are sections that vary among individuals, which can be compared and analyzed Can be identified in the gel by nucleic acid probes: a radioactive nucleotide sequence complementary to the DNA sequence searched for They can occur in alleles for diseases, other traits, or even in noncoding regions (the last is what is typically used for rigorous court evidence) Created through PCR & gel electrophoresis First, a person's DNA is replicated several times over with PCR and cut with restriction enzymes. Then gel electrophoresis is used to separate the various fragments by size The results of #2 are analyzed
Explain how the structure of DNA lends itself to replication.
DNA, or deoxyribonucleic acid, is composed of nucleotides in the shape of a double helix, and obeys the base pairing rules of CG/GC and AT/TA. Because each base only has one other pair, if DNA is 'unzipped' into two separate strands, two new pieces of DNA can be formed, each with one strand from the original DNA and one newly replicated strand. E.g. if the original DNA had C, then you can reconstruct the other antiparallel, which could only be G.
Relate the structure of a gene to the processes of genes being expressed or turned "on" or "off". Be able to use the lac operon as an example. In prokaryotes:
Each gene has a promoter and operator before it. This promoter-operator-gene sequence is called an operon. The promoter acts as the site showing the starting position where RNA polymerase can attach to the DNA and replicate the gene following it. The operator follows the promoter, and acts like a switch that determines whether or not RNA polymerase can transcribe the gene. There is also a nearby protein called a repressor, which binds to the operator to prevent RNA polymerase from attaching to the promoter. E.g. for the lac operon in E. coli. (often found the human gut), when lactose is present, it binds to and changes the shape of the lac repressor, preventing it from binding to the operator and disabling the operon as it normally does. Note that promoters do not always disable the operon by default—e.g. the promoter often used in GMOs, CaMV, is on by default. In eukaryotes: It's just way more complicated. Some genes still have promoter sequences before them. Proteins called transcription factors exist, which regulate transcription by binding to these promoters or to RNA polymerase. (RNA polymerase is the enzyme that helps transcribes DNA into mRNA) E.g. some hormones signal cells to express genes by attaching to transcription factors
Explain the difference between introns and exons
In eukaryotic cells, the initial mRNA transcripts contain sections of noncoding DNA, introns (think of them as random letters pasted into a document in strange places). Before the mRNA leaves the nucleus, the introns have to be removed in a process called RNA splicing, which removes the introns and connects the exons, which are the functional parts of the gene that will be translated and expressed. Remember, the EXons are EXpressed. Also, not all of the introns are always removed; sometimes leaving in introns results in a different protein!
How does polymerase chain reaction (PCR) utilize the basic process of DNA replication:
PCR has 3 main steps: denaturation, annealing, and extension. Denaturation (96°C): DNA heated, unzipped (like the start of DNA replication) Annealing (~58°C): primers identify and bind to desired sequences Extension (~72°C): replication begins from the primers' locations Similar to when the DNA is copied and then rezipped in replication. PCR occurs in a specific section many times over and over, whereas DNA replication happens once for the entire DNA molecule. They both also use the same enzyme to form the covalent bonds between nucleotides—DNA polymerase.
Compare and contrast the genomes of prokaryotes and eukaryotes
Prokaryotes have a single circular DNA molecule, with simple structure (operons) and it's fairly short. Eukaryotic genomes are split into several chromosomes, and have much more complex regulatory sequences, proteins, and controls (see below), and are larger. Prokaryotes have additional genes on independent circular or linear DNA plasmids, while eukaryotes do not. Prokaryotes do not have introns, while eukaryotes do; they make up the majority of eukaryotic genetic material
Contrast recombinant DNA technology and the process of cloning
Recombinant DNA technology only takes a few genes and inserts them into another organism's DNA/the animal's fertilized egg cell. In cloning, the nucleus of an unfertilized egg cell is removed and replaced with an adult nucleus (which contains all the donor's genetic material), creating an individual with a completely identical genome to the donor. Recombinant DNA technology can be utilized across species, while the donor and the embryo must be of the same species. For animals, both involve modifying an egg cell of the animal.
Transcription
Transcription is the conversion of DNA's nucleotide sequence into a single-stranded mRNA molecule. RNA polymerase binds to DNA and separates its two strands. RNA polymerase uses one strand as a template for mRNA (used in the 3′ to 5′ direction, forms mRNA in the 5′ to 3′ direction). E.g. 3′ - TTCAGT - 5′ DNA→ 5′ - AAGUCA - 3′ mRNA DNA strands rejoin. Note: when transcribing, uracil (U) replaces thymine (T), the nucleotide that usually matches to adenine (A)
Translation
Translation is the conversion of 'nucleic' language into 'amino acid' language. In eukaryotes, introns (non-coding sections of DNA) are removed in the mRNA before it exits the nucleus. mRNA meets up with a ribosome in the cytoplasm, and the ribosome moves along the mRNA strand while tRNA pair up with their complementary codons and build an amino acid chain which eventually becomes a polypeptide.
Describe the basic process of DNA replication and how it relates to the transmission and conservation of the genetic code
Welcome to Interphase. S phase, to be precise. You are in the nucleus. DNA helicase unzips the DNA strand in a small bubble called a replication bubble. (Many replication bubbles form at same time to speed things up.)' DNA polymerase joins each base on each original strand with a complementary base using nucleotides in the cytoplasm. On the leading strand, the polymerase synthesizes continuously from 5′ → 3′. (This means that it forms a new strand from 5′ → 3′. However, this strand is built off of the original strand, running in the 3′ → 5′ direction. Nucleotides are added on the 3' end of the NEW strand). On the lagging strand (3′ → 5′, note the strand it's following is 5′ → 3′), RNA primers (short strand of genetic material, serves as a starting point for DNA replication, necessary because DNA polymerase needs a starting point) are put down to form Okazaki fragments (short, newly synthesized DNA fragments complementary to the template DNA strand, separated by primers), synthesizing them in the opposite direction of the entire replication. This way, it joins up with the previous fragment and forms a continuous DNA strand. The place where the DNA is unzipping to replicate is called the replication fork. The replication bubbles merge and eventually entirely split the two parental DNA strands into 2 new DNA molecules, each with one old strand and one new strand. DNA ligase connect (glues) Okazaki fragments. ^Process is called semi-conservative: one old strand + one new strand
Mutation
any change in this e nucleotide sequence of DNA. In the case of a silent mutation, the DNA sequence of a gene does not result in a phenotypic change. Since multiple codons code for the same amino acid, substitution of a base might not change which amino acid is coded for. Also, if mRNA codes for an amino acid that has similar chemical properties as the original amino acid, there will be little effect on the protein's function as a whole.
Replication:
the biological process of producing two identical replicas of DNA from one original DNA molecule. End product is identical strand of DNA.
Recombinant DNA technology
the process of inserting a foreign gene into a DNA molecule that is then inserted into a target organism. Helps add beneficial traits.
Inversion:
when a fragment is flipped/reversed in the chromosome. Less harmful than deletions/duplications because most genes are still there
Deletion:
when a fragment of a chromosome is lost. Large deletions can be very bad. Both can occur during an error in synapsis
Translocation:
when a fragment of one chromosome attaches to a nonhomologous chromosome, potentially resulting in 2 different chromosomes exchanging incompatible parts
Missense mutation:
when the changed nucleotide changes the amino acid produced. E.g. sickle-cell disease: DNA codon GAG (Glu) → GTG (Val)
Nonsense mutation:
when the changed nucleotide makes its codon a STOP codon (DNA codons UAA, UAG, or UGA), truncating the gene and the protein product. The earlier in the gene it is, the more likely it is that the protein will not function.