Unit 5 - DNA , Biotechnology and Protein Synthesis Flashcards
Explain the role of DNA polymerase in DNA replication.
DNA polymerase add nucleotides to form a complementary strand of DNA, but it can only add nucleotides to the 3’ end of an existing strand. Therefore, to start at the 5’ end, it must ad nucelotides to an RNA primase.
What are the steps of DNA replication?
DNA is unzipped, and a new strand is composed of complementary bases by RNA polymerase. On the lagging strand, Okazaki fragments are small chunks of complementary bases. These are then connceted by DNA ligase.
Describe the structure of a double helix.
The double helix looks like a long twisted ladder.
What is gel electrophoresis?
Gel electrophoresis separates DNA fragments according to their molecular weight. Because DNA is negatively charded, it moves towards the positive end.
What is euchromatin?
Euchromatin is genetic material in a loose form, with active genes available for transcription.
What is an exon?
Exons are coding regions of DNA.
What is a frameshift mutation?
A frameshift mutation is a genetic mutation caused by insertions or deletions of a number of nucleotides in a DNA sequence that is not divisible by three.
How is gene expression regulated?
Operons can regulate gene expression.
What is genetic engineering?
Genetic engineering is the branch of technology that produces new organisms or products by transferring genes between cells.
What function does a guanine cap serve?
The 5’G cap serves to protect the mRNA strand from degradation by enzymes.
What is the start codon in eukaryotes?
AUG (MET)
What is the role of transcription factors?
Transcription factors control the transfer of genetic information from DNA to RNA by binding to specific DNA sequences.
What are the three steps of protein synthesis?
Transcription, RNA processing, and translation
What occurs at the P site of a ribosome?
At the P site, an initiator tRNA serves to activate translation and occupies the site.
What occurs at the E site of a ribosome?
At the E site, the uncharged tRNA molecule exits, after giving away its amino acids.
What is a mutation and what are the two groups of mutations?
All mutations fall into two groups: base substitutions and gene rearrangements. A mutation is a change in the nucleotide sequence of an organism’s DNA or in the DNA or RNA of a virus.
What are nucleotides the building blocks of?
Nucleotides are the building blocks of nucleic acids, consisting of a five-carbon sugar covalently bonded to a nitrogenous base and one or more phosphate groups.
What is the role of rRNA?
A ribosome consists of a large subunit and a small subunit, each made up of proteins and one or more ribosomal RNAs (rRNAs). Ribosomal RNA genes are transcribed, and the RNA is processed and assembled with proteins imported from the cytoplasm. rRNA is essential for protein synthesis of all living organisms.
What is the function of RNase and what does it stand for?
RNase stands for ribonuclease. RNase is a type of nuclease that catalyzes the degradation of RNA into smaller components.
What is the role of RNAi and what does it stand for?
RNA interference is a technique used to silence the expression of selected genes. RNAi uses synthetic double-stranded RNA molecules that match the sequence of a particular gene to trigger the breakdown of the gene’s messenger RNA.
Explain the function of okazaki fragments in DNA replication.
An okazaki fragment is a short segment of DNA synthesized away from the replication fork on a template strand during DNA replication. Many such segments are joined together to make up the lagging strand of newly synthesized DNA.
Explain the components of an operon.
An operon is a unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway.
What is the function of an operator?
In bacterial and phage DNA, an operator is a sequence of nucleotides near the start of an operon to which an active repressor can attach. The binding of the repressor prevents RNA polymerase from attaching to the promoter and transcribing the genes of the operon.
Explain primer in DNA replication.
Primer is a short stretch of RNA with a free 3’ end, bound by complementary base pairing to the template strand and elongated with DNA nucleotides during DNA replication.
What is a plasmid and how is it used in DNA cloning?
A plasmid is a small, circular, double-stranded DNA molecule that carries accessory genes separate from those of a bacterial chromosome. In DNA cloning, it is used as vectors carrying up to about 10,000 base pairs of DNA. Plasmids are also found in some eukaryotes, such as yeasts.
What is the role of snRNPs in splicing?
snRNPs are small nuclear ribonucleoproteins. They are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs.
Describe an example of a corepressor.
Tryptophan functions in the trp operon as a corepressor, a small molecule that cooperates with a repressor protein to switch an operon off.
Explain the function of miRNAs and how they are made.
miRNAs are capable of binding to complementary sequences in mRNA molecules. The miRNAs are made from longer RNA precursors that fold back on themselves, forming one or more short double-stranded hairpin structures, each held together by hydrogen bonds.
What is the function of an inducer?
An inducer inactivates the repressor. For the lac operon, the inducer is allolactose, an isomer of lactose formed in small amounts from lactose that enters the cell.
What is CAP and what does it function as?
The regulatory protein, called catabolite activator protein (CAP), is an activator, a protein that binds to DNA and stimulates transcription of a gene.
Describe the anti-parallel structure of DNA.
DNA molecules have two strands that form a double helix. The two sugar-phosphate bacakbones run in opposite 5’–>3’ directions from each other, which is referred to as antiparallel.
Explain the role of anticodons during the process of translation, and give an example.
As it arrives at a ribosome, a tRNA molecule carries a specific amino acid at one end. At the other end of the tRNA is an anticodon, which a nucleotide triplet that base-pairs with a complementary condon on the mRNA. For example, the mRNA codon GGC base-pairs with a tRNA CCG anticodon. As the mRNA molecule moves through a ribosome, glycine will be added to the polypeptide chain after translation.
Explain how biotechnology is used to express a gene of interest in any species.
DNA can be artificially made so an organism can express a gene that it originally did not have. Several components of different plasmids, such as the pBAD and rfp genes from the pKAN-R plasmid and the ori site and ampR and ara C genes of the pARA plasmid, can be combined and rearranged to form a recombinant plasmid that expresses the gene of interest.
Explain the role of cAMP as a second messenger during signal transduction, as well as its role in positive gene regulation.
Many signaling pathways also involve small, non-protein, water-soluble molecules or ions called second messengers. Adenylyl cyclase converts ATP to cAMP in response to an extracellular signal. The immediate effect of cAMP is usually the activation of protein kinase A, which phosphorylates various other proteins. In terms of gene regulation, cAMP accumulates when glucose is scarce. cAMP binds to the regulatory protein CAP to activate it, which increases the rate of trancription of the lac genes.
What are chromosomes, and what do all eukaryotic chromosomes consist of?
Chromosomes are located in the nucleus, and they are structures that carry genetic information. Each eukaryotic chromosome consists of one very long, linear DNA molecule associated with many proteins. The DNA molecule carries genes that specify an organism’s inherited traits.
Give a brief overview of gene cloning, as well as what a cloning vector is.
Gene cloning is the multiple copies of a single gene. First, a gene is inserted into a plasmid. The plasmid is then put into a bacterial cell, which is then grown in culture to form a clone of cells containing the “cloned” gene of interest. Proteins are then expressed from this gene of interest, and basic research can be done on these proteins or the gene itself. Genes are cloned in plasmids; a cloning vector is a DNA molecule that carries foreign DNA into a host cell, where it replicates.
How are codons along an mRNA molecule decoded/translated into amino acids that make up a polypeptide chain?
Codons are nucleotide triplets that are read by the translation machinery in the 5’–>3’ direction along mRNA. Each codon specifies which one of the 20 amino acids will be incorporated in a polypeptide. The number of nucleotides must be three times the number of amino acids in the protein made.
Give an example of a corepressor and how it works.
An example of a corepressor is tryptophan, as it cooperates with a repressor protein to turn an operon off. As tryptophan accumulates, more tryptophan molecules associate with trp repressor molecules, which then bind to the trp operator. This blocks transcription, as production of the tryptophan pathway enzymes is shut down.
Describe the monomers and function of DNA.
DNA is made of nucleotides, each of which has a phosphate group, a deoxyribose sugar, and one of four types of nucleotide bases. DNA carries the genetic/hereditary information of an organism, as well as the instructions needed for an organism to develop, survive and reproduce. Sequences of DNA must be converted into messages (mRNA during transcription) that can be used to make proteins (during translation).
Describe the effect of DNA methylation, as well as how it accounts for genomic imprinting in mammals.
During DNA methylation, methyl groups are added to DNA, which modifies its function. DNA methylation can act to reduce gene transcription since the DNA is more tightly packed together, making it more difficult for DNA to be transcribed. In terms of genomic imprinting, methylation permanently regulates expression of either the maternal or paternal allele of particular genes at the start of development.
Who are some contributors of the discovery of DNA, and what were their contributions?
In 1928, Frederick Griffith discovered that bacteria can transfer genetic information. In the 1940s, Erwin Chargoff discovered that the number of purines (A, G) must equal the number of pyrimidines (T, C). In 1952, Hershey and Chase found that DNA is a genetic/hereditary material. In the early 1950s, Rosalind Franklin found that DAN has a helical structure with 2 strands and a sugar phosphate backbone. During the same time, Watson and Crick introduced the central dogma, which is the idea that genetic information flows as DNA is transcribed into RNA, which is then translated to make proteins.
What are the steps required to set-up the plasmid restriction digest?
A plasmid map is used to identify where the restriction enzymes are. The restriction sites identify where the enzymes are cut out and removed.
All cells follow the same central dogma. Explain what this is and how it can be used to explain how a gene from a human or sea anemone can be expressed in bacteria to make a new product.
The central dogma explains the order of protein production. First, DNA is transcribved into RNA, which is then translated into proteins. Because bacterial cells, sea anemone cells, and human cells make proteins the same way, this means that a gene from humans or sea anempne can be expressed in bacteria to make a product never before made in bacteria.
