Term
| Why do E. coli exhibit a biphasic growth curve when cultured in an environment with both glucose and lactose present? |
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Definition
| The first phase represents their use of the glucose as fuel, followed by a plateau as the lac operon becomes activated through lactose introduced to the cells. Then, a second phase of growth occurs following activation of the lac operon and production of lactase within the cells. |
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Term
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Definition
| An operon is a group of genes, regulated together by transcription from a single promoter that produces a polycistronic mRNA. |
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Term
| What is a Shine-Dalgarno sequence? |
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Definition
| This is analogous to the eukaryotic 5' cap in an mRNA molecule. It allows initiation at internal start codons. |
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Term
| The lac operon has both a repressor site and an activator site. What does this mean in terms of when the operon will be able to be active? |
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Definition
| The operon will be active only when the activator molecule is bound and the repressor molecule is not bound. Even if the activator molecule is bound, if the repressor site is still occupied, the operon will not function. |
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Term
| What is the difference between the lac and trp opera in bacteria? |
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Definition
| The trp operon is modified by repression only; if the repressor molecule is not bound, then the operon is active. This differs from the lac operon, which has an activator site. |
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Term
| True or False: the trp operon provides an example of helix-loop-helix transcription regulation. |
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Definition
| False - it's an example of helix-turn-helix transcription regulation. |
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Term
| What happens when you methylate a gene? |
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Definition
| Methylated genes are usually silenced. |
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Term
| Daughter cells in eukaryotes have DNA that retains the methylation patterns of the previous generation. Define and explain this form of inheritance. |
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Definition
| Epigenetic inheritance - the inheritance of chemical structure rather than gene sequence. |
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Term
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Definition
| Barr bodies are the silenced X chromosome found in female somatic cells. The silencing occurs via methylation and the whole process is referred to as Lyonization. |
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Term
| The MLH1 protein is a human homolog of MutL, which functions in determining the new strand from the template strand in strand-directed mismatch repair. When MLH1 is methylated during early onset colon cancer, what would you expect as a result? |
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Definition
| Faulty copies of MLH1 are made, leading to increased errors in replication and increased production of microsatellites in the genome of new cells. |
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Term
| Describe the three basic steps of strand-directed mismatch repair. |
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Definition
1. Recognition of a mismatched pair by proteins.
2. Excision of the DNA segment containing the mismatch from the newly synthesized strand.
3. Resynthesis of the excised segment using the old strand as a template. |
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Term
| Why is strand-directed mismatch repair only effective in repairing replication errors? |
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Definition
| The scanning protein works by looking for a nick in the new strand where an error is detected. Nicks like this are only present following replication, in the lagging strand (Okazaki fragments). |
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Term
| Since DNA is bound up in chromatin and wound into tight formations, how does the transcription machinery gain access to the DNA sequence? |
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Definition
| Chromatin remodeling complex, consisting of a variety of enzymes and chaperones that can modify or temporarily remove histones, reconfigures the DNA sequence to make the material more accessible. |
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Term
| True or False: only general transcription factors are required to transcribe protein-coding genes. |
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Definition
| False - there are gene-specific factors that can also activate or suppress transcription, in complex patterns that are specific to each gene. |
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Term
| Name and briefly describe the three main functional domains in a transcription factor. |
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Definition
1. DNA-binding domain (DBD). This binds to enhancer proteins and allows the factor to sit near a promoter and ensure that transcription will occur from that promoter.
2. Dimerization domain. These are protein-protein interaction domains.
3. Activation domain. This domain actually interacts with RNA Pol to start transcription. |
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Term
| DNA is flexible. If it takes on a new conformation to enhance transcription when bound to transcription factors, what is one way that proteins can act to inhibit gene expression? |
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Definition
| Proteins can block or slow down the assembly of the new conformation, or the coming together of the transcription factors themselves. |
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Term
| Give an example of a helix-turn-helix transcription factor. |
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Definition
| The trp repressor operon. Hox genes code for HTH transcription factors... these control cranial-caudal and anterior-posterior body patterning. |
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Term
| What type of receptors are associated with zinc fingers? |
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Definition
| Steroid hormones, thyroid, Vitamin D, retinoids, GATA, Sp1, Kruppel family |
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Term
| What genetic receptors are associated with helix-turn-helix domains? (Leucine zippers) |
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Definition
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Term
| What gene receptors are associated with HLH domains? |
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Definition
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Term
| What type of regulation domain is a zinc finger? |
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Definition
| It is a DNA-binding domain (DBD). |
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Term
| Abuse of androgens causes sterility and increases cardiovascular disease in men. Estrogen and progesterone are used in birth control. Both of these relationships involve genes that are transcribed with factors that include what type of domain? |
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Definition
| Zinc finger DNA-binding domains. |
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Term
| At a protein level, inflammation is caused by proteins with glucocortacoid response elements. What would happen if asthma was treated with a glucocortacoid drug? |
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Definition
| Inflammation in the tissues decreases, providing more surface area for respiration and a better patient prognosis. |
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Term
| Leucine is a hydrophobic amino acid. How does this affect the structure of the leucine zipper? |
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Definition
| Leucine residues are located along one side of the structure, enclosed on the inside of the final protein and exposing positive charges to bind the negatively-charged DNA. |
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Term
| Helix-loop-helix domains promote the formation of what structures? What is the result of their binding DNA? |
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Definition
| They promote dimerization and regulate temporal expression of genes. |
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Term
| Describe the mechanism by which miRNA silences genes. (2 methods) |
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Definition
1. miRNA binds in an RNA-induced silencing complex (RISC)and causes mRNA degradation
2. binds mRNA and clogs the translational machinery by different mechanisms. |
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Term
| Why are miRNAs important to the molecular phenotype of a tissue? |
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Definition
| They fine tune the level of protein expression in a given cell type. This is a crucial role during normal development, as well as in the disease process (cancers, CV, lung, neuro). |
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