Unit 6: Gene expression and Regulation review

Differentiate between purines and pyrimidines

- Purines (A & G) have double-ring structure while pyrimidines (C,U,T) have a single ring

List 3 differences between DNA and RNA

1. Sugar composition: RNA = ribose sugar DNA = deoxyribose sugar 2. Number of strands: RNA = 1 strand DNA= 2 strand 3. Bases: RNA and DNA contain A, C, and G but RNA contains U instead of T.

The DNA from a certain plant species is analyzed. The DNA contains 22% Thymine. Determine the percent of the other bases.

28%

An mRNA sequence reads: 5'- CGAUGCAGA- 3'Translate this sequence.

: Arginine - Cysteine - Arginin

What is a promoter region? Are promoter regions upstream or downstream of the gene?

A promoter region is a specific sequence of DNA located upstream of a gene

After fertilization a zygote forms. THe cells then go through mitosis. Explain how this bundle of cells eventually forms a human with specialized cells.

After fertilization a zygote forms. THe cells then go through mitosis. Explain how this bundle of cells eventually forms a human with specialized cells.

What does it mean that DNA strands are antiparallel and complementary? Draw a strand of DNA with 6 nucleotides to support you answer.

Antiparallel: In DNA, the two strands run in opposite directions along the 5' to 3' axis. One strand runs in the 5' to 3' direction (from the 5' end to the 3' end), while the other runs in the opposite direction, from 3' to 5'. Complementary: The bases on one strand of DNA form specific hydrogen bonds with the bases on the opposite strand.

If one bacterial cell has a gene that is promoting its survival, explain how other bacterial cells can benefit from it.

Bacterial cells can share beneficial genes with other bacterial cells through horizontal gene transfer mechanisms, such as conjugation, transformation, and transduction. Here's how other bacterial cells can benefit from a gene that promotes the survival of one bacterial cell:

Identify major classes of macromolecules and then identify their monomers and polymers

Carbohydrates (monosaccharides) Protein (amino acids) Lipids (fatty acids and glycerol) Nucleic acid (nucleotides)

Describe the process of conjugation

Conjugation is a mechanism of horizontal gene transfer in bacteria whereby genetic material, typically in the form of plasmids, is transferred from one bacterial cell (the donor) to another bacterial cell (the recipient). This process allows for the exchange of genetic material between bacterial cells, contributing to genetic diversity and the spread of advantageous traits, such as antibiotic resistance.

Is DNA positively or negatively charged? How could you tell just by looking at a strand of DNA?

DNA is negatively charged. This negative charge arises from the phosphate groups in the back bone which each carry a negative charge due to negatively charged oxygen atoms.

In which stage of the cell cycle does DNA replicate?

DNA replication occurs in the S phase

In which direction does DNA move during gel electrophoresis?

During gel electrophoresis, DNA molecules move from the negative electrode (cathode) towards the positive electrode (anode).

why does DNA move during gel electrophoresis?

During gel electrophoresis, DNA molecules move through a gel matrix when an electric field is applied across the gel. The movement of DNA occurs due to the interaction between the negatively charged DNA molecules and the electric field, resulting in migration towards the positive electrode.

During gel electrophoresis, which size of DNA will move the farthest? Why?

During gel electrophoresis, smaller fragments of DNA will generally move the farthest through the gel matrix. This occurs because smaller DNA fragments encounter less resistance as they navigate through the pores of the gel, allowing them to migrate more quickly and travel farther distances compared to larger DNA fragments.

True or False: The genetic code is read in groups of two nucleotides at a time called the doublet code.

False

True or False: only the template strand of DNA is transcribed during transcription

False

If the tRNA anticodon read 3' - CUU - 5' then what does the mRNA codon read that it can bind to? Knowing this, what amino acid will the tRNA carrying. ( remember the amino acid the tRNA is based on the mRNA codon.)

GAA = lysine

What would be the immediate effect to transcription if a cell was exposed to a drug that mutated the promoter region?

If a cell were exposed to a drug that mutated the promoter region of a gene, the immediate effect on transcription would likely be a decrease or complete cessation of transcription of that particular gene.

What does it mean if a gene/trait is evolutionary conserved

If a gene or trait is evolutionarily conserved, it means that it has remained relatively unchanged across different species over long periods of evolutionary time. In other words, the gene or trait has been preserved, or conserved, throughout evolution because it performs a critical function that is essential for the survival or fitness of organisms.

If the bacterial cell uses up its tryptophan and it builds up inside of the cell, what would happen to the trp operon?

If the bacterial cell uses up its tryptophan and it builds up inside the cell, the increased concentration of tryptophan would act as a corepressor for the trp operon. In a repressible operon like the trp operon, the presence of tryptophan would trigger the repressor protein to bind to the operator region of the operon. This binding would block the access of RNA polymerase to the promoter, inhibiting transcription of the trp genes. As a result, the expression of the trp operon would be repressed, and the synthesis of tryptophan would decrease to maintain cellular homeostasis.

Referring to question 10: imagine if the coding strand were transcribed and translated instead. Determine the mRNA sequence and translate it. How would this error affect the polypeptide produced.

If the coding strand were mistakenly transcribed and translated instead of the template strand, it would lead to the production of a polypeptide with a premature stop codon. As a result, translation would terminate prematurely, and the synthesized polypeptide would be truncated, likely lacking functional domains or critical regions necessary for proper protein function. This could potentially disrupt the normal cellular processes in which the protein participates, leading to dysfunctional or non-functional protein products.

What if you were performing gel electrophoresis and the molecules you were examining moved towards the negative electrode? What does this mean about the charge of the molecule you are analyzing?

If the molecules being examined in gel electrophoresis move towards the negative electrode (cathode), it means that these molecules are positively charged. In gel electrophoresis, DNA molecules typically migrate towards the positive electrode (anode) because they are negatively charged due to the phosphate backbone of the DNA. However, certain molecules or conditions may result in the opposite behavior, where molecules move towards the negative electrode.

Differentiate between silent, missense, and nonsense mutations. Predict which would be most detrimental and why?

In general, nonsense mutations are often the most detrimental because they result in the production of truncated and nonfunctional proteins. These truncated proteins may lack essential functional domains or structural motifs required for proper protein function, leading to loss-of-function phenotypes. Missense mutations can also be detrimental if they occur in critical regions of the protein or result in drastic changes in protein structure or function. However, silent mutations typically have no discernible effect on protein function or organismal phenotype.

Why do introns exist if they are just spliced out of the mRNA during pre-mRNA modifications?

In summary, although introns are removed from mRNA during RNA processing, they play critical roles in gene expression regulation, protein diversity, evolutionary innovation, and genetic recombination. Their presence within genes reflects the intricate and multifaceted nature of eukaryotic genomes and is essential for the complexity and adaptability of eukaryotic organisms.

Differentiate between a repressible and inducible operon.

In summary, repressible operons are normally active but can be inhibited by the presence of a corepressor, while inducible operons are normally inactive but can be activated by the presence of an inducer.

What are the two reproductive cycles of bacteriophages. Describe each.

In summary, the lytic cycle results in the immediate replication and lysis of host bacterial cells, while the lysogenic cycle involves the integration of the phage genome into the host chromosome and the potential for long-term coexistence between the phage and the host cell.

Why do errors in DNA replication lead to natural selection. Would natural selection still occur if all errors were corrected? Why or why not?

In summary, while perfect error correction might alter the dynamics of genetic variation and the rate of evolution, natural selection would still occur as long as there are selective pressures and heritable variation within populations.

Describe the meselson and stahl experiments that supported the semi-conservative model of DNA replication

In the experiment, Meselson and Stahl created and manipulated E. coli bacteria containing a heavy isotope of nitrogen N-15. Through DNA extraction and replications, they concluded that each new DNA molecule contains one strand from the parent molecule and one newly synthesized strand.

What is the center of DNA composed of?

It is composed of nucleotide pairings

What is the backbone of DNA composed of?

It is composed of sugar phosphate

What is redundancy in the genetic code important

It is when a codon codes for multiple different amino acids

In eukaryotic cells where does transcription occur?

Nucleus

Trace the path of a newly produced polypeptide that will leave the cell?

Overall, the path of a newly produced polypeptide that will leave the cell involves complex intracellular trafficking and processing mechanisms to ensure proper folding, modification, and delivery to its destination outside the cell.

Describe the consequences of a chemical that prevents the 5' cap and poly-A tail from forming on eukaryotic mRNA?

Overall, the prevention of 5' cap and poly-A tail formation on eukaryotic mRNA would have profound effects on mRNA stability, export, translation initiation, and overall gene expression, ultimately impacting cellular function and homeostasis.

Describe how it is possible for only one identical twin to express an inherited disease

Overall, while identical twins share the same genetic blueprint, differences in genetic, epigenetic, environmental, and stochastic factors can lead to variations in gene expression and disease manifestation between them. These factors contribute to the complexity of genetic inheritance and disease susceptibility in individuals.

How does the transcription and translation differ between prokaryotes and eukaryotes?

Overall, while the basic processes of transcription and translation are similar between prokaryotes and eukaryotes, there are significant differences in the details of how these processes occur and are regulated.

The very first tRNA will enter at which site on the ribosome (A,P,or E)

P site

How can PCR be used to produce copies of a gene?

PCR allows for the rapid and specific amplification of target genes by repeatedly cycling through denaturation, annealing, and extension steps, using specific primers and a DNA polymerase enzyme. This technique has revolutionized molecular biology and is widely used in research, diagnostics, forensics, and other fields.

If one DNA strand reads: 3' - ACTAG - 5' what would be the complementary DNA strand read?

TGATC

Provide an example that illustrates the importance of apoptosis

The importance of apoptosis in digit formation is highlighted by experiments where apoptosis is disrupted. For example, inhibiting apoptosis in the interdigital regions can lead to webbed digits, where the digits fail to separate properly, resulting in fused or partially fused fingers or toes. Conversely, inducing apoptosis inappropriately in the developing digits can lead to abnormal digit shapes or missing digits

Describe the mutation that causes cystic fibrosis.

The most common mutation that causes cystic fibrosis is a deletion of three nucleotides (CTT) in the CFTR gene. This mutation leads to the loss of the amino acid phenylalanine at position 508 (Phe508del or ΔF508). This specific mutation accounts for approximately 70% of CF cases worldwide.

What does it mean that DNA strands are antiparallel?

The strands run in opposite direction. One strand going 5' to 3' and the other 3' to 5'. Despite running in opposite direction the strands pair in a complementary manner: A with T, and C with G

What are the three parts of an operon?

Together, the promoter, operator, and structural genes comprise the basic components of an operon, allowing for efficient and coordinated regulation of gene expression in prokaryotic cells.

A section of the template strand of DNA reads: 5'- CAACACTAA - 3' Determine the mRNA sequence and translate it.

Transcribed mRNA sequence: 5'- GGUUGUGAU - 3' and the translated amino acid sequence is: Glycine - Leucine - Stop.

List and describe the steps of transcription

Transcription involves 4 steps. First, is initiation where RNA polymerase binds to the promoter region of DNA and unwinds that section to reveal the template strand. Next is Elongation where the enzyme adds complementary RNA nucleotides along the strand. Then termination when the polymerase reaches a termination sequence, and the RNA script is synthesized. Finally, is Processing where the mRNA gets its 5' and 3' ends capped and the introns are removed through splicing.

Fill in the blank: The process of____ converts DNA to RNA. The process of _____ turns RNA into proteins.

Transcription, translation

Dsecirbe the process of transduction

Transduction is a mechanism of horizontal gene transfer in bacteria where genetic material is transferred from one bacterium to another by bacteriophages (viruses that infect bacteria). This process allows for the exchange of genetic material between bacterial cells, contributing to genetic diversity and the spread of advantageous traits, such as antibiotic resistance. Here's an overview of the process of transduction:

Describe transformation. Are all bacteria competent?

Transformation is a process by which bacteria can take up and incorporate foreign DNA from their environment into their own genome. This mechanism allows bacteria to acquire new genetic material, such as genes encoding antibiotic resistance or other advantageous traits, through horizontal gene transfer. not all bacteria are competent.

Summarize the purpose of translation in 1-2 sentences.

Translation is the process in which the genetic information encoded in mRNA is decoded to synthesize a specific sequence of amino acids, ultimately resulting in the production of a functional protein. It is a key step in gene expression and is essential for the synthesis of proteins that carry out various cellular functions.

Where does translation occur?

Translation occurs in the cytoplasm of eukaryotic cells and in the cytoplasm or cytoplasmic region of prokaryotic cells.

When does translation stop?

Translation stops when a stop codon is encountered in the mRNA sequence.

True or False: morphogenesis is the process that gives an organism its shape.

True

True or False: plasmids replicate separately from chromosomal DNA

True.

Using a codon chart determine what UAU codes for

Tyrosine

If an error occurs in DNA replication, how is it fixed?

With DNA polymerase checking for and correcting errors in the nucleotides

Fill in the blanks: tRNA has an ____ region which is complementary and antiparallel to ____.

anticodon and mRNA codons

What are restriction enzymes? Where do they come from?

are enzymes that recognize specific DNA sequences and cleave the DNA at or near these sequences. They are essential tools in molecular biology for cutting DNA molecules into specific fragments for various applications, such as cloning, DNA sequencing, and genetic engineering.Restriction enzymes are naturally produced by bacteria and archaea as part of their defense mechanisms against invading viruses, known as bacteriophages

Fill in the blank: the mRNA nucleotide triplets are called ____. These code for_____ ______.

codons and amino acids

What role do cytoplasmic determinants play in early embryonic development?

cytoplasmic determinants play essential roles in early embryonic development by regulating cell fate specification, pattern formation, and the establishment of gene expression patterns. They contribute to the complexity and precision of developmental processes, ensuring the proper formation of tissues, organs, and body structures.

What functional group defines the 3' end of DNA?

free hydroxyl group

How does gel electrophoresis separate DNA fragments?

gel electrophoresis separates DNA fragments based on their size and charge by applying an electric field across a porous gel matrix. Smaller fragments migrate more rapidly through the gel, resulting in their separation from larger fragments. This process allows for the visualization and analysis of DNA fragments within a sample.

differentiate between histone acetylation and DNA methylation.

histone acetylation and DNA methylation are two distinct epigenetic modifications that regulate gene expression by altering chromatin structure. Histone acetylation generally promotes gene activation by loosening chromatin structure, while DNA methylation generally leads to gene silencing by compacting chromatin structure.

If a bacterial cell is grown in nutrient rich, lactose free medium, what would you expect to see at the lac operon?

in nutrient-rich, lactose-free medium, the lac operon is typically repressed, and the expression of the lac genes is low or inactive. The lac repressor prevents unnecessary expression of the lac genes when lactose is not present as a substrate for metabolism.

In reference to question 8, what would happen if you then add lactose to the medium?

in the presence of lactose, the lac operon would be induced, leading to the expression of genes required for lactose metabolism and utilization by the bacterial cell.

Circle the correct item: The lac operon is repressible/inducible

inducible

How can mutations lead to natural selection?

mutations can give rise to an adaptation that leads to survival and reproduction for individuals in their environment. those with these advantageous mutations will survive and reproduce, while those without them will die

Fill in the blank: A change in an organisms genotype can cause a change in the organsims _____.

phenotype

Circle the correct item: The trp operon is repressible/inducible.

repressible

Circle the correct option: substitutions are small/large scale mutation

small

Referring to question 3, what is the codon that the tRNA binds to?

the complementary 3 nucleotide sequence

What functional group defines the 5' end of DNA?

the free phosphate group

Can a transformed organism pass on its new traits to its offspring?

the heritability of newly acquired traits in transformed organisms depends on whether the modifications are made to germline cells and the reproductive mechanisms of the organism. If modifications are made to germline cells and the organism reproduces sexually, the modified traits can be passed on to offspring. However, if modifications are made to somatic cells or the organism reproduces asexually, the heritability of the modified traits may vary.

Fill in the blanks: Protein synthesis occurs in two stages ___ and ___.

transcription and translation

Circle the correct option: microRNAs and siRNAs block transcription/translation.

translation