Genetics Exam 2

What is a genome? Where are the genomes in a eukaryotic cell?

A genome is all the genetic materials of an organism. The genomes are housed in the nucleus of a eukaryotic cell.

What is a chromosome? What is found on chromosomes?

Chromosomes are the genetic materials that are passed from cell to cell during the formation of gametes. Genes are found of chromosomes.

What different compositions may viral genomes have?

Smooth strains and rough strains. The smooth strains create a capsule of the cell, making it more dangerous.

Describe the shape and organization of bacterial chromosomes.

Bacterial chromosomes are circular and are found in the nucleoid region of a bacterial chromosome. They can be folded into loop domains to be able to fit into the cell.

What is DNA supercoiling? What is a topoisomer of DNA? Why are these structural changes of DNA important to functionality of the genome?

DNA can supercoil in order to be more compact, but it decreases the functionality of the genome. If an area is heavily supercoiled, it cannot be functional. A topoisomer of DNA is a different topographical shape of DNA conformations (More turns vs less turns)

Do eukaryotic chromosome number and size correlate to organism complexity? Why?

No. This phenomena is called the c-value paradox which states that a large genome size does not equal a high complexity.

Understand the basic structure of eukaryotic chromosomes.

Eukaryotic chromosomes contain multiple origins of replication with a centromere and two telomeres.

Understand the C0t curve and how these renaturation experiments give one information about genome complexity.

C0t curves show the ability of renaturation after the DNA double helix was broken apart. The resulting graph shows how much the DNA is composed of highly repetitive, moderately repetitive, and unique DNA.

What is a nucleosome? What did Noll demonstrate about nucleosomes?

A nucleosome is a structure composed of a histone protein with DNA wrapped around it (8 histone proteins + 146/147 base pairs). Noll determined this by showing how the DNA is broken up into roughly 200 base pair fragments, which consist of the histones and base pairs in one nucleosome.

Describe the higher orders of structure present in eukaryotic chromatin.

Nucleosomes with linker DNA -> 30 nm fibers (solenoid or zigzag) -> radial loop domains -> euchromatin (less acetylation, more active) or heterochromatin (more acetylation, less active)

What is heterochromatin? How is it different from euchromatin? What determines this structural remodeling of chromatin?

Heterochromatin is the more compact portion of DNA and euchromatin is less compact. Acetylation determines the structural remodeling of chromatin.

Explain how Meselson and Stahl demonstrated that DNA replication is semiconservative.

Shows "half-heavy" DNA strands in F1, consistent with the semi-conservative model and dispersive model. In F2, two types "light" and "half-heavy" are shown, consistent with only semi-conservative.

Explain the initiation of DNA replication at oriC. What are the functions of the DnaA proteins, helicase, and the AT rich regions?

DnaA protein bonds to DnaA boxes, initiated negative supercoiling, which causes the AT-rich regions to separate. Helicase then keeps the separation consistent in both directions.

What is topoisomerase? Why is it necessary?

Topoisomerase induces negative supercoiling to alleviate the positive supercoiling from the replication fork.

What is DNA polymerase? How does it polymerize DNA?

DNA polymerase III synthesizes a complementary strand of DNA from the template strand.

How are the leading and lagging different? What is an Okazaki fragment? Why are these differences necessary? What is a T1 sequence? What is Tus?

The leading strand is a continuous strand of 5' to 3', while the lagging strand also runs 5' to 3', but in Okazaki fragments that are put together by DNA ligase. This is necessary because DNA can only be synthesized from 5' to 3'. Tus "blows up" the replication fork by binding to the T1 site.

What is DNA primase? Why is it necessary?

DNA primase creates an RNA primer on the lagging strand for DNA polymerase III to start synthesizing on. It is necessary because the lagging strand needs constant initiation sites to be able to make the lagging strand work.

How does the proofreading activity of polymerase enzymes work?

DNA Polymerase II, IV, V, and III all have proofreading abilities. This is done by an exonuclease digesting the error present until the incorrect nucleotide is removed.

How do methylation and DnaA boxes help regulate the rate of DNA replication?

The DNA needs to wait for all the adenicines to be methylated, as well as enough DnaA proteins to be made.

How were most of the enzymes involved in DNA replication discovered?

Mutagenesis: "Breaking them" to see their function.

Contrast DNA replication in eukaryotes with that seen in prokaryotes.

Eukaryotic chromosomes have long, linear chromosomes that are tightly compact and have more complicated cell cycles. All of the same enzymes as prokaryotes, but there are multiple origins of replication with high proportions of A and T bonds.

What are the functions of the alpha, delta, and epsilon in eukaryotic DNA replication?

They are the core polymerase types and they all function to replicate non-damaged DNA during S phase. The polymerase switch is when the polymerase alpha lays down the RNA primer and then switches to the delta to take over elongating the lagging strand.

What are telomeres? Why are they necessary?

Telomeres have repeat sequences that degrade and are lost during DNA replication. They are necessary to protect the important genes of the genome and if the genome is lost, the cell would go into apoptosis.

What is telomerase?

Telomerase extends telomeres to replenish them for new generations.

What is gene expression? What is the central dogma (yuk) of gene expression?

DNA->RNA->Protein/Product.

Understand the concept of a regulatory sequence, a promoter, and a terminator.

A regulatory sequence is a binding site for regulatory proteins that influence when, where, and how much of the product is made. Promoters are sites for RNA polymerase to bind and signal the beginning of transcription. A terminator signals the end of transcription.

What are transcription factors?

Transcription factors recognize the promoter and regulatory sequences to control transcription.

What are the three stages of transcription?

Initiation, elongation, and termination.

What are some of the varied functions of RNA in cells?

mRNA, tRNA, rRna

How are bases in the promoter numbered? What is a consensus sequence?

They are generally numbered by the consensus sequence, which is an average of the bases in different species.

What is RNA polymerase? What is the role of the -10 and -35 promoter sequences in initiation of transcription?

RNA polymerase binds to the -35 and -10 sequences to begin transcription.

Describe the elongation stage of transcription.

The binding of the RNA polymerase to the promoter regions creates a closed complex that includes the sigma factor. Then, the open complex is formed when the TATAAT box in the -10 region is unwound, and the sigma factor is released. Then the core enzyme slides down the DNA to synthesize an RNA strand.

Compare and contrast the processes of rho-dependent and rho-independent termination.

Rho-dependent termination happens when the rho recognition site (rut) binds to the rho protein and causes the rho protein (a helicase) to cause a stem-loop, then makes RNA polymerase pause. Rho-independent occurs when a stem-loop causes RNA polymerase to pause, then the u-rich region bonds break.

What is the core promoter of eukaryotes?

The TATA box.

What is meant by “regulatory element”?

Regulatory elements affect the binding of RNA polymerase to the promoter. There are enhancers that stimulate transcription and silencers that inhibit transcription.

Contrast cis and trans acting elements.

Cis-acting elements are next to the location of transcription, while the trans-acting elements are coded for somewhere else far away.

Contrast initiation of transcription in eukaryotes with what you have learned about prokaryotes.

Initiation begins when TFIID binds to the TATA box, when then TFIIB binds to D, and then F, which brings in RNA polymerase.

What are introns? Exons?

Introns are intruders, exons are the important coding sequences.

What is the 5’ cap? The poly-A tail?

Modification that keep the mRNA from wearing away.

How is mRNA processed in eukaryotes? rRNA? tRNA?

Splicing, 5' capping, 3' poly-A tailing, then RNA editing and base modification for rRNA or tRNA.

What is a spliceosome? How are introns excised and exons spliced?

A spliceosome is made of ribozymes and is how RNA is processed and the introns are cut out. There are 5' and 3' splice sites where the introns begin and end, and the spliceosomes create a lariat structure, which gets cut off and then the two exons connect.

How did Crick show that the genetic code is triplet?

He discovered that if he deleted a single base or two bases, an entire frame shift would occur, but if three were taken out, then everything would still be in the frame, making 3 the magic number.

How were synthetic RNA and copolymers used to further elucidate the code?

Synthetic RNA was made and the codon possibilities were then incorporated into polypeptides.

What is the structure of a polypeptide?

A polypeptide has an amino terminus, an r group, a carboxyl terminus, a hydrogen, and a central carbon.

What is an anticodon? What is tRNA wobble?

An anticodon is the part of tRNA that is recognized my mRNA to get the correct amino acid for a specific polypeptide chain. tRNA wobble is when the 3' closest bond in a codon has a weaker interaction, leading to some mistakes in that bond.

What is the structure of a ribosome?

E = exit, P = peptidyl, A = aminoacyl. There is a large and small subunit.

How is translation initiated?

Initiation occurs at the ribosome binding site, which is a few base pairs before the AUG. The start codon AUG is then brought to the P site. Initiation also requires several initiation factors (mRNA ->small subunit -> IF3 binds -> IF2 binds -> large subunit is brought in and kicks out IF3 and IF2).

How does elongation during translation work? What are the functions of the E, P, and A

The next tRNA goes into the A site, and then a full shift 5' to 3' of the ribosome occurs, making the A site open again. the tRNA's amino acid is binded to the polypeptide chain, and is then shifted to the E site to exit.

How is translation terminated?

A stop codon goes into the A site and brings in a release factor, which makes the polypeptide be released from the tRNA in the P site. Then, everything dissociates.

What are sorting signals? What is the difference between co-translational and posttranslational sorting?

Sorting signals direct a protein to is correct location. Cotranslational sorting occurs during translation and posttranslational sorting occurs after translation.