DNA Replication & Transcription and Translation

1) DNA polymerase always reads the template strand in the _____ direction 2) DNA polymerase creates the complimentary strand in the _____ direction

1) 3' --> 5' 2) 5' --> 3'

1) Histones are _____ charged 2) DNA is _____ charged

1) positively 2) negatively

DNA polymerase can only add DNA nucleotides off an existing _____

3' hydroxyl group

RNA polymerase synthesizes a daughter strand of RNA in the _____ direction

5' --> 3'

The end products of translation are: A. polypeptides B. amino acids C. lipids D. RNA E. DNA

A. Translation is the process in which ribosomes conduct the matching of tRNA with mRNA, producing an amino acid chain, or polypeptide.

Centrifuge

Centrifugation is one of the most useful and frequently employed techniques in the molecular biology laboratory. Centrifugation is used to collect cells, to precipitate DNA, to purify virus particles, and to distinguish subtle differences in the conformation of molecules

Gel Electrophoresis Steps

DNA fragments are cut up, DNA fragments are then put into the gel, electric current is ran through the gel, organizing the DNA fragments from smallest to largest the slight negative charge of DNA reacts with the positive electric current, with the DNA organized, it is then put back together in a easier way to be analyzed

Initiation of DNA replication

During DNA replication, the enzyme helicase unwinds the DNA helix, forming the replication fork. Singlestrand binding proteins attach to each strand of the uncoiled DNA to keep them separate. As helicase unwinds the DNA, it forces the double-helix in front of it to twist. A group of enzymes, called topoisomerases, break and rejoin the double helix, (always in front of the enzyme helicase) allowing the twists to unravel and preventing the formation of knots.

central dogma

The theory that states that, in cells, information only flows from DNA to RNA to proteins

What a problems occur when we arrive at the telomere (end of the chromosome in eukaryotic cells)

Two problems can occur when replication reaches the end of the DNA strand: 1) One occurs when not enough template strand remains to which primase can attach. 2) Another problem occurs when the last primase is removed. If there is no next Okazaki segment to which DNA polymerase can attach, the empty space left by the removal of the primer is left unfilled. Video: https://www.youtube.com/watch?v=i6nE6gUp2cw

_____ are extra sequences of nucleotides that are not necessary to create the corresponding protein

introns

The _____ is a short DNA sequence found upstream from the site where transcription of a specific RNA is going to take place

promoter region

exonuclease vs endonuclease enzymes

Exonucleases are a broad class of enzymes that cleave off nucleotides one at a time from the 3' or 5' ends of DNA and RNA chains. endonucleases, which hydrolyze internal phosphodiester bonds.

What is the function of polypeptides

Many polypeptides are enzymes that regulate chemical reactions, and these chemical reactions influence the resulting characteristics of the cell.

What is the wobble hypothesis

The Wobble Hypothesis explains why multiple codons can code for a single amino acid, tRNAs recognize more than one codon (the codons differ in their third nucleotide)

describe the differences between activators and repressors

activator proteins bind enhancers. These elements increase transcription repressor proteins bind silencers. These elements decrease transcription

Codons are translated from mRNA into _____

amino acids

Review: name the components of DNA (amino acids)

Both DNA and RNA are polymers of nucleotides. The nucleotide monomer consists of three parts—a nitrogen base, a sugar, and a phosphate. DNA is called deoxyribonucleic acid, while RNA is ribonucleic acid because DNA is missing the extra oxygen therefore DNA is deoxygenated

Microarray analysis

Microarray analysis is a method that uses microchips containing anchored arrays of short DNA elements (known as probes) for the large-scale interrogation of gene expression.

_____ proteins bind _____, and they work to decrease transcription

repressor; silencers

What is the process where DNA gene sequences are copied into mRNA?

transcription

Steps of DNA replication (synthesis)

1. Helicase unwinds the DNA, producing a replication fork (1A, 1B). •Single-strand binding proteins prevent the single strands of DNA from recombining (1C). •Topoisomerase removes twists and knots that form in the double-stranded template as a result of the unwinding induced by helicase (1D). 2. Primase (2A) initiates DNA replication at special nucleotide sequences (called origins of replication) with short segments of RNA nucleotides, called RNA primers (2B). 3. DNA polymerase III attaches to the RNA primers and begins elongation, the adding of DNA nucleotides to the complement strand ( 3'→ 5' direction). 4. The leading (complementary) strand is assembled continuously as the double-helix DNA uncoils. 5. The lagging strand (5A) is assembled in short Okazaki fragments (5B). Primase sets down RNA primers for each fragment and DNA polymerase begins to replicate the DNA on the lagging strand (5' → 3' direction). 6. DNA Polymerase I replaces the RNA primers on the Okazaki fragments wit the corresponding nucleotides and the DNA is joined together by ligase.

Transcription

1. In initiation, the RNA polymerase attaches to a promoter region on the DNA and begins to unzip the DNA into two strands. A promoter region for mRNA transcriptions often contains the sequence T-A-T-A (called the TATA box). 2. Elongation occurs as the RNA polymerase unzips the DNA and assembles RNA nucleotides using one strand of the DNA as a template. As in DNA replication, elongation of the RNA molecule occurs in the 5' → 3' direction. In contrast to DNA replication, new nucleotides are RNA nucleotides (rather than DNA nucleotides), and only one DNA strand is transcribed. 3. Termination occurs when the RNA polymerase reaches a special sequence of nucleotides that serve as a termination point. In eukaryotes, the termination region often contains the DNA sequence AAAAAAA.

1. Three kinds of RNA molecules are produced during transcription, as follows: (mRNA)

1. Messenger RNA (mRNA) is a single strand of RNA that provides the template used for sequencing amino acids into a polypeptide. A triplet group of three adjacent nucleotides on the mRNA, called a codon, codes for one specific amino acid. Since there are 64 possible ways that four nucleotides can be arranged in triplet combinations (4 × 4 × 4 = 64), there are 64 possible codons. However, there are only 20 amino acids, and thus, some codons code for the same amino acid. The genetic code provides the decoding for each codon. That is, it identifies the amino acid specified by each of the possible 64 codon combinations. For example, the codon composed of the three nucleotides cytosine-guanine-adenine (CGA) codes for the amino acid arginine. By aligning the C found in the first column with the G in the center part of the table and the A in the column at the far right. Note that three of the codons in the genetic code are stop codons. They signal an end to translation rather than code for an amino acid. Therefore, only 61 of the codons actually code for amino acids.

2. Three kinds of RNA molecules are produced during transcription, as follows: (tRNA)

2. Transfer RNA (tRNA) is a short RNA molecule (consisting of about 80 nucleotides) that is used for transporting amino acids to their proper place on the mRNA template. Interactions among various parts of the tRNA molecule result in base-pairings between nucleotides, folding the tRNA in such a way that it forms a three-dimensional molecule. (In two dimensions, a tRNA resembles the three leaflets of a clover leaf.) The 3' end of the tRNA (ending with cytosine-cytosine-adenine, or C-C-A-3') attaches to an amino acid. Another portion of the tRNA, specified by a triplet combination of nucleotides, is the anticodon. During translation, the anticodon of the tRNA base pairs with the codon of the mRNA. Exact base-pairing between the third nucleotide of the tRNA anticodon and the third nucleotide of the mRNA codon is often not required. This wobble allows the anticodon of some tRNA's to base-pair with more than one kind of codon. As a result, about 45 different tRNA's base-pair with the 61 codons that code for amino acids.

3. Three kinds of RNA molecules are produced during transcription, as follows: (rRNA)

3. Ribosomal RNA (rRNA) molecules are the building blocks of ribosomes. The nucleolus is an assemblage of DNA actively being transcribed into rRNA. Within the nucleolus, various proteins imported from the cytoplasm are assembled with rRNA to form large and small ribosome subunits. Together, the two subunits form a ribosome that coordinates the activities of the mRNA and tRNA during translation. Ribosomes have three binding sites— one for the mRNA, one for a tRNA that carries a growing polypeptide chain (P site, for "polypeptide"), and one for a second tRNA that delivers the next amino acid that will be inserted into the growing polypeptide chain (A site, for "amino acid").

Types of Point Mutations

A mutation may or may not have a significant effect. If an mRNA is produced from a DNA segment that contains a point mutation, one of the following results. 1. A silent mutation occurs when the new codon still codes for the same amino acid. This occurs most often when the nucleotide substitution results in a change of the last of the three nucleotides in a codon. For examples of codons that differ by their third nucleotide but code for the same amino acid. 2. A missense mutation occurs when the new codon codes for a new amino acid. The effect can be minor, or it may result in the production of protein that is unable to fold into its proper three-dimensional shape and, therefore, is unable to carry out its normal function. The hemoglobin protein that causes sickle-cell disease is caused by a missense mutation. 3. A nonsense mutation occurs when the new codon codes for a stop codon. Mutations can occur as a result of replication errors, or they may result from environmental effects such as radiation (for example, ultraviolet or x-ray) or reactive chemicals. Radiation or chemicals that cause mutations are called mutagens. Carcinogens are mutagens that activate uncontrolled cell growth (cancer).

Describe ribosomal binding sites and how they synthesized polypeptide chains

A ribosome has: mRNA binding site, and three tRNA binding sites: A, P, E Polypeptide synthesis takes place at the peptidyl and aminoacyl sites... or the P and A site. The P site holds the tRNA attached to the growing polypeptide chain. The A site holds the tRNA with its associated amino acid to the polypeptide chain. tRNA is discharged at the E site.

The lac operon in E. coli is involved in: A. regulating the expression of a gene B. regulating the translation of mRNA C. controlling the formation of ribosomes D. controlling DNA replication E. preventing the transfer of the F. plasmid

A. Operons are DNA segments that include a promoter region, an operator region, and a series of structural genes. Together with a regulatory gene lying outside the operon, the three parts of an operon work collectively to control transcription, which results in a regulation of gene expression.

Translation

After transcription, the mRNA, tRNA, and ribosomal subunits are transported across the nuclear envelope and into the cytoplasm. In the cytoplasm, amino acids attach to the 3' end of the tRNA's, forming an aminoacyl-tRNA. The reaction requires an enzyme specific to each tRNA and the energy from one ATP. The amino acid-tRNA bond that results is a high-energy bond, creating an activated amino acid-tRNA complex. As in transcription, translation is categorized into three steps—initiation, elongation, and termination. Energy for translation is provided by several GTP molecules. GTP acts as an energy supplier in the same manner as ATP. 1. Initiation begins when the small ribosomal subunit attaches to a special region near the 5' end of the mRNA. 2. A tRNA (with anticodon UAC) carrying the amino acid methionine attaches to the mRNA at the start codon AUG. (You can remember that the start codon is AUG because school often starts in August.) 3. The large ribosomal subunit attaches to the mRNA, forming a complete ribosome with the tRNA (bearing a methionine) occupying the P site. 4. Elongation begins when the next tRNA (bearing an amino acid) binds to the A site of the ribosome. The methionine is removed from the first tRNA and attached to the amino acid on the newly arrived tRNA. Figure 8-6 shows elongation after several tRNAs have delivered amino acids. The growing polypeptide is shown at 4. 5. The first tRNA, which no longer carries an amino acid, is released. After its release, the tRNA can again bind with its specific amino acid, allowing repeated deliveries to the mRNA during translation. 6. The remaining tRNA (together with the mRNA to which it is bonded) moves from the A site to the P site (translocation). Now the A site is unoccupied and a new codon is exposed. This is analogous to the ribosome moving over one codon. 7. A new tRNA carrying a new amino acid enters the A site. The two amino acids on the tRNA in the P site are transferred to the new amino acid, forming a chain of three amino acids. Figure 8-6 shows a chain of four amino acids. 8. As in step 5, the tRNA in the P site is released, and subsequent steps are repeated. As each new tRNA arrives, the polypeptide chain is elongated by one new amino acid, growing in sequence and length as dictated by the codons on the mRNA. 9. Termination occurs when the ribosome encounters one of the three stop codons. At termination, the completed polypeptide, the last tRNA, and the two ribosomal subunits are released. The ribosomal subunits can now attach to the same or another mRNA and repeat the process. Once the polypeptide is completed, interactions among the amino acids give it its secondary and tertiary structures. Subsequent processing by the endoplasmic reticulum or a Golgi body may make final modifications before the protein functions as a structural element or as an enzyme.

Components of the Operon and Control Mechanisms

Among prokaryotes, an operon is a unit of DNA that controls the transcription of a gene. It contains the following components. The kinds of operons described are in the bacterium E. coli, a common bacterium that lives in the digestive tracts of humans. 1. The promoter region is a sequence of DNA to which the RNA polymerase attaches to begin transcription. 2. The operator region can block the action of the RNA polymerase if this region is occupied by a repressor protein. 3. The structural genes contain DNA sequences that code for several related enzymes that direct the production of some particular end product. 4. A regulatory gene, lying outside the operon region, produces repressor proteins, substances that occupy the operator region and block the action of RNA polymerase. Other regulatory genes produce activator proteins that assist the attachment of RNA polymerase to the promoter region.

The two strands of a DNA molecule are connected by: A. hydrogen bonds between the codons and anticodons B. hydrogen bonds between the bases of one strand and the bases of the second strand C. hydrogen bonds between deoxyribose sugar molecules of one strand and deoxyribose molecules of the second strand D. covalent bonds between phosphate groups E. covalent bonds between the nitrogen bases

B. Weak hydrogen bonds form between bases of the two strands. In particular, a pyrimidine (a base with one nitrogen ring) in one strand bonds to a purine (a base with two nitrogen rings) in the second strand.

mRNA Processing

Before an mRNA molecule leaves the nucleus, it undergoes the following alterations: 1. A 5' cap (-P-P-P-G-5') is added to the 5' end of the mRNA. The 5' cap is a guanine nucleotide with two additional phosphate groups, forming GTP. Capping provides stability to the mRNA and a point of attachment for the small subunit of the ribosome. 2. A poly-A tail (-A-A-A . . . A-A-3') is attached to the 3' end of the mRNA. The tail consists of about 200 adenine nucleotides. It provides stability to the mRNA and also appears to control the movement of the mRNA across the nuclear envelope. 3. RNA splicing removes nucleotide segments from mRNA. A transcribed DNA segment contains two kinds of sequences—exons, which are sequences that express code for a polypeptide, and introns, intervening sequences that are noncoding. The original unprocessed mRNA transcript contains both the coding and the noncoding sequences. Before the mRNA moves to the cytoplasm, small nuclear ribonucleoproteins, or snRNP's, and splicosome delete the introns and splice the exons. 4. Alternative splicing allows different mRNA's to be generated from the same RNA transcript. By selectively removing different parts of an RNA transcript, different mRNA's can be produced, each coding for a different protein product.

All viruses consist of: A. DNA and a protein coat B. RNA and a protein coat C. a nucleic acid and a protein coat D. a nucleic acid and a phospholipid bilayer membrane E. proteins and polysaccharides

C. Viruses consist of a nucleic acid (DNA or RNA) surrounded by a protein coat. Some viruses contain an envelope made from lipids or glycoproteins obtained from the membranes of their hosts but they do not have the phospholipid bilayer membrane typical of cells.

Mechanisms of gene expression in eukaryotic cells include the following

Chromatin structure can be regulated to Promote or Demote Transcription: A) Genes with heterochromatin are highly condensed and not normally expressed where as euchromatin is much more loosely packed B) Histones are acetylated: allowing for less tightly packing of chromatin, hence allowing for better transcription... Histone acetylation promotes transcription! C) DNA methylation: when CH3 groups are added, tighter packing occurs, thus we can see a reduction in gene expression. In other words, inactivated genes are usually heavily methylated, and certain genes are activated by removal of the CH3 group called demethylation.

ATP, the common energy-carrying molecule, most resembles the: A. adenine DNA nucleotide B. adenine RNA nucleotide C. adenine DNA nucleotide with two extra phosphates D. adenine RNA nucleotide with two extra phosphates E. adenine nitrogen base

D. Since ATP contains the adenine nitrogen base, the sugar ribose (not deoxyribose), and three phosphate groups, it is equivalent to the adenine RNA nucleotide with two extra phosphate groups. In contrast, an adenine DNA nucleotide with two extra phosphates contains a deoxyribose sugar and would be written as dATP

Types of Mutations

DNA replication is not perfect, and errors occur. If an error is not repaired, it becomes a mutation. A mutation is any sequence of nucleotides in a DNA molecule that does not exactly match the original DNA molecule from which it was copied. A point mutation is a single nucleotide error and includes the following. 1. A substitution occurs when the DNA sequence contains an incorrect nucleotide in place of the correct nucleotide. 2. A deletion occurs when a nucleotide is omitted from the nucleotide sequence. 3. An insertion occurs when a nucleotide is added to the nucleotide sequence. 4. A frameshift mutation occurs as a result of a nucleotide deletion or insertion. Such mutations cause all subsequent nucleotides to be displaced one position. If a frameshift mutation occurs in a DNA segment whose transcription produces an mRNA, all codons following the transcribed mutation will change. 5) Transposons: Some DNA segments within a DNA molecule can move to new locations. These transposable genetic elements, called transposons (or jumping genes) can move to a new location on the same chromosome or to a different chromosome. Some transposons consist only of DNA that codes for an enzyme that enables it to be transported. Other transposons contain genes that invoke replication of the transposon. After replication, the new transposon copy is transported to the new location. Wherever they are inserted, transposons have the effect of a mutation. They may change the expression of a gene, turn on or turn off its expression, or have no effect at all.

Which of the following would most likely cause a mutation with the greatest deleterious effect? A. An insertion of a nucleotide triplet into a DNA strand that codes for an mRNA B. A deletion of a nucleotide triplet from a DNA strand that codes for an mRNA C. A single substitution of a nucleotide in a DNA strand that, when transcribed, results in a change in the nucleotide occupying the third codon position in an mRNA D. A single substitution of a nucleotide in a DNA strand that, when transcribed, results in a change in the nucleotide occupying the first codon position in an mRNA E. A single addition of a nucleotide in a DNA strand that codes for an mRNA

E. An addition of a nucleotide in a DNA strand that codes for mRNA produces a frameshift mutation. As a result, the first nucleotide in every codon will become the second; the second nucleotide will become the third; and the third nucleotide will become the first nucleotide of the next codon. Such an arrangement is likely to change many of the amino acids in the sequence (depending upon where in the sequence the frameshift begins) and, thus, considerably affect the final sequence of the polypeptide. Answer choice C may have no effect at all because a change in the third position of a codon will often code for the same amino acid. (This results from the wobble of the third position of the tRNA anticodon.) Answer choices A and B will result in an additional amino acid and a missing amino acid, respectively, and answer choice D will change one amino acid to a different amino acid. These changes may change the effectiveness of the polypeptide, but not as severely as changing many amino acids, as would occur in answer choice E. The inherited disorder sickle-cell disease is caused by the replacement of one amino acid by another in two chains of the hemoglobin protein, severely reducing the effectiveness of hemoglobin in carrying oxygen. However, a frameshift in the mRNA coding for hemoglobin would certainly make it entirely ineffective.

Where are ribosomes synthesize andsynthesize eukaryotes

Eukaryote ribosomes are made in the nucleolus of the cell

DNA (chromosomal) organization in eukaryotes

In eukaryotes, DNA is packaged with proteins to form a matrix called chromatin. The DNA is coiled around bundles of eight or nine histone proteins to form DNA-histone complexes called nucleosomes. Through the electron microscope, the nucleosomes appear like beads on a string. During cell division, DNA is compactly organized into chromosomes. When the cell is not dividing, the DNA is arranged as either of two types of chromatin, as follows. 1. Euchromatin: describes regions where the DNA is loosely bound to nucleosomes. DNA in these regions is actively being transcribed. 2. Heterochromatin: represents areas where the nucleosomes are more tightly compacted and where DNA is inactive. Because of its condensed arrangement, heterochromatin stains darker than euchromatin.

Describe transcription factors

In eukaryotic cells, RNA polymerases cannot directly detect and bind to the promoter region. They require the binding of transcription factors. Transcription factors are regulatory proteins that bind to promoter DNA and affect the recruitment of RNA polymerases. Eukaryotic promoter sequences tend to contain a region known as the TATA box. TATA boxes are recognized by transcription factors. Transcription factors can either increase rate of transcription (Up Regulation) or decrease the rate of transcription (Down-Regulation).

What is semiconservative replication?

In semiconservative replication, the original two strands of the double helix serve as templates for new strands of DNA. When replication is complete, two double-stranded DNA molecules will be present. Each will consist of one original template strand and one newly synthesized strand that is complementary to the template.

PCR (polymerase chain reaction)

Instead of using a bacterium to clone DNA fragments, fragments can be copied millions of times by using DNA polymerase directly. This method, called polymerase chain reaction, or PCR, uses synthetic primers that initiate replication at specific nucleotide sequences.

what is the difference between a nucleotide and a nucleoside

Nucleotide: a compound consisting of a nucleoside linked to a phosphate group. Nucleotides form the basic structural unit of nucleic acids such as DNA. Nucleoside: a compound (e.g., adenosine or cytidine) commonly found in DNA or RNA, consisting of a purine or pyrimidine base linked to a sugar.

Composition of Ribosomes

RNA ribosome is a complex of rRNA molecules (RNA nucleotides) and proteins (amino acids). The remaining choices are incorrect because a messenger RNA molecule is single-stranded (not a double helix), the uracil nucleotide contains a ribose sugar (not a deoxyribose sugar), adenine nucleotides base-pair with uracil nucleotides, and both DNA and RNA are produced in the nucleus. More Info: Eukaryotic ribosomes are larger. They consist of a 60S large subunit and a 40S small subunit, which come together to form an 80S particle. Prokaryotic 70S ribosome. The 40S subunit contains an 18S RNA that is homologous to the prokaryotic 16S RNA.

In the initial nucleotide chain primase adds a primer is this primer made up of RNA or DNA

The initial nucleotide chain is actually a small RNA stretch, not DNA. This is what is called an RNA primer and uses the enzyme primase. This enzyme starts an RNA chain using the parental DNA strand as a template.

The lac Operon

The lac operon in E. coli controls the breakdown of lactose (catabolism). A regulatory gene produces an active repressor that binds to the operator region. When the operator region is occupied by the repressor, RNA polymerase is unable to transcribe several structural genes that are consecutively expressed (lac Z, lac Y, lac A) and code for enzymes that control the uptake and subsequent breakdown of lactose. When lactose is available, however, some of the lactose (in a converted form) combines with the repressor to make it inactive. When the repressor is inactivated, RNA polymerase is able to transcribe the genes that code for the enzymes that break down lactose. Since a substance (lactose, in this case) is required to induce (turn on) the operon, the enzymes that the operon produces are said to be inducible enzymes.

Describe the origin of replication in eukaryotes and prokaryotes

The origin of replication is a particular sequence in a genome at which replication is initiated. Propagation of the genetic material between generations requires timely and accurate duplication of DNA. Eukaryotes have multiple origins of replication. Prokaryotes have a single origin.

The trp Operon

The trp operon in E. coli (anabolism, negative feedback loop) produces enzymes for the synthesis of the amino acid tryptophan. A regulatory gene produces an inactive repressor that does not bind to the operator. As a result, the RNA polymerase proceeds to transcribe the structural genes necessary to produce enzymes that synthesize tryptophan. When tryptophan is available to E. coli from the surrounding environment, the bacterium no longer needs to manufacture its own tryptophan. In this case, rising levels of tryptophan induce some tryptophan to react with the inactive repressor and make it active. Here tryptophan is acting as a corepressor. The active repressor now binds to the operator region, which, in turn, prevents the transcription of the structural genes. Since these structural genes stop producing enzymes only in the presence of an active repressor, they are called repressible enzymes.

Mechanisms to Prevent Mutations

There are various mechanisms to repair replication errors, including the following. 1. Proofreading of a newly attached base to the growing replicate strand is carried out by DNA polymerase. DNA polymerase checks to make sure that each newly added nucleotide correctly base pairs with the template strand. If it does not, the nucleotide is removed and replaced with the correct nucleotide. 2. Mismatch repair enzymes repair errors that escape the proofreading ability of DNA polymerase. 3. Excision repair enzymes remove nucleotides damaged by mutagens. The enzymes identify which of the two strands of the DNA contain a damaged nucleotide and then use the complementary strand as a template to repair the error.

How do we solve the problem that occurs at the telomere of the chromosome

To solve these problems and to prevent the loss of DNA in the replicate strand, the enzyme telomerase is used. •Telomerase attaches to the end of the template strand and extends the template strand by adding a short sequence of DNA nucleotides over and over again. This allows elongation of the lagging strand to continue. •Eventually, telomerase stops elongating the template strand, and ultimately DNA polymerase will be unable to replicate the new, extended portion of the template (for the same reasons as cited previously). •However, the DNA in the extended region of the template strand is just repeating short segments of nucleotides (generated from the built-in template of telomerase or telomeric repeat sequences) and merely acts to prevent the loss of important coding DNA that precedes it.

How does RNA polymerase differ from DNA polymerase

Unlike DNA polymerase, RNA polymerase does not proofread for any errors... thus more errors occur during transcription than for replication. Luckily, an error during transcription gives a "bad" protein and not transmitted to the entire progeny if it occurred with DNA

Protein Structure

What stabilizes the alpha Helix has within proteins? A) ionic bonding this option is incorrect because ionic bonds play an important role in tertiary and quaternary structures B) disulfide bonds this option is incorrect because these are observed and tertiary structures C) hydrophobic effect this option is incorrect because it is mostly observed in tertiary structures D) hydrogen bonding this auction is correct because the secondary structure is driven and reinforced by hydrogen bonding between a carbonyl oxygen and an amino hydrogen E) non-covalent interaction this option is incorrect because these are observed and quaternary structures and also and secondary structures but not to the extent of hydrogen bonding

different mRNA molecules are produced from the same pre-mRNA primary transcript due to _____

alternative splicing

In tRNA, triplet sequences of nucleotides that are complementary to mRNA codons are called _____

anticodons

1 side of the DNA helix runs in the opposite direction to the other (5' to 3' and 3' to 5') - this is known as the _____ _____ of DNA

antiparallel arrangement

DNA is transcribed into mRNA and arranged into triplets known as _____

codons

_____ occurs when transcription factors decrease rates of transcription

down regulation

_____ are the nucleotides necessary to make the protein

exons

a 5' _____ _____ and a 3' _____ _____ are post-transcriptional modifications to mRNA, which provide protection against enzyme degradation after the mRNA leaves the nucleus

guanine cap, poly-A tail

the trp operon is an example of a _____ operon

repressible

The nucleotide structural component of ribosomes is _____

ribosomal RNA (rRNA)

the introns are _____ out by the _____ leaving only the exons behind

spliced, spliceosome (enzyme only found in eukaryotes)

_____ do not code for amino acids; rather, they signal the ribosome to stop translation (termination)

stop codons UAG, UAA, or UGA (they do not code for amino acids)

in translation initiation, the ribosome scans the mRNA until it binds to the _____

the start codon is the codon that signals the start of translation - what is it and what amino acids does it code for? start codon (AUG)

_____ creates small nicks within the DNA double helix ahead of the replication fork, to relieve tension created by DNA helicase

topoisomerase

in eukaryotic cells, RNA polymerases cannot directly detect and bind to the promoter region - they require the binding of _____

transcription factors regulatory proteins that bind to promoter DNA and affect the recruitment of RNA polymerases in eukaryotes

mRNA sequences pass through how many ribosomal subunits during translation

two

____ occurs when transcription factors increase rates of transcription

up regulation

Lagging Strand DNA Replication

•For the 5' → 3' template strand, however, the DNA polymerase moves away from the uncoiling replication fork. This is because it can assemble nucleotides only as it travels in the 3' → 5' direction. •As the helix is uncoiled, DNA polymerase assembles short segments of nucleotides along the template strand in the direction away from the replication fork. •After each complement segment is assembled, the DNA polymerase must return back to the replication fork to begin assembling the next segment. These short segments of complementary DNA are called Okazaki segments. •The Okazaki segments are connected by DNA ligase, producing a single complement strand. Because this complementary strand requires more time to assemble than the leading strand, it is called the lagging strand.

Leading Strand DNA Replication

•Since a DNA double-helix molecule consists of two opposing DNA strands, the uncoiled DNA consists of a 3' → 5' template strand and a 5' → 3' template strand. •The enzyme that assembles the new DNA strand, DNA polymerase III, moves in the 3' → 5' direction along each template strand. •A new (complement) strand grows in the antiparallel, 5' → 3' direction. •For the 3' → 5' template strand, replication occurs continuously as the DNA polymerase follows the replication fork, assembling a 5' → 3' complementary strand. (The complementary strand is called the leading strand).