exam 6 final test review
Why might the genomic analyses of dogs be particularly useful for investigating the genes responsible for body size and other physical characteristics?-
Within a single species, individual dogs show enormous variation in body size and substantial diversity in other physical characteristics. Therefore, genomic analyses of individual dogs would provide valuable clues concerning the genes responsible for the diversity within the species.
6) What is Ricin and what does it do?
- A Ribosomal inhibiting protein that cleaves an adenine from the 28S rRNA molecule in eukaryotes. This prevents the binding of elongation factor, disrupting protein synthesis.
16) What are codons and anti-codons?
- A codon is a three-base sequence (three nitrogen bases in a row) on mRNA. It calls for a specific amino acid to be brought to the growing polypeptide. - An anticodon is a three-base sequence on tRNA. It matches the codon. That's how the right amino acid is put onto the polypeptide next. The tRNA must fit its anticodon onto the mRNA codon like a jigsaw puzzle piece. Each tRNA can only bring one kind of amino acid.
10) What is a micro array?
- A microarray is a sequence of dots of DNA, protein, or tissue arranged on an array for easy simultaneous analysis. The most famous is the DNA microarray, which plays an integral role in gene expression profiling.
5) What are DNA vectors?
- A piece of DNA readily taken up and replicated by bacteria
7) How does the peptide bond formation occur?
- A region on the 23S rRNA molecule of the Large Subunit enables a peptide bond to form between the carboxyl terminus of the fMet and the free amino terminus of the aminoacyl-Trna
2) What is the Ames test? How was it formulated? What organism is used? What modifications make it more relevant to eukaryotes?
- A strain of Salmonella typhimurium that has a defect in its histidine biosynthetic pathway (and must grow on media supplemented with the amino acid histidine) is exposed to the potential carcinogen. The number of revertants (above background levels) that grow on media that does not contain histidine, is a measure of the strength of mutagenic agent.
12) What is the start codon?
- AUG is the "start" codon and codes for the amino acid Methionine
6) What is alternative splicing?
- Alternative splicing is a mechanism by which multiple protein products can be produced from a single primary transcript by alternating how the transcript is spliced
2) What is a helicase?
- An enzyme that binds and unwinds DNA
What is ligase?
- An enzyme that seals the "nicks" by making phosphodiester bonds between Okazaki fragments.
14) Why do eukaryotes have to compact their DNA? How do they use it? How do they do it?
- Because the linear length of DNA is nearly 1,000 times the length of a single cell. They use supercoiling to compact the DNA. Eukaryotes wind around proteins like wire around a bale of hay.
14) Why are aminoacyl tRNA synthetases really the only enzyme that knows the genetic code?
- Because they use the anticodon bases and other nucleotides on the tRNA molecule to ensure that the correct amino acid gets on the correct tRNA and also because they're very specific.
11) What is Watson-Crick Base Pairing? Which DNA did they use A,B or Z?
- Cytosine binds with Guanine via 3 hydrogen bonds Adenine binds with Thymine via 2 hydrogen bonds They used B DNA
6) Why is DNA synthesis semi-discontinuous?
- DNA replication is called semi-discontinuous because one strand is synthesized continuously (the leading strand) and the other strand is synthesized discontinuously in small fragments (the lagging strand).
What are the forces that stabilize DNA structure?
- DNA structure is stabilized by the hydrogen bonding between base pairs and by van der Waals interactions that result from the stacking of bases
3) Why do organisms use Thymine instead of Uracil in DNA?
- Despite uracil's tendency to pair with adenine, it can also pair with any other base, including itself. By adding a methyl group (which is hydrophobic) and turning it into thymine, its position is reorganized in the double-helix, not allowing those wrong pairings to happen
8) What is Sanger or Dideoxy sequencing
- Dideoxy sequencing (also called chain- termination or Sanger method) uses an enzymatic procedure to synthesize DNA chains of varying lengths, stopping DNA replication at one of the four bases and then determining the resulting fragment lengths.
17) What are stem-loop structures?
- Double stranded regions within a single RNA molecule, involved with regulation. RNA will form double-stranded regions within a single molecule that are called secondary structural elements. These secondary structural elements are termed stem-loop structures
2) What are the 3 important sites of a ribosome and what occurs in each one?
- E Site (Exit): Exit site where empty tRNA molecules leave the ribosome - P Site (Peptidyl): Site where the Methionine-tRNA initially bind - A Site (Aminoacyl): Site where the Aminoacyl-tRNA molecule designated by the second codon on the mRNA binds
19) What are telomeres?
- Ends of chromosomes which keep the linear chromosome from shortening each time they are replicated
2) What is the genetic structure of eukaryotic genes (introns and exons)? What extra burden do these impose on transcription?
- Exons are regions of the gene that code for the amino acids that make up the protein that is produced in translation (they are expressed). - Introns are intervening sequences in the genes that although they are part of the primary transcript, are spliced out during processing and do not code for amino acids in the protein product.
10) What are post-transcriptional modifications of ribosomal RNA and tRNA in prokaryotes?
- For rRNA and tRNA molecules post-transcriptional modifications are usually required. A primary transcript may contain more than one gene product which all need to be cleaved out of larger molecules. Ribonucleases are responsible for these cleavages
7) Why are GC and AT pairs important?
- GC bonds via 3 hydrogen bonds while AT bonds with only 2
1) What did Griffith have to do with the concept of transformation?
- Griffith used Streptococcus pneumoniae in mice and inserted a dead (heated) III-S smooth (virulent) and II-R rough (nonvirulent) strain into the mouse and the mouse died. When the II-R strain was put in the mouse by itself, the mouse lived; and vice versa for the III-S strain. He concluded that the II-R strain transformed into the III-S using DNA as a "transforming factor."
16) What proteins make up the octamer of the nucleosome? What does H1 do?
- Histone proteins form an octamer with a + charge. The (-) phosphodiester backbone of the linear DNA wraps around the octamer. - Histone protein H1 then helps the DNA-protein octamers associate. Other proteins then help the further condensation of DNA to form chromatin
4) What are some examples of hormones that affect transcription? (estrogen, estradiol, thyroid)
- Hormones (like estradiol) are hydrophobic and can diffuse across the cell membrane and attach to receptor proteins inside the cytoplasm or nucleoplasm. - When estrogen is not bound to the receptor protein, it is inactive and transcription is not initiated while. - In the case of thyroid hormone when their receptors are bound transcription is repressed because the proteins can bind corepressor proteins that inhibit transcription.
9) What holds the DNA double helix together?
- Hydrogen bonding and Van Der Waal interactions
15) What are the mechanisms that ensure the correct amino acid is put on the correct tRNA molecule?
- In addition to the specificity of incorporation due to specific active site interactions with the incoming amino acid, the aminoacyl-tRNA synthetase also has an editing site separate from the active site. - The CCA-amino acid "arm" can swing from the active site to the editing site so that it can check to see if the correct amino acid is attached. If it is not, then the bond is hydrolyzed and the enzyme can try to attach the correct amino acid again. - Amino acids larger than the correct amino acid won't fit into the active site, and only smaller amino acids will fit into the editing site. This is an elegant economy of function. - Aminoacyl-tRNA synthetases also use the anticodon bases and other nucleotides on the tRNA molecule ( to ensure that the correct amino acid gets on the correct tRNA.
13) What are inducible and repressible operons? What is Catabolite Activator Protein?
- Inducible Operons - transcription is normally shut off, and can be turned on under certain circumstances - Repressible Operons - When an inducer binds to a repressor, it changes the conformation so that it can no longer bind to the operator - CAP - Catabolite Activator Protein - bind cAMP and changes its conformation so that it can bind to promoter regions and recruit RNA polymerase
1) What are the 3 steps of translation?
- Initiation: The initiator codon (AUG) is lined up correctly by using a region upstream of AUG start codon to position it (Shine-Dalgargno Sequence). Once the mRNA is lined up correctly with the 30S subunit, the Met-tRNA in the P site of the ribosome. - Elongation: the A site is unoccupied and has the second codon on the mRNA molecule in it. Elongation factor Tu brings in the amionacyl tRNA-synthetase whose anticodon will correctly complementary base pair with the second codon. - Termination: When a stop codon is reached, Release Factor interacts with the ribosome to hydrolyze the bond in the final aminoacyl tRNA molecule.
13) What enzymes help prokaryotes supercoil their DNA? Why do they even have to supercoil their DNA?
- It is done in order to compact the DNA - supercoiling it is achieved by enzymatic activity by topoisomerases. Prokaryotes anchor their DNA and wind like a rubber band
7) What is the function of the 7-methyl guanosine cap? polyA tail?
- It stabilizes mRNAs by protecting their 5' ends from phosphatases and nucleases. Caps enhance the translation of mRNA by eukaryotic protein-synthesizing systems. - The presence of the polyA tail enhances the translation efficiency of the mRNA as well as increases its stability.
7) What are Complementary (cDNA) libraries
- Library that contains only the expressed genes
6) What is a genomic library?
- Library that contains the entire Genome
4) For Eukaryotes, know what eukaryotic ribosomes small subunits use to position the start codon in the P site in eukaryotic RNA
- Met-tRNA is used instead of FMet-tRNA for initiation. The small subunits use the 5' cap on the mRNA molecule as a starting point and just moves down until it finds the first AUG codon and starts there.
1) What do the terms mismatch repair, base excision repair, and nucleotide excision repair mean?
- Mismatch Repair - the template strand is methylated, and the newly synthesized strand has not been methylated. An exonuclease excises out a region around and including the error. - Base Excision Repair - the nucleotide base is clipped from the DNA backbone by a glycosylase. AP endonuclease nicks the backbone. DNA pol I inserts a replacement nucleotide and ligase seals the nick - Nucleotide Excision Repair - UvrABC enzyme system cuts out a region of DNA including the dimer and DNA pol I fills the gap and ligase seals it.
11) What is the tri-nucleotide sequence and where all tRNA's ended?
- NA Polymerase III transcribes transfer RNAs (tRNAs). The 5' end is trimmed by RNase P, the 3' end is trimmed and the trinucleotide sequence CCA is added (if necessary), and ribose sugars and nucleotide bases are extensively chemically modified. - Many eukaryotic tRNAs also undergo splicing to remove internal sequences. - Nucleotides may be added to the 3' ends of some RNA molecules. ALL tRNA molecules end in the sequence CCA, which is added to tRNAs that do not already have it. - In tRNAs a variety of chemical modifications occur, including the conversion of uracil to pseudo uracil, or thymine
3) What are Southern, Northern and Western blotting
- Northern: The Northern blot is a technique used in molecular biology to study gene expression by detection of RNA - Southern: The same thing but for DNA - Western: It's an adaptation of the Southern Blot, used to identify specific amino-acid sequences in proteins.
2) Be able to tell if a DNA sequence is palindromic or not
- Palendromic means that the DNA sequence reads the same in either direction (right to left or left to right). Example: racecar, mom.
3) How many RNA polymerases are there in prokaryotes and eukaryotes?
- Prokaryotes - 1 - Eukaryotes - 3
18) What are the differences in the sizes of large and small subunits in prokaryotes vs eukaryotes?
- Prokaryotes: 70S ribosome made of: 50S Large Subunit (consisting of the 23S rRNA, the 5s rRNA, and 34 proteins) and a 30s Small Subunit (consisiting of the 16S rRNA and 21 proteins). - Eukaryotes: 80S ribosome made of: 60S large subunit (5S rRNA and 28S rRNA, 5.8S rRNA and 46 proteins) 40S small subunit (18S rRNA and 33 proteins)
3) In prokaryotic replication: where is it done, what enzymes are involved, and how is it done? What is primase?
- Prokaryotic replication takes place at an origin or replication (eg. in E. coli - OriC) DnaB (an ATP-hydrolyzing helicase) unwinds DNA strands and single-strand-binding proteins stabilize the single stranded regions - Primase synthesizes a short region of RNA complementary to the DNA strand to provide a free 3' OH group for DNA synthesis. Primers are removed by 5' 3' exonuclease prior to the completion of replication
What are promoters, sigma factors, terminators and Rho proteins?
- Promoters - The regions that occur in the 5' region before genes and are recognized by the sigma factor of RNA polymerase in prokaryotes. - Termination of RNA synthesis may also occur due to the interaction of Rho proteins, which bind to the growing RNA chain and finds regions rich in Cytosine and poor in Guanonine. Rho moves down the chain and finds the RNA pol causing the RNA to dissociate from the DNA template.
12) What are major and minor grooves in DNA structure? Where do proteins usually interact? Why?
- Proteins usually interact with DNA through the major groove, since they have greater access and the opportunity to hydrogen bond with the nitrogenous bases. This enables the proteins to find and interact with specific sequences in the DNA double helix.
4) What classes of genes do eukaryotic RNA polymerases I, II, and III synthesize?
- RNA Polymerase I transcribes ribosomal RNAs - RNA Polymerase II transcribes messenger RNAs and small nuclear RNAs - RNA Polymerase III transcribes the 5S ribosomal RNA and tRNAs.
7) What subunits make up the core and holoenzyme of RNA polymerase?
- RNA polymerase in prokaryotes consists of 5 subunits (α2ββ'σ). - The sigma subunit (σ) finds the promoter region (where transcription begins) and the α2ββ' subunits are called the core enzyme. - The catalytic site is at the interface of the β and β' subunits.
4) What is homologous and non-homologous recombination?
- Recombination - Two "parent" DNA molecules exchange sections of DNA to form two "daughter" molecules. - Homologous - (between regions that are somewhat similar in sequence) - Non-homologous - (regions share no similarity)
4) What does topoisomerase do?
- Relax supercoiled DNA so that helicases can unwind the DNA strands - Type 1 topoisomerases relax supercoiling - Type 2 topoisomerases (gyrase) add supercoils to DNA and require ATP hydrolysis
4) What is reverse transcriptase?
- Reverse Transcriptase (RT) is an anzyme used to generate complementary DNA (cDNA) from an RNA template, a process termed reverse transcription.
10) What are the 4 things you need for translation to occur?
- Ribosome - Messenger RNA (mRNA) molecule - Aminoacyl-tRNA molecule - Enenrgy
17) What are ribosomes?
- Ribosomes are organelles that consist of RNA and proteins. Ribosomes are composed of a large subunit and a small subunit. Ribosomal subunits are synthesized by the nucleolus. These two subunits join together when the ribosome attaches to messenger RNA (mRNA) during protein synthesis. Ribosomes along with another RNA molecule, transfer RNA (tRNA), help to translate the protein-coding genes in mRNA into proteins.
12) What antibiotics interfere with transcription?
- Rifampicin binds to a pocket in RNA Polymerase, blocking chain elongation - Actinomycetes binds to DNA by intercalating between the base pairs of DNA, making it a poor template for transcript
8) What are ribozymes?
- Self-splicing RNAs
What are Okazaki fragments?
- Short segments of DNA that are synthesized on the lagging strand of DNA. These fragments are subsequently joined by DNA ligase, forming a continuous segment of DNA
5) What is splicing out of introns? How does it happen? Associated factors?
- Splicing - the excision of introns from the primary mRNA transcript. - Takes place at the ribonucleoprotein complex called the spliceosome consisting of small nuclear RNAs (snRNA) and specific proteins called small nuclear ribonucleoproteins (snRNP) - U1 snRNP binds at the 5' splice site, followed by U2 snRNP binding at the branch site. - Binding of U4-U5-U6 tri-snRNP completes spliceosome formation.
3) What is TATA Binding Protein?
- Tata Binding Protein starts the process of initiation by binding to the TATA box. It is a saddle shaped protein and induces conformational changes in the DNA when it bind, unwinding it and opening up the minor groove
3) What is the Shine-Delgarno sequence in prokaryotes?
- The Initiator codon is lined up correctly by using a region upstream of the AUG start codon to position it. This region on the mRNA is called the Shine-Dalgarno Sequence and is complementary to a region on the 3' end of the 16S SSU rRNA molecule in the 30S fragment of the ribosome.
2) What are the prokaryotic replication structures?
- The Replisome is a complex of proteins that includes two DNA pol III enzymes, Primase, Helicase, DNA polymerase I, and DNA ligase
7) What is the clamp for DNA polymerase III? What does clamp-loading protein do?
- The b2 subunit of DNA Polymerase III forms a DNA clamp on the template and keeps DNA Polymerase III from falling off the template. A clamp loader protein helps the clamp get on the template
1) What is RNA polymerase II in eukaryotes? What are some special things about it?
- The eukaryotic RNA Polymerase II contains a unique Carboxyl-Terminal Domain that enables it to be regulated via phosphorylation of Serine residues.
14) What is the lac operon and how does it work?
- The lac operon consists of genes for the β-Galactosidase, a lactose permease, and a transacetylase. "is an operon required for the transport and metabolism of lactose in E coli and some other enteric bacteria" - One of the genes encoded by the lac operon produces the enzyme β -Galactosidase, which hydrolyzes the β 14 bond in the disaccharide lactose (galactose β 14 glucose).
What are the four bases in DNA and RNA?
DNA - A-T C-G RNA - A-U C-G
9) Know about PCR -
- The polymerase chain reaction (PCR) is a technique for copying a piece of DNA a billion-fold. As the name suggests, the process creates a chain of many pieces, in this case the pieces are nucleotides, and the chain is a strand of DNA. - General Outline: 1. Double Helix containing the targer sequence and flanking regions (primers) is heated to 95oC to denature the double helix and form single strands. 2. Mixture is cooled (55oC) to allow the primers to anneal (bond) to template DNA. 3. Mixture is heated to 72oC, allowing the polymerase to synthesize DNA. - The 3 steps are repeated 20-30 times to generate large amounts of target DNA.
1) What are restriction enzymes nucleases?
- They are enzymes that cuts DNA at or near specific recognition nucleotide sequences known as restriction sites.
13) What are aminoacyl tRNA synthetases?
- They are enzymes that link specific amino acids to specific tRNA molecules
5) RNA polymerase makes errors much more often than DNA polymerase. Why is that not a problem?
- This is acceptable since the mistakes are not passed on to progeny - Due to the degeneracy of the genetic code and the fact that often most amino acid changes do not have a measurable effect on protein function, - Finally due to the fact that mRNA molecules can be used multiple times in translation
1) Review the Messelson and Stahl experiment that is in the book
- This is called semiconservative replication, and was determined by a series of experiments conducted by Meselson and Stahl where they labeled parental strands of DNA with the "heavy" isotope of Nitrogen (N15). They then switched the cells to the light isotope (N14) for one generation. They detected one band, which meant that replication could have been either semiconservative or random (also called dispersive), but eliminated the possibility of replication being conservative. By continuing the experiment they were able to determine that replication was semiconservative and not random.
2) What are the similarities between DNA polymerase and RNA polymerase? Where are the catalytic sites? What divalent cation is important in catalytic mechanism?
- Transcription is the process by which the information stored in DNA is transferred to a soluble RNA molecule. - The enzyme that catalyzes the polymerization of ribonucleotide triphosphates into a polymeric RNA molecule is called RNA Polymerase. - RNA polymerase is a multimeric enzyme that requires a template molecule that is usually DNA (but can be RNA in some cases), ribonucleotide triphosphates, and a divalent cation (Mg2+) in its catalytic mechanism. - In RNA, the thymine used in DNA is replaced by uracil. - The synthesis of RNA is like that of DNA, in that when each nucleotide monophosphate is incorporated into the growing polymer, pyrophosphate (PPi) is released. - The direction of synthesis is 5' 3' and requires a free 3' OH group for the continuation of the chain. RNA polymerase does NOT require a primer. - Genes are segments of DNA that encode RNA transcriptional products.
9) How is mRNA processed?
- mRNA molecules are translated in the cytoplasm. There is a spatial and temporal disconnect between transcription and translation in eukaryotes that is not seen in prokaryotes. This disconnect enable eukaryotes to regulate transcription and translation much more finely that prokaryotes are able to.
1) What are the four types of RNA?
- mRNA, rRNA, tRNA and small micro RNA's
11) What does it mean when the code is said to be degenerate?
- multiple codons code for the same amino acid
20) What is telomerase?
- the enzyme that synthesizes telomeres on the 3' ends of chromosomes, enabling primers to be made for replication without shortening the chromosomes each time they are replicated. - Adds nucleotides to the leading strand so that the lagging strand will always maintain its approximate length. Contains an RNA molecule that acts as a template for extending the leading strand.
18) When you replicate eukaryotic DNA, what are the three challenges of replication in eukaryotes that are different form prokaryotes? How are they Solved?
1 Eukaryotic genomes are 100-1000X larger than Prokaryotic genomes 2 Eukaryotes have multiple chromosomes 3 Eukaryotic chromosomes are linear, not circular - Multiple origins of replications solve the first 2 problems - The presence of telomeres solve the 3rd problem
6) In what direction does DNA synthesis proceed? RNA synthesis proceed? In what direction is mRNA read by the ribosome?
5' - 3' Direction
10) What are A, B, and Z DNA? Which is Most Important?
B - The DNA double helix studied by Watson and Crick is called "B" DNA (Figure 32.17) and is the most common structure. It is a right-handed double helix. A - DNA can also adopt the "A" conformation, which is a right-handed double helix, but the basepairs are tilted. "A" DNA is the form dehydrated DNA adopts, but is also that formed by DNA-RNA hybrids (important in regulation) and by double-stranded RNA molecules. Z - DNA can adopt the "Z" conformation, which is a left-handed double helix. The biological import of "Z" DNA is still being determined.
1) What are DNA polymerase III and DNA polymerase I and what are their enzymatic activities? Where are they used? What is the main one used in replication? Which one is used to get rid of Okazaki fragments? Which activities go with each one?
DNA pol I 5' → 3' polymerization activity (Removes Okazaki fragments) 5' → 3' exonuclease activity (nick translation) 3' → 5' exonuclease activity (proofreading) DNA pol III 5' → 3' polymerization activity (Main polymerase involved in replication) 3' → 5' exonuclease activity (proofreading)
Who is Rosalind Franklin and why are scientists ticked off that she got screwed out of a Nobel Prize?
In 1953, Watson and Crick published there ground-breaking paper describing the structure of DNA (Figure 32.1), for which they received the Nobel Prize. They used X-Ray crystallography data of Rosalind Franklin in their analysis, and they received this data by questionable means. Franklin did not share in the Nobel Prize, and this is one of the major embarrassments in Science. Essentially, Franklin's data was stolen and she got hosed.
*Know about RNA processing, . This is different in eukaryotes why?-where does transcription and translation occur in prokaryotes and where do those processes occur in space and time in eukaryotes:
In prokaryotes, mRNA molecules can be translated as soon as they are produced and require no further processing. In fact, translation may start before transcription is even finished. For rRNA and tRNA molecules, however, post-transcriptional modifications are usually required. Since prokaryotes do NOT have a nucleus, replication, transcription, and translation all take place in the cytoplasm. In Eukaryotes replication and transcription occur in the nucleus, and the mature mRNA molecules are translated in the cytoplasm. Therefore, there is a spatial and temporal disconnect between transcription and translation in eukaryotes that is not seen in prokaryotes. This disconnect between transcription and translation also enables eukaryotes to regulate transcription and translation much more finely than prokaryotes are able to.
Distinguish between a closed promoter complex and an open promoter complex
In the closed promoter complex, the DNA is in the form of a double helix. In the open promoter complex, RNA polymerase has separated the two DNA strands in order to expose the template, and RNA synthesis has begun
5) Know how the STEC (Streptomycin, Tetracycline, Erythromycin & Chlorampenicol) affect protein synthesis at the ribosome (they all affect the ribosome somehow).
Streptomycin (inhibits initiation and cause the misreading of mRNA in bacteria), Tetracycline (binds to the small ribosomal subunit of bacteria and inhibits the binding of aminoacyl-tRNAs), Erythromycin (Binds to the large ribosomal subunit bacteria and inhibits translocation) and Chloramphenicol (inhibits the peptidyl transferase activity of the large ribosomal subunit in bacteria)
*Prokaryotes for synthesis: Promoters, operators, are where RNA synthesis starts. Know where it ends (regions) and know how transcription ends
Termination of RNA synthesis occurs when the growing RNA molecule can form a hairpin structure from an inverted palindromic sequence, that usually consists of a GC-rich region followed by numerous U's. This hairpin causes the RNA Polymerase to pause and the weakly bound poly-U sequence allows the RNA to dissociate from the DNA template. OR there are Rho proteins that cause the RNA to dissociate from the DNA template
What would be the likely effect of a mutation that would prevent σ from dissociating from the RNA polymerase core?
The core enzyme without σ binds more tightly to the DNA template than does the holoenzyme. The retention of σ after chain initiation would make the mutant RNA polymerase less processive. Hence, RNA synthesis would be much slower than normal.
What is the difference between DNA and RNA?
The difference between DNA and RNA is centered on the ribose sugar moiety (Figure 32.3). In ribose, both the 2' and 3' carbons have hydroxyl (-OH) groups. In deoxyribose, the 3' carbon has a hydroxyl (-OH) group but the 2' carbon has a Hydrogen (-H).
*Know how the repressor molecule is the bolder on train tracks (know how it is removed):
The lac repressor protein is constitutively produced (i.e., all the time) and in the absence of allolactose it binds to the operator, preventing RNA Polymerase from transcribing the operon (so it just sits on the operon like the boulder on train tracks). When an inducer molecule (allolactose) binds to the repressor, it changes its conformation so that it can no longer bind to the operator, clearing the way for RNA Polymerase to transcribe the operon. There is a whole catabolized activator protein system that brings in RNA polymerase: RNA Polymerase can also be recruited to promoter regions by Catabolite Activator Protein (CAP). When CAP binds cAMP (which will increase in concentration when glucose runs out), it changes its conformation so that it can bind to promoter regions and recruit RNA Polymerase. If lactose is also present, then the way is clear for transcription of the lac operon. This selectively turns on only those operons for the metabolism of available carbon substrate.
Eukaryotes: 20 pounds of DNA in 5 pound organism: linear DNA
The linear DNA is wound around proteins. -Histone proteins form an octomer (+ charge). -The negative phosphodiester backbone of the linear DNA wraps around the octomer. -Histone protein H1 helps DNA-protein octomers (nucleosomes) associate -Histone octomer protein tails stick out so they can interact with other proteins to enable transcription -DNA wrapped around histone octomers forms a left-handed superhelix
