Genetics 3000 Week 7 Notes
Genetics 3000 Week 7 Notes 85033 - GEN 3000 - 002
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85033 - GEN 3000 - 002
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This 7 page Class Notes was uploaded by Lisa Blackburn on Sunday February 28, 2016. The Class Notes belongs to 85033 - GEN 3000 - 002 at Clemson University taught by Kate Leanne Willingha Tsai in Fall 2015. Since its upload, it has received 29 views. For similar materials see Fundamental Genetics in Biomedical Sciences at Clemson University.
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Date Created: 02/28/16
Key Terms Key Ideas Important things to remember/note Chapter 9: DNA Structure and Analysis (Cont.) 1. Key Terms: a. Phosphodiester Bonds: bond between phosphate group and sugar on a DNA strand. This bond is not within a nucleotide, it connects the phosphate group of one nucleotide to the sugar of another nucleotide. Very strong bond. b. Alpha Helix: DNA is a right handed/clockwise spiral c. DNA forms: come in different forms, they have different lengths/properties d. A Form: Shorter and wider than the form discovered by Watson and Crick (B form). Has an alpha helix. Probably does not exist in nature. Located outside of the cell. As change of the environment occurs, the structure can be modified. e. B Form: the DNA structure discovered by Watson and Crick. Right handed helix. Located in the cell. Exists in the presence of water. Most stable of DNAs under physiological conditions. Regions of B form can change to Z form. i. Why to change to Z form: Two possibilities: protein binding to DNA puts tension on the outside, Z form releases some of this pressure. OR changes to this form allows for proteins to attach to bases. f. Z Form: longer and narrower than B form. Left handed helix. Has a backbone that zigzags. Sites of active genes can make Z DNA (the change from B form to Z form). This structure is a dramatic change and found inside the cell. 2. Key Ideas: a. DNA polynucleotide strand: i. The “backbone” of the DNA strand is antiparallel, meaning the strands run in opposite directions but parallel. Strands go from 5’ to 3’ (this is how we know the sides go in different directions. ii. The phosphodiester bonds on the bonds between the sugar and the phosphate. This is a very strong bond. iii. The sugars and the phosphates are hydrophilic, meaning that they are water loving and want to be on the outside while the bases are hydrophobic, meaning water fearing, and want to be on the inside. This makes the outside wrap around the inside. b. Genomes are Different: i. Different organisms = different genomes ii. Genome size does not correlate to complexity for Eukaryotes iii. Why do some organisms have so much more information? (look below at Reassociation Kinetics) c. Reassociation Kinetics: melting of DNA. A double stranded DNA is denatured through heat, separating the strands into single stranded DNA. This is done by breaking the H-bonds between the bases. These single stranded DNA are then cooled down and they rejoin, creating a double stranded DNA that is renatured. i. By using this, we can determine how quickly a DNA strand can renature. ii. Adenine-Thymine bases break at a low temperature, due to there only being 2 hydrogen bonds. Cytosine-Guanine bases break at a high temperature due to there be 3 hydrogen bonds. The more H-bonds, the more heat needed to break them. 1. This tells you that it takes a little longer to be able to break C-G bases from each other iii. The graph resulting from the process of going from denatured to renatured is a downhill slope with different sections that have “bumps” (see slide for clarification) 1. The first bump: highly repetitive meaning that there are a lot of copies of something, doesn’t have to be an exact copy. Meaning, that when the strands are lining up, since there is a lot of copies of one nucleotide, there are many nucleotides that can fit here so it does not take up as much time finding the other side. 2. The second bump: moderately repetitive. This doesn’t have to be an exact copy, however, there aren’t as many repetitions. Meaning, that there are a lot of copies of one nucleotide, so multiple nucleotides can fit there, but there are other nucleotides that do not appear as much and takes a little longer for the pairing to occur. 3. The third bump: unique. This has to have an exact copy to pair with it. d. Electrophoresis: separated DNA fragments based on the sizes of the fragments. i. Utilizes the negative charge of DNA ii. DNA piece will go into the well and then voltage is applied (the voltage is a negative charge) iii. This pulls DNA to the positive end. The gel slows DNA iv. If the fragments are small, the closer they will get to the bottom of the gel v. If the fragments are big, the farther from the bottom of the gel they will be Chapter 11: Chromosome Structure and Organization 1. Key Terms: A lot of terms for this chapter, some will be explained again during the Key Ideas section. If a term seems unclear, go to this section to be able to understand the term better. Some terms are not listed under Key Terms that are highlighted under the Key Ideas. They are still important to know! a. Primary Structure of DNA: nucleotide sequences (A, C, T, G) b. Secondary Structure of DNA: double stranded helix c. Tertiary Structure: higher order packing d. Chromatin: complex of DNA and proteins in Eukaryotic chromosomes. Proteins are always interacting with DNA. During interphase, DNA is called chromatin because of the proteins interacting with the DNA e. Heterochromatin: a highly condensed chromatin. Such as inactive X chromosomes, which are highly condensed and turned silent/off f. Euchromatin: chromatin can be transcriptionally active or “open” chromatin. i. DNA being used is called active/open. Certain segments of chromatin can be open/active even when condensed, they need to be available to interact with proteins. This part is called Euchromatin. g. Scaffold Proteins: are non-histone proteins. They play a role in the folding and packing of DNA into a chromatin structure. i. They hold chromosome structure in metaphase. Allows for structures of chromosomes to be seen. h. Linker DNA: DNA segment that is in between the histone wrapped by DNA i. Nucleosome: made of four different histones and two copies of each (8 total histones). The first thing to happen when condensing is for DNA to wrap around these histones j. Chromatin Remodeling: structure must change to allows for access of DNA. This means that DNA needs to be accessible even when it is compacted. k. Histone tails: targets for binding. Holds onto the DNA. Positive charge on arms and is attracted to the negative charge of DNA l. Acetylation: neutralizes the positive charge of histones which will relax the histone hold on the DNA, allowing for access m. Methylation: when added, it tightens the histone tails grip on the DNA. “closes down” the DNA and allows for the chromosome to condense (heterochromatin) n. Chromosome banding: quick identification of chromosomes. Kind of like a “finger print” for chromosomes, bond order is the same for every sister chromosome in every one. Also allows for identification of specific regions of a chromosome, gives the regions names as well. o. Polytene Chromosomes: specialized chromosomes, very rare p. Telomeres: maintain ends of chromosomes, caps to prevent the chromosome from unraveling. 2. Key Ideas: a. NOTE: cells have a ton of DNA that needs to fit into a tiny cell. The cell doesn’t have enough space within it to be able to fit all of the DNA. How does the cell cope with this? By CONDENSING DNA. b. DNA Structure has three levels: i. Primary structure ii. Secondary structure iii. Tertiary structure c. DNA without free ends can be supercoiled: for prokaryotes i. Prokaryote DNA is a circular DNA meaning that there are no free ends. ii. The DNA strand needs to be able to compress to keep from tangling up. iii. First thing it does: supercoiling. 1. Overrotate: adds two extra turns 2. Underrotates: removes two turns iv. An overrotated coil creates a positive super coil: look at the way the overlapping is in the bottom depiction of positive supercoil v. An underrotated coil creates a negative super coil: look at the way the overlapping is in the bottom depiction of negative supercoil. vi. NOTE: most DNA is negatively supercoiled. 1. Why: Since there are two less coils in the strand (negative supercoil=underrotate=removal of two coils), then it is easier to access the DNA. When DNA wants to be accessed, removal of rotations must occur. Therefore, since two coils are already removed, it is uncoiling less DNA than a positive supercoil would. (positive supercoil=overrotate=addition of two coils) d. Bacterial DNA is packaged with proteins, NOT histones. (histones are used in Eukaryotes) i. The twisted loops of DNA bind to proteins. This allows for further organization of DNA and to keep the DNA strands from tangling with each other e. Viruses and compacted DNA: viruses also have to compact DNA. i. The head of the virus has to hold a lot of DNA (even though it is a small segment compared to DNA of a cell) f. Eukaryotic Chromosomes are complex: i. Chromatin: complex of DNA and proteins in eukaryotic chromosomes. Proteins are always interacting with DNA. During interphase, DNA is called chromatin because of the proteins interacting with the DNA ii. Heterochromatin: a highly condensed chromatin. Such as inactive X chromosomes, which are highly condensed and turned silent/off iii. Euchromatin: chromatin can be transcriptionally active or “open” chromatin. 1. DNA being used is called active/open. Certain segments of chromatin can be open/active even when condensed, they need to be available to interact with proteins. This part is called Euchromatin. iv. Scaffold Proteins: are non-histone proteins. They play a role in the folding and packing of DNA into a chromatin structure. 1. They hold chromosome structure in metaphase. Allows for structures of chromosomes to be seen. v. Chromatin is a highly complex structure with many parts to it. A histone is positively charged and is attracted to DNA, since DNA is negatively charged. vi. Beads-on-a-String: 1. DNA wraps around a histone. This forms a Nucleosome. The segment of DNA between the wrapped histones is called linker DNA (it links the wrapped histones) a. Histones protect DNA. Histones are repetitive. They occur every so many base pairs. 2. Nuclease comes in and cuts the linker DNA, the parts cut then wrap around the histone. 3. There are then a ton of histones wrapped with DNA, a photo of this looks like beads on a string because the histones are shaped like a ball and are in a linear fashion. vii. Nucleosomes: there are two copies of four different histones and DNA. (H2A, H2B, H3, and H4) 1. The first thing to happen when DNA is condensing, is for DNA to wrap around these histones (8 total histones) viii. Solenoid: another histone will come and interact with the linker DNA of this nucleosomes to create a solenoid (DNA becomes more compacted). ix. Scaffold proteins: come and bind to the solenoid x. Chromatid: is the end product of this process, it is the most condensed DNA can become. g. Chromatin Remodeling: structure must change to allows for access of DNA. This means that DNA needs to be accessible even when it is compacted. i. Histone Tails: histones have multiple tails coming off of the histone. These tails are positively charged (is what gives the histone a pos. charge). They grab onto DNA and since DNA is negatively charged, the tails are attracted to the DNA and hold on tightly to the DNA strand. ii. NOTE: DNA needs to be able to be accessed, so the histone tails are a site for target binding to allow for DNA to be accessed. 1. Acetylation: this can be added to the histone tails to neutralize the positive charge of the tails, relaxing the histone hold on the DNA. This results in the DNA segment to be accessed. 2. Methylation: this can be added to the histone tail to “close down” the DNA. This means that when this is added to a histone tail, it makes the histones grab the DNA tighter, making the segment more unavailable. This is used to condensing DNA even more (Heterochromatin: a highly condensed chromatin) h. Chromosome Banding: this allows for quick identification of a chromosome or of a part of a chromosome. i. “Finger-print” of chromosome. ii. All subjects of a species have the same banding of the same chromosomes. 1. Chromosome 21 will have the same banding for all humans. iii. Banding between homologous sister chromosomes will be the same as well. iv. This allows for us to identify chromosomes and even gives names to regents of chromosomes. v. Staining of centromere: staining of centromeres of chromosomes allows for chromosomes to be identified. Remember: we have learned that the position of centromeres allows for us to identify chromosomes. 1. By looking at the stained centromeres, you can match the chromosomes by where the centromere is located, these will be sister homologous chromosomes. i. Polytene Chromosome: a specialized and rare chromosome. i. Found in certain cells for tissues at certain times (which is why it is rare) ii. By studying rare chromosomes, we can understand normal chromosomes iii. These can be seen in interphase (normal chromosomes cannot) iv. We can determine what these chromosomes do: 1. They are replicated many times and never divide. Instead they stick together. This results in a banding pattern that is the same for every chromosome being copied. 2. Puff: region of Polytene chromosome that is relaxed and pulled out (the middle part of the above depiction) a. Allows for a ton of product to be made very quickly b. Has a high amount of gene activity in the Puff i. Transcription 3. Chromomeres: the individual bands of the above depiction. j. Centromeres are important for chromosomal segregation: i. Remember: centromeres is a region of chromosome where spindle fibers attach. Chromosomes without centromeres will be lost. ii. Point Centromere: small iii. Regional Centromere: in most plants and animals. A large “region” iv. CEN Region: critical regions. Without this, the chromosome will not work (located within centromere) v. Centromeres are very repetitive. The CEN region is also very repetitive and is the same for all chromosomes. Can vary from one organism to the next. vi. If you try to stain a centromere of a single chromosome, you will end up staining all centromeres of all chromosomes, because all of the centromeres look the same. k. Telomeres maintain ends of chromosomes: the caps on the ends of the chromosomes to prevent them from unraveling. i. Function: 1. Structural: serve as a cap to prevent unraveling 2. Replication of ends: this can be tricky a. Generally does not occur in somatic cells (results in beings shortened to death) b. Single celled organisms and germ cells do have to deal with this function ii. Problem: 1. Replicative enzymes cannot replicate ends of chromosomes. 2. Chromosomes would get shorter to the point of loss of function iii. Solution: have an enzyme that replaces ends. iv. Telomeres repeats are very large. Heterochromatic ends of chromosomes v. TERRA: transcribed regions. (Telomeric repeat containing RNA) contribute to methylation. vi. Do most somatic cells have telomerase activity? 1. Telomerase allows for elongation of telomeres. If not working, you will see the telomeres being shortened continuously. l. Transposable Sequences: a transposon is a “jumping gene.” It is a segment of a gene that can move within a genome. i. SINE: short interspersed element 1. Alu family: most common SINE in humans ii. LINE: long interspersed element iii. SINE and LINE: add to repetitive nature of genome iv. Retrotransposons: RNA intermedia using reverse transcriptase 1. Uses reverse transcription, exception of central dogma v. Pseudogenes: risen through duplications, but no longer functional genes.
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