1. What is “genomics”?
A. The human genome is the complete set of genetic information we all carry. This created the field genomics where scientists study the origin and function of genes. B. Genomics is the study of the organization, function and evolution of genomics. 2. Where do you find the genomes of humans?
A. It is found in all cells that contain a nucleus.
3. Whereas DNA is an abbreviated, short-hand version, how do you spell and say the long-handed version of this genetic material?
A. Deoxyribonucleic acid.
4. What was the Human Genome Project all about?...when was it begun?...when did it end? What was accomplished by the HGP?
A. The Human Genome Project is known for its work towards detecting, diagnosing and treating cancer. They used recombinant DNA technology to gather the entire set of genetic information we all carry.
B. It began in 1990 and ended in 2003.
5. Among the four common nucleotides of DNA, Can you say/write what A stands for? … what T stands for? … what G stands for? … what C stands for?
A. A for adenine, T for thymine, G for guanine and C for cytosine.
6. What is a gene? Approximately, how many genes are there in the human genome? What fraction of the genome is accounted for by genes that actually get expressed as RNA? What is the significance of “non-gene” DNA?
A. A gene is the basic and functional unit of genetics and at the molecular level it is a DNA sequence that is transcribed into a RNA molecule. We also discuss several other topics like the sign of four quiz
B. An extremely small fraction of the genome is actually expressed by RNA (1%). C. There is about 26,000 putative genes or genes with functions we know. The rest have a molecular function that is unknown.
7. What is the relationship of phosphate groups (P) to the nitrogenous bases (A,T,G and C) in the DNA double helix? (Figure 1.1 in Cummings) Which is on the outside of the helix? Which is on the inside of the helix?
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A. The phosphate groups link the nucleotides (ATGC) together and it’s residue brings negative charge, giving it an acidic character. Don't forget about the age old question of enec 201 unc
B. The nitrogenous bases connect with the hydrogen bonds to hold the double stranded polynucleotide together.
C. Phosphate groups are outside the helix and the nitrogenous bases are in the inside. 8. How can you account for the β-hemoglobin gene being composed of ~1700 nucleotides, whereas only ~450 of those are expressed as β-hemoglobin protein?
A. There are 10 nucleotides that are the promoters, about 454 nucleotides that are responsible for gene coding and the rest do nothing. If you want to learn more check out microeconomics notes chapter 1
9. Within the cell nucleus of a cell actively expressing genes, what does RNA processing accomplish? How does the ‘final’ mature RNA compare to the newly made one? A. RNA is translated to proteins and those proteins carry out our life functions. B. Introns are deleted from the mRNA since they are considered “junk” and only exons are left.
10. Among the approximate 20-25,000 genes of the human genome, does to the largest class of genes have any function? (Fig 15.10)
A. Their molecular function is not know.
11. What is a genetic map of a human chromosome? What sort of “probe” must be in hand before such a map can be made? (Fig 15.4) (Fig 13.9)
A. The genetic map of a human chromosomes consist of locations of the genes in the chromosome, marked by the promoter of that gene.
B. The probe is a complementary single stranded RNA or DNA molecule, they indicate for specific genes.
12. Where in cells does transcription (making RNA from DNA) take place? Where does translation (making proteins, i.e. polypeptides, from RNA) take place? A. Transcription occurs in the nucleus of a cell.
B. Translation occurs in the cytoplasm.
13. What features of an organism’s chromosome make-up are taken into account in defining its karyotype? What is the normal human male karyotype? ... female karyotype?Don't forget about the age old question of math109
A. The number of chromosomes and the sex chromosomes, characteristics of the chromosome like it’s size and structure, such as where the centromere is located and length of p and q arm.
B. Normal male is 46, XY
C. Normal female is 46, XX
14. Consider the chromosomes of a human karyotype. Which is the largest, which is the smallest? Are X and Y similar (homologous)? Define the term: autosome. How many pairs of autosomes are there in the human diploid karyotype? What is the definition of a homologous chromosome? We also discuss several other topics like cems uta
A. Chromosome 1 is the largest chromosome. Chromosome 21 is the smallest. B. X and Y are partially homologous.
C. Autosome is a non sex chromosome. There are 22 pairs of autosome. D. Homologous chromosomes are chromosome pairs (one from each parent) that are similar in length, gene position, and centromere location.
15. How many double-stranded (ds) DNA helices are in human chromosome 1?….in human chromosome 15?...in human X?
A. Every chromosome consists of one long DNA molecule.
16. How many chromosome haploid sets constitute the normal human female karyotype? …the normal male karyotype? What is the definition of diploid? What is the ploidy (haploid, diploid, etc.) of a normal male karyotype before replication? ... after replication?
A. There are 23 haploid sets + XX for females and same but XY for males B. Diploid is two complete sets of chromosomes, two haploids put together, one from each parent.
C. Before replication there will be 23 sets of haploid, after will be 46.
D. Before replication there will be 46 diploid, after will be 92.
17. Name the nitrogenous bases that are found in DNA. (Fig8.5) How are the following configured within double-stranded (ds) DNA: deoxyribose sugars, phosphate ions, and nitrogenous bases (A,T,G,C)? (Fig 8.9) … Which contributes to the acidic character of
DNA? (Fig 8.10) What is a nucleotide? … a polynucleotide? How does the acidic nature of DNA influence its linear structure?
A. The nitrogenous bases include A for adenine (purine) , T for thymine (premadine), G for guanine (purine) and C for cytosine (premadine).
B. Covalent bonds hold the deoxyribose sugars and phosphate ions together and nitrogenous bases are held together by hydrogen bonds.
C. Phosphate contributes to DNA’s acidic character.
D. The negative charge of phosphate repels off other DNA which gives it that linear look. 18. What is the nature of the bonds that hold the two strands of DNA together? How can these bonds be broken? What is bond-breaking called?...hint: de----------
A. Hydrogen bonds hold the two strands together, as well as histone proteins that are polyions, so the negative charges attract to its positive charges because of electrostatic charged attraction.
B. Bonds can be broken at 60 degrees celsius.
C. Bond breaking is called denaturation.
19. How is the structure of dsDNA conserved during the process of semi-conservative DNA replication? How does DNA polymerase figure into the mechanism underlying the process of DNA replication? (Fig 8.13)
A. The dsDNA splits into two, creating two templates.
B. It uses the old DNA strand as a template, by doing this the DNA polymerase successfully creates and matches nucleotides with preexisting ones from the template (replicon). Thus creating a sister chromatid.
20. What is the magnitude of the distance (in nanometers) between base pairs within the “spiral staircase” of DNA? How wide (in nanometers) is that staircase?...i.e. what is the diameter of a DNA double helix?
A. 0.34 nm between base pairs of a DNA.
B. The staircase is 2nm wide (thick)
C. Diameter of a DNA double helix is 2nm.
21. What is the total length of DNA in the haploid human genome?...in the diploid genome? How many base pairs does each of those lengths include? Given that an adult human body is estimated to consist of ~50 trillion (5 x 1013) cells, what is the total length of DNA in an entire adult human body? How can this distance be expressed in relation to the distance from the earth to the sun?...in terms of the size of an ice cube? A. 1 meter for haploid human genome - 3.2 billion base pairs
B. 2 meters for diploid human genome - 6 billion base pairs
C. 10-50 billion miles is the total length of DNA in the human genome. D. You can go to the sun and back 70 times with total length of DNA.
E. DNA can fit into a single ice cube.
22. What is the molecular composition of chromosomes? How are the two general morphological states of chromosomes --- interphase (non-mitotic) vs. mitotic --- distinguished from each other? What is a “chromosome territory”?
A. Chromosomes are half DNA and half protein.
B. In mitotic chromosomes, they are stuffed together, but distinct from one another, shapes can be seen, like arms and centromere and nuclear membrane is broken for for mitosis. C. In interphase chromosome, dispersed in the nucleus and can’t be seen without “paint”, the shapes can’t be seen, surrounded by the nuclear membrane.
D. Chromosome territory refers to the different sections chromosomes have in the nucleus during interphase.
23. How do the terms – metacentric, submetacentric and acrocentric -- relate to chromosomes of the human karyotype? … relate to the terms: “p arm” and “q arm”? (Fig 6.3)
A. Metacentric where centromere is in the middle of telomeres (tips of the chromosomes, has two) , p and q arms are generally equal in size. Chromosomes #1 and #3 B. Submetacentric is where p arm is significantly smaller than q arm. Centromere is closer to one arm than the other. Chromosomes #2-#12, #16-#20 and X
C. Acrocentric is where there is a satellite connecting small p arm to the centromere, #13-#15 #21, #22 and Y.
D. P is the short arm and q is the longer arm.
24. What is “chromosome banding”, and what is the significance of banding techniques to human karyotype analysis? (fig 6.5) Where are telomeres located?
A. Chromosome banding is the line pattern, which helps to see if the chromosome is homologous.
B. It can identify specific regions which indicate what genes it carries.
C. Telomeres are the tips of the chromosomes.
25. What is a nucleosome? (Fig 8.14) What is the role of nucleosomes in packaging DNA into chromatin and chromosomes? How do the ionic properties of DNA and histone core particles (lysine-rich and arginine-rich) contribute to establishing and maintaining the nucleosomal association of DNA to histone proteins? What is the protein subunit composition of histone core particles? What are H1 linker histones?
A. Nucleosome is a bread like structure composed of histones (octomers) wrapped with DNA.
B. DNA wraps around the nucleosome like a center spool.
C. Since DNA is negatively charged, it attracts to the positive charges of histones where lysine and arginine are clustered to.
D. The protein subunits are lysine and arginine.
E. H1 linkers link all the histone together.
26. What effects do acetylation and phosphorylation of histone proteins have on DNA-histone bonding? What is the relationship of histone phosphorylation and/or acetylation to reversible chromatin remodeling? What is the significance of remodeling to activation of transcription …activation of DNA replication?
A. Acetylation of histone proteins changes their charge properties, making them less basic, this happens by the acetylase enzymes adding acetate to the sites near lysine and arginine to neutralize the positive charge (loses its positive charge).
a. Makes the bonding between DNA and histone less strong.
B. Phosphorylation of histone proteins changes their charge properties, making them less basic, this happens by the kinase enzymes adding phosphate to the sites near lysine and arginine to neutralize the positive charge (loses its positive charge).
a. Makes the bonding between DNA and histone less strong.
C. Phosphorylation and acetylation change the histone proteins to make it less basic, they are protein modification mechanism.
D. This allows DNA activation and replication possible.
27. What is the diameter (in nanometers) of a nucleosome ‘bead’? What is the relationship of nucleosomes to 30nm fibers?…of 30nm fibers to mitotic chromosomes? (Fig 8.16) A. The diameter of a nucleosome bead is 10 nm.
B. A nucleosome going from a 30nm fiber that is too compacted for expression going to 10nm beads to be unpackaged DNA (Naked DNA) so that DNA transcription, expression and replication is possible.
C. Going from 10nm beads to 30nm fibers is the process of packaging DNA. D. Interphase chromosomes are less compacted compared to mitotic chromosomes. 28. What are the general features of the mechanism underlying replication of DNA? What is the identity of the enzyme that facilitates DNA replication? Name the building blocks that polymerize during DNA replication to make a new polynucleotide strand. Replication of DNA:
A. Tracing the Flow of Genetic Information from Nucleus to Cytoplasm a. Transferring genetic information from from nucleotides in a DNA to the amino acids in a protein is done by:
b. Info inside a gene is copied into a RNA molecule called pre-messenger RNA, this step is called transcription.
c. This pre-mRNA is turned into the finished mRNA, when introns are deleted and moves to the cytoplasm.
d. Info in the mRNA turns into amino acids in a polypeptide chain to be folded into a protein, this step is called translation.
B. Transcription Produces Genetic Messages
a. Transcription starts when one strand of the DNA in a chromosome is used to make a pre-mRNA molecule.
b. 1st step is the RNA polymerase enzyme bind to a nucleotide sequence (promoter 5’) which is the beginning of a gene.
c. This enzyme moves along the DNA to unwind it and links RNA nucleotides to a strand of RNA based on a base sequence -- called elongation.
d. The polymerase creates covalent bonds between the nucleotides to make a RNA strand. This base sequence of the RNA is complementary to the DNA base sequence.
e. The last part of the new transcript unwinds and separates from the DNA template, this is the termination.
C. Messenger RNA is processed and spliced
a. pre-mRNAs are processed in the nucleus to remove introns, which DNA sequences that are in some genes but removed so not present in mature mRNA. b. Exons are DNA sequences that are transcribed to join other exons so when mRNA is processing, it is translated into the amino acid sequence of a protein. c. During this processing, a nucleotide cap is put on the 5’ end, and a tail of 30-100 A nucleotides are added to the 3’ end, called the Poly- A tail.
d. During splicing, exons can be cut off along with introns, allowing mature mRNAs to contain different combinations of exons. (Chapter 9 notes).
D. Basically, DNA replication occurs during the interphase state, where it can serve as a template for synthesis of RNA (transcription) for a transcription factor to bind to the promoter of its target gene, leading to a series of changes that lead to making mRNA from the gene.
E. Polymerase is the enzyme that facilitates DNA replication.
F. Nucleotides are ATCG.
29. When DNA replication is completed, what is the specific term (hint: sister ----------) given to the two daughter DNA polymers that are generated from the parental DNA? Subsequent to DNA replication, what mechanism holds the two daughter double helices together?
A. Sister chromatids.
B. Cohesion hold the two daughter double helices together.
30. If a human somatic cell DNA is diploid and unreplicated (i.e., ~6 x 109 bp), what is its DNA content (bp) after DNA replication? If in the same nucleus there are 46 double stranded DNA molecules before replication, how many double stranded DNA molecules are there after replication in that nucleus?
A. 12 x 10^9 bp.
B. There will be 92 double stranded DNA molecules.
31. If in a human somatic cell nucleus there are 32 million nucleosomes before DNA replication, how many are there after replication?
A. There will be 64 million nucleosome after replication.