Bio 97: Midterm 1
Explain the differences in the chromosome structure between sexually reproducing animals and bacteria using the words chromosomes, haploid, diploid, and homologs.
Sexually reproducing animals have haploid gametes (sperm and egg) that once undergone fertilization become diploid. The chromosomes of sexually reproducing organisms are in pairs called homologs. The sexually reproducing animal itself is diploid as its a eukaryote. Diploid- containing two copies of each gene In comparison Bacteria are prokaryotes, typically prokaryotes are haploid. Haploid- containing one copy of each gene Bacteria undergo mitosis - create genetically identical daughter cells
If complementary DNA strands were arranged in a parallel manner, what would you expect to see?
Some regions of the two strands may form atypical hydrogen bonds, but the overall structure of the two DNA strands would not be stable.
Explain why the structure of DNA's double helix suggested a mechanism for DNA replication.
Watson and Crick noted that the structure of DNA suggests a possible copying mechanism. DNA replication follows a semiconservative model. The two DNA strands separate. Each strand is used as a pattern to produce a complementary strand, using specific base pairing. Each new DNA helix has one old strand with one new strand
A sample of double-stranded DNA is found to contain 20% cytosine. Determine the percentage of the three other DNA nucleotides in the sample.
20% cytosine, 20% guanine, 30% of adenine and thymine
Besides the nucleus, where else do plants and animals have DNA?
Mitochondria and chloroplasts have their own genetic material Proteins produced by the above work with proteins produced by nuclear genes to perform cell functions Mitochondria - essential to make ATP (adenosine triphosphate) Chloroplasts - essential for photosynthesis During cell division they are released into the cytoplasm and their random distribution is called : cytoplasmic inheritance
Compare and contrast the cells that result from mitosis and meiosis.
Mitosis: the process of cell division in somatic cells that produces genetically identical daughter cells through a single nuclear division The cells are genetically identical to the parent cell. Two daughter cells Diploid daughter cells Creates all body cells Meiosis: the process of cell division occurring in germline cells. Produces four haploid gametes(sex cells)/spores through two successive nuclear divisions in diploid species. The cells are genetically unique Four daughter cells Haploid daughter cells Creates only germ cells
How has next generation sequencing affected the price of sequencing a human genome?
Next-generation and third-generation DNA sequencing are much faster and far cheaper methods that have paved the way for large numbers of genome sequencing projects and personal human genome sequencing.
The following segment of DNA is the template strand transcribed into mRNA: 5'-...GACATGGAA...-3' a) What is the sequence of mRNA created from this sequence? b) What is the amino acid sequence produced by translation?
a) mRNA: 3'-...CUGUACCUU...-5' In other words: 5'-...UUCCAUGUC...-3' b) Starting from 5'... to ...-3': Phe-His-Val
How many hydrogen bonds does an A-T base pair have? How many does a G-C base pair have?
two stable hydrogen bonds form for each A-T base pair, and three hydrogen bonds are formed by each G-C base pair
What are the three components of a DNA nucleotide?
A five carbon deoxyribose sugar, one of four nitrogenous bases, and up to three phosphate groups.
What is the purpose of gel electrophoresis? What is the one molecular characteristic that DNA or RNA molecules are separated on in gel electrophoresis?
A process to separate different fragments from one another using an electrical field. Molecular weight is one molecular characteristic that they are separated on. (Other characteristics are molecular charge and shape, and EtBr can be used as the tag (color))
What is "massively parallel" about next generation sequencing? In NGS, is one DNA molecule sequenced at a time? Or many?
Massively parallel sequencing means that the technology sequences DNA fragments in parallel, hundreds of thousands of DNA fragments simultaneously. In NGS the whole genome is sequenced at once, a much faster and less costly version of DNA sequencing
central dogma
DNA -(transcription)> RNA -(translation)> Protein
Southern blotting
DNA gel to membrane transfer
What is a dideoxynucleotide triphosphate? How does it get used to sequence DNA? (Please note your book describes a sequencing method where each ddNTP is added to a separate reaction. Since this method is outdated, in the lecture, I cover the current version of Sanger sequencing, in which all 4 ddNTPs are added to a single reaction.)
Dideoxynucleotides triphosphate (ddNTP) is different from deoxynucleotides (dNTP) as ddNTP lack two oxygen's whereas dNTP lacks one (it has OH and and one deoxygenated site whereas ddNTP has two H in place of the OH and in the deoxygenated site) When ddNTP is added into a growing strand synthesis of the strand is terminated (as there is an absence of the OH to form the phosphodiester bond) The dNTP is needed to keep the strand growing as the presence of the OH allows for the phosphodiester bond
What are the three steps of a PCR reaction?
During the denaturation step of a PCR cycle, the template DNA strands are separated or denatured. Next, during the annealing step, the single-stranded primers hybridize to the denatured DNA template. Finally, during the elongation step, Taq polymerase synthesizes a new strand of DNA from the DNA template in a 5' to 3' direction, starting at the 3' end of the primers, by adding dNTPs to the 3' end of the new DNA strand. - Denaturation. The reaction mixture is heated to approximately 95°C, causing double-stranded DNA to denature into single strands as the hydrogen bonds between complementary strands break down. The step duration is usually 1 to 2 minutes. - Primer annealing. The reaction temperature is reduced to between about 45°C and 68°C to allow primer annealing—the hybridization of the two short, single-stranded DNA primers to complementary sequences bracketing the target sequence. These primers have the same function as RNA primers in DNA replication. They are, as mentioned, short (12 to 24 nucleotides), and one primer binds to each of the denatured DNA strands. The step duration is usually 1 to 2 minutes. - Primer extension. Raising the temperature of the reaction to 72 which allows primer extension, during which a specialized DNA polymerase know as Taq polymerase synthesizes DNA, beginning at the 3' end of each primer. Taq polymerase, described in more detail below, synthesizes new DNA at the rate of about 1000 bp per minute. This step duration is usually 3-5 minutes.
Which of the following equations are true for the percentages of nucleotides in double-stranded DNA?
G+A=C+T
If thymine makes up 21% of the DNA nucleotides in the genome of a plant species, what are the percentages of the other nucleotides in the genome?
If thymine makes up 21% percent then cytosine also makes up about 21%. This means adenine and guanine will both be about 29%
Physical units of heredity
Located on chromosomes composed of DNA sequences (contain complex instructions) that is transcribed and encodes a polypeptide or another functional molecule Control gene transcription Contain info to produce RNA molecules
What is the difference between a genotype and phenotype? Are alleles part of a genotype or phenotype?
Phenotype - visible/observable characteristics Genotype - genetic makeup of an organism, not visible All the alleles of all the genes Alleles - are part of genotype, they are alternate forms of a gene Contains DNA sequence that alter the product of the gene
Western blotting
Protein gel to membrane transfer
Northern blotting
RNA gel to membrane transfer
With respect to transcription describe the relationship and sequence correspondence of the RNA transcript and the DNA template strand. Describe the relationship and sequence correspondence of the mRNA transcript to the DNA coding strand.
The RNA-synthesizing enzyme RNA polymerase pairs template-strand nucleotides with complementary RNA nucleotides to synthesize new transcript in the 5' → 3' direction; the transcript is antiparallel to the DNA template strand Because the coding strand is both complementary and antiparallel to the DNA template strand, it has the same 5' → 3' polarity as the RNA transcript synthesized from the template strand; moreover, the RNA transcript and the DNA coding strand are identical in nucleotide sequence, except for the appearance of U in the place of T Textbook answer: The template DNA strand is complementary and antiparallel to the RNA transcript. The coding DNA strand is parallel and identical to the mRNA transcript, except that thymidine is located in the DNA strand where uridine is located in RNA.
A portion of a polypeptide contains the amino acids Trp-Lys-Met-Ala-Val. Write the possible mRNA and template-strand DNA sequences. (Hint: Use A/G and T/C to indicate that either adenine/guanine or thymine/cytosine could occur in a particular position, and use N to indicate that any DNA nucleotide could appear.)
Trp - Lys - Met - Ala - Val mRNA: UGG-AA(A/G)-AUG-GCN-GUN DNA: ACC- TT(T/C)- TAC- CGN-CAN
Identify two differences in chemical composition that distinguish DNA from RNA.
Two differences in chemical makeup of DNA and RNA are that DNA is made of deoxyribose sugar and RNA is made of ribose sugar, and that in RNA there is Uracil instead of thymine.
Figure 1.14a, lane 4. Which band represents the DNA molecules that are longer - the top band or the bottom band?
The top band. The bigger the molecule/fragments (the more base pairs) the closer to the beginning it will stay due to it not being able to travel as far.