Term
| how many base pairs are in a typical human haploid sperm or egg cell? how many in a diploid cell? |
|
Definition
| 3x10^9 base pairs for haploid, 6x10^9 base pairs for diploid |
|
|
Term
| About how much of our DNA actually codes for genes? |
|
Definition
|
|
Term
| all DNA is in the nucleus with one exception. what is it? |
|
Definition
| mitochondrial DNA is found in the cytoplasm |
|
|
Term
| What is the central dogma of molecular biology? |
|
Definition
| the flow of information always goes from DNA to RNA to Proteins. |
|
|
Term
|
Definition
| copying the original DNA transcript |
|
|
Term
|
Definition
| making an RNA copy from a DNA template |
|
|
Term
|
Definition
| producing a protein (an amino acid sequence) from an RNA template using a ribosome. |
|
|
Term
| Name the 3 pyrimidines. Do these have a single ring or a double ring? |
|
Definition
| cytosine, thymine, and uracil. these have a single ring. |
|
|
Term
| what is the difference between thymine and uracil? |
|
Definition
| thymine has a methyl group off the ring, and uracil does not. Uracil bonds with adenine in RNA, thymine bonds with adenine in DNA |
|
|
Term
| Name the two purines. are these single ring or double ring? |
|
Definition
| adenine and guanine. double ring, one of 6 members, and one of 5 members. |
|
|
Term
| When purines break down, what compound is produced? what does this lead to? |
|
Definition
| Uric acid. this can lead to gout. |
|
|
Term
| What is a nitrogenous base? a nucleoside? a nucleotide? |
|
Definition
| the nitrogenous bases are GTACU, nucleosides have ribose added, but no phosphoates. nucleotides have the ribose + 1 or more phosphates. |
|
|
Term
| deoxyribose and ribose. whats the difference? |
|
Definition
| in deoxyribose, carbon number 2 does NOT have a hydroxyl group attached (no oxygen). Ribose has an OH group attached to carbon number 2. |
|
|
Term
| What carbon #'s are used for attaching each nucleotide to the next in the chain? |
|
Definition
| the 3' and 5' C's are used. |
|
|
Term
| How many hydrogren bonds form between Adenine and Thymine? |
|
Definition
|
|
Term
| how many hydrogen bonds form between cytosine and guanine? |
|
Definition
|
|
Term
| if we want to unzip a strand of DNA at a certain point, would we expect to find a lot of AT pairs or a lot of GC pairs? why? |
|
Definition
| AT pairs. The AT pairs only have 2 hydrogen bonds, and are easier to unzip than GC pairs which have 3 hydrogen bonds. |
|
|
Term
| The nitrogenous bases are pretty exposed in the major groove. what purpose does this serve? |
|
Definition
| regulatory proteins and transcription factors can recognize the pattern of bases and H bonding possibilities in the major groove. |
|
|
Term
| What happens when we apply a lot of heat to double stranded DNA? |
|
Definition
| we break the hydrogen bonds between the bases and get single stranded DNA. a high GC content (3 H bonds) would increase the dissociation temperature. |
|
|
Term
|
Definition
| taking two pieces of single stranded nucleic acid (usually 1 DNA 1 RNA) with complimentary sequences and allow them to cool and reform a double helical structure |
|
|
Term
|
Definition
| a primer is a single stranded RNA sequence that are complementary to a desired piece of single stranded DNA. (used in PCR) |
|
|
Term
| How to we amplify dna with PCR? |
|
Definition
| we separate the sample dna into single strands with heat. We add a primer, polymerase, and NT bases. we allow it to cool a bit and the sample and primer hybridize, and now the polymerase can attach and start synthesizing a new strand. |
|
|
Term
| What are the 3 steps in PCR? |
|
Definition
| denaturing (high heat), annealing (low heat), extension (mid-heat, polymerase optimum temp) |
|
|
Term
|
Definition
| probes are single strands of DNA or RNA that are complimentary and labelled in some way. We allow the sample and the probe to hybridize, and we can determine how much of our probe is bound to the sample by measuring the label. |
|
|
Term
| How do probes help us detect SNP's (single nucleotide polymorphisms)? |
|
Definition
| a probe with imperfect base-pairing would have a lower melting temp than a perfect match, so by comparing melting temps we can determine the number of SNPs |
|
|
Term
| what do we mean by semi-conservative replication? |
|
Definition
| each daughter molecule of DNA contains 1/2 of our original molecule. The original molecule is not conserved, it is semi-conserved! |
|
|
Term
| how did meselson and stahl demonstrate semi-conservative replication? |
|
Definition
| they labeled the parental DNA with Nitrogen-15. then by centrifugation you could see the results matched with what you would expect in semi-conservative replication. |
|
|
Term
| what enzyme opens up the replication fork? |
|
Definition
|
|
Term
| what other proteins besides helicase are involved in unraveling the helix and keeping it apart? |
|
Definition
| we have topoisomerase which breaks and rejoins the helix to relieve coiling stress, and Single strand binding proteins that keep the strands apart. |
|
|
Term
| how do we synthesize both strands if we can only go from 5' to 3'? |
|
Definition
| the leading strand works normally, but the lagging strand we synthesize in small bits caleld okazaki fragments. |
|
|
Term
| what does DNA polymerase need in order to bind to the DNA and start doing its job of adding nucleotides? |
|
Definition
| There has to be an RNA primer on our DNA strand in order for DNA polymerase to attached. |
|
|
Term
| what enzyme makes to RNA primer for us? |
|
Definition
|
|
Term
| What enzyme removes the RNA primer from the lagging strand and replaces it with DNA? |
|
Definition
|
|
Term
| After DNA polymerase I replaces the rna primer with DNA, how do we join the two okazaki fragments? |
|
Definition
|
|
Term
| what is the catalytic potency of polymerases? |
|
Definition
| about 1000 nucleotides/second |
|
|
Term
| what is the error rate of dna replication? |
|
Definition
| 1 mutation for every 10^9 to 10^12 nucleotides. |
|
|
Term
| what do the exonucleases do? |
|
Definition
| one of them removes the RNA primer, and another checks for errors |
|
|
Term
|
Definition
| two thymines next to each other on a strand and be caused to spontaneously bond together to form a dimer by UV light. This makes it very difficult to replicate or transcribe correctly. |
|
|
Term
| how does DNA damage get repaired? |
|
Definition
| mismatches get removed by endo or exo nucleases. DNA polymerase replaces bad nucleotides using the other strand as a template. DNA ligase recconects these damaged bits after repair. |
|
|
Term
| What are telomeres and how do they limit the number of times replication can occur? |
|
Definition
| telomeres are repeating dna sequences at the end of chromosomes that get shortened slightly with each chromosome replication. eventually if they get too short the cell cannot replicate |
|
|
Term
| is greater telomere length associated with anything? |
|
Definition
| yes. immortal cell lines such as embryonic stem cells and cancer cells have long telomeres. |
|
|
Term
| what enzyme replaces or lengthens telomeres? |
|
Definition
|
|
Term
| why do the telomeres get shortened anyway? |
|
Definition
| dna polymerase requires a primer, it cannot start at the very end of a telomere, leaving a primer gap. telomerase repairs this gap, but it eventually gets turned off! |
|
|
Term
| How does telomerase actually work? |
|
Definition
| the enzyme has an RNA primer with the telomere sequence built in, so it gives a place for the dna polymerase to extend the telomere. |
|
|
Term
| how does stress affect telomere length and telomerase activity? |
|
Definition
| low stress is associated with long telmeres and high telomerase activity! don't stress out, you'll live longer. |
|
|
Term
| how can antibodies to millions of different molecules be created from limited DNA? |
|
Definition
| we have genes for antibody molecules, but we also have the ability to cut and paste the DNA together to make new antibodies. |
|
|
Term
| What does the RAG enzyme do? |
|
Definition
| they are the enzymes that recombine and edit antibody DNA segments in order to make novel antibodies. |
|
|
Term
| What do deficiencies in RAG1 and RAG2 result in? |
|
Definition
| SCID's severe combined immunodeficiency disease (bubble boy) |
|
|
Term
| How is the finished DNA packaged? |
|
Definition
| it is wrapped around histone proteins. These proteins are acetylated and DNA is methylated. methylation inhibits transcription |
|
|
Term
| if the DNA is highly packaged how do we find the DNA we want? |
|
Definition
|
|
Term
| What direction is synthesis of new DNA and RNA chains? What direction is the enzyme reading? |
|
Definition
| We always add bases to the 3' end, so synthesis goes from 5' to 3'. We are reading the template strand in the opposite direction, so we are reading from 3' to 5' |
|
|
Term
| Is the gene actually on the coding strand or the template strand? |
|
Definition
| the gene is on the coding strand. |
|
|
Term
| So if the gene is on the coding strand, how do we synthesize the RNA from the template strand? |
|
Definition
| the template is complimentary to the coding strand. When we transcribe it to a complimentary RNA sequence, it becomes the same as the coding strand! |
|
|
Term
| What is the promoter sequence? |
|
Definition
| This is the TATA box where the RNA polymerase binds. it is close to the initiate sequence for transcription. enhancer sequences are even farther upstream and can influence transcription. |
|
|
Term
| How do the DNA binding proteins identify the promoter from outside the helix? |
|
Definition
| by reading it through the major groove |
|
|
Term
| Where does translation start on the mRNA transcript? |
|
Definition
|
|
Term
| What is a polycistronic mRNA? |
|
Definition
| bacteria use this method to transcribe several proteins with one mRNA transcript. this does not happen in humans. |
|
|
Term
| Introns and Exons, which stays and which goes? |
|
Definition
| exons are snipped out, and introns stay in to be coded. |
|
|
Term
| Why is the promoter site AT rich instead of GC rich? |
|
Definition
| We want to unzip the helix at the promoter site, and its easier to pull apart AT pairs which only have 2 H bonds, versus GC pairs which have 3 H bonds. |
|
|
Term
| which RNA polymerase transcribes genes in humans? |
|
Definition
|
|
Term
| How do steroids affect transcription? |
|
Definition
| the steroid either binds to DNA itself to promote or inhibit transcription, or it binds to an intracellular receptor which then binds to DNA |
|
|
Term
| How do peptide hormones affect transcription? |
|
Definition
| peptide hormones intitiate a phosphorylation cascade which activates a transcription factor. |
|
|
Term
| After transcription, how is the mRNA processed in the nucleus? |
|
Definition
| it is capped as it is being transcribed, the poly A tail is added. Introns are removed and exons are ligased together. Then it is shipped out for translation by ribosomes |
|
|
Term
|
Definition
| heterogeneous nuclear RNA. this is the RNA that still has the introns |
|
|
Term
| what is a snRNA + protein complex actually cuts out the introns? |
|
Definition
|
|
Term
|
Definition
| it is a Guanine with an extra methyl group attached to a backwards ribose which is attached by three phosphates to the first base in the sequence. |
|
|
Term
| What is the poly A tail and what does it do for us>? |
|
Definition
| it is a sequence AAUAAA that signals for cleavage of the transcript 10-20 bases downstream. mRNAs without a poly A tail don't get translated as much. |
|
|
Term
| How does our body accomplish extremely high levels of protein production? where does this take place? |
|
Definition
| we have 1000 rRNA genes close together in the nucleus, with spacer regions that are the termination sequence of one gene and the promoter sequence of the next. This allows us to pump out huge amounts of ribosomes very quickly. this takes place in the nucleolus |
|
|
Term
| The rRNAs are transcribed all at once. how is it processed? |
|
Definition
| the three subunits are all transcribed at once, but when the introns are removed, the genes are not joined, they are each translated/processed seperately. |
|
|
Term
| What are the components of a ribosome? |
|
Definition
| it consists of 83 proteins and four pieces of rRNA |
|
|
Term
| What is the function of a tRNA? |
|
Definition
| it is to get attached to the appropriate amino acid, and present itself to the ribosome at the right time. |
|
|
Term
| What is the sequence on a tRNA right before the amino acid attachment site? where is this site in relation to the anticodon? |
|
Definition
| CCA. it is on the opposite side as the tRNA |
|
|
Term
| What are the steps in processing of tRNA? |
|
Definition
| removal of extra pieces on the 5' and 3' end. removal of an intron next to the anticodon. modification of individual bases. the addition of the CCA sequence at the 3' end. |
|
|
Term
|
Definition
| it is the uneven synthesis of alpha and beta hemoglobin subunit genes. it is the most common single gene disorder in the world. 7% carrier state. mutations affect synthesis rate. |
|
|
Term
| how is thalessemia different from sickle cell? from affinity mutations? |
|
Definition
| in sickle cell we have no change in synthesis rate, it is just defective. thalessemia hemoglobin subunits work perfectly fine, we're just not making enough of them. affinity mutations are defective |
|
|
Term
| what problems can cause a thalessemia? |
|
Definition
| problems with: noncoding sequences (improper splicing), protomer sequence (decrease expression), deletion of gene or protion of gene, termination sequence (increase in mRNA length, decrease in translation), early termination. |
|
|
Term
| What is one of the main goals of an effective antibiotic? |
|
Definition
| we want to inhibit bacterial transcription, but not human transcription. some drugs do this by binding to bacterial RNA polymerase, or maybe to bacterial rRNA subunits. |
|
|
Term
| proteins are translated by the ribosome from the ____ end to the _____ end, just like transcription. |
|
Definition
|
|
Term
|
Definition
|
|
Term
| What are the 3 sites on the ribosome? |
|
Definition
| A site, P site, E site. The A site is where the new amino acid binds. the P site is where the growing peptide chain (peptide bond formation) is found, and the E site is where the outgoing tRNA exits, or is released. |
|
|
Term
| Our peptide grows from the ____ terminus to the _____ terminus |
|
Definition
|
|
Term
| What is the error rate in DNA replication? in transcription? in translation?> |
|
Definition
| replication - 1 in a billion or trillion. transcription - 1 in 10,000 to 100,000. translation - 1 in 10,000 |
|
|
Term
| What enzyme actually attaches the amino acid to the tRNA? |
|
Definition
|
|
Term
| the acid group of an amino acid plus the alcohol group of ribose yields a ______ bond |
|
Definition
|
|
Term
| How does the initiation of bacterial translation differ from eukaryotic initiation of translation? |
|
Definition
| bacteria initiate their protein synthesis with a formyl methionine rather than normal methionine like in eukaryotes. (our mitochondira use formyl MET, just like bacteria! ) |
|
|
Term
| How does the initiation of bacterial translation differ from eukaryotic initiation of translation? |
|
Definition
| bacteria initiate their protein synthesis with a formyl methionine rather than normal methionine like in eukaryotes. (our mitochondira use formyl MET, just like bacteria! ) |
|
|
Term
| The start codon is AUG, what does AUG code for? |
|
Definition
|
|
Term
| what controls the cell cycle? |
|
Definition
| cyclins and cyclin dependent kinases. |
|
|
Term
| what cyclin is required for entrance into mitosis? |
|
Definition
|
|
Term
| What cyclin is required to begin DNA replication? |
|
Definition
|
|
Term
| what can set in motion a chain reaction that causes a cell to re-enter the cell cycle from the G-zero stage? |
|
Definition
| growth factors or proto-oncogene (which induce cyclins) |
|
|
Term
| what molecules turn on/off a few genes that are usually transcription factors that end up turning on/off many many more genes in a secondary response? |
|
Definition
|
|
Term
| growth factors ultimately, after all those responses, end up phosphorylating what? |
|
Definition
|
|
Term
| cytokines bind to what type of cell membrane signal protein? |
|
Definition
| tyrosine kinases, which starts the phosphorylation cascade |
|
|
Term
|
Definition
| B cells are part of the immune system that have a specialized receptor protein allows a B cell to bind to a specific antigen. |
|
|
Term
|
Definition
| plasma cells pump out huge quantities of antibodies |
|
|
Term
| After a helper T-cell has identified some foreign antigen, it hopefully interacts with a resting B-cell that has the correct antibody to cause what response? |
|
Definition
| helper t cell interacts with a b cell. helper t cell releases cytokines which tell the b cell to differentiate into either a plasma cell or a memory cell |
|
|
Term
| Why is an IGF like insulin? |
|
Definition
| it activates a tyrosine kinase receptor! this end up phosphorylating some things, that increase synthesis of proteins and lead to hypertrophy. |
|
|
Term
| what is a proto-oncogene? |
|
Definition
| A proto-oncogene is a normal gene that can become an oncogene due to mutations or increased expression. Proto-oncogenes code for proteins that help to regulate cell growth and differentiation |
|
|
Term
| What are tumor suppressor genes? |
|
Definition
| they are barriers to proliferation (usually dna repair proteins). one, p53, is a defect in over 70% of all tumors. |
|
|
Term
| What are 4 common but not mutually exclusive characteristics of cancer cells? |
|
Definition
| 1. mutations that activate proto-oncogenes. 2. mutations that stop tumor suppression limits on proliferation. 3. mutations that stop contact inhibition. 4. mutations that "optimize" genetic instability |
|
|
Term
| what is the philadelphia chromosome error? |
|
Definition
| it is a specific chromosomal abnormality that is associated with chronic myelogenous leukemia (CML). It is the result of a reciprocal translocation between chromosome 9 and 22. This causes an error which leads to a BCR/ABL fusion protein which phosphorylates leading to additional growth and proliferation. |
|
|
Term
| What drug blocks the BCR-ABL fusion protein? |
|
Definition
| gleevec, a competitive inhibitor. |
|
|
Term
|
Definition
| It is a tumor suppressor gene that limits uncontrolled cell proliferation. APC eliminates cyclin and halts the cell cycle. (so obviously an error in this gene would make the cell continue the cell cycle when it should've stopped) |
|
|
Term
| What does the Rb protein do? |
|
Definition
| it blocks continuation of the cell cycle. when this protein is modified by a growth factor, the cell cycle can continue |
|
|
Term
|
Definition
| similar to Rb, it blocks the cell cycle. When it is modified/phosphorylated by growth factors the cell cycle can continue |
|
|
Term
| retinablastoma results in 2 mutations to which gene? |
|
Definition
|
|
Term
| the Ras and Myc genes that affect cancer support what model of cancer? |
|
Definition
| supports the"two-hit" model of gene mutations leading to cancer |
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