study guide questions
What is the probability of you and another person independently flipping pennies and both landing on heads? What rule of probability are you applying here?
.25. Applying rule of multiplication
Following the Law of Segregation, what alleles will an individual with Aa genotype put into each gamete? What about AA genotype? Or aa?
Aa will produce A,A,a,a. AA will produce A,A,A,A. aa will produce a,a,a,a
Explain the process of acetylation. Where are acetyl groups added? How does it impact the packaging of DNA? Why does acetylation change the structure of chromatin? How does that regulate transcription? Can acetylation be undone?
Acetylation is the addition of acetyl groups to the end of histone tails, neutralizing their charges, and opening up condensed DNA. Process: 1) Histone acetyltransferases add acetyl groups, allowing transcription 2) histone deacetylases remove acetyl groups, repressing transcription. Makes genes accessible. Is reversible.
What are the two ways that damaged DNA can be repaired? How does each work?
Can be repaired by excision repair and direct repair. Excision repair removes damaged nucleotides and replaces them with correct ones, DNA polymerase adds the correct nucleotides, DNA ligase repairs the remaining nick. Direct repair photolyase breaks the dimer bond and is released from the DNA, the DNA returns to its original structure.
What happens if DNA polymerase causes a base pair mismatch and doesn't catch its mistake?
Can result in a point mutation
What are the two ways that mismatched repair proteins can make a mistake? What are the results of each of these mistakes?
Can result in a tautomeric shift or Deamination. A tautomeric shift is when a base temporarily forms its rare teutomer (same chemical formula, different arrangement), which can pair with a different base. Deamination is the loss of an amino (NH2) group in cytosine, forming uracil (a base in RNA).
Describe the elongation of DNA during replication. Compare/contrast the elongation of the leading and lagging strands. Which one is composed of Okazaki fragments? What does that mean, and how are they combined into a single, continuous DNA strand? Explain this process and the components involved.
DNA polymerase attaches to primers and adds nucleotides to the 3' end to build a new strand (a primer is required). During DNA synthesis the template strand is read in the 3'-to-5' direction but the complementary strand is built in the 5'-to-3' direction. The helicase only unwinds a single replication fork but both strands, leading strand (built continuously) and lagging strand (built discontinuously in separate okazaki fragments), are synthesized simultaneously. A different DNA polymerase replaces the RNA primers with DNA and the DNA ligase joins Okazaki fragments.
Describe the discovery regarding the structure of DNA that Francis Crick and James Watson found that Rosalind Franklin also discovered.
Double helix structure and antiparallel
Explain how genes are expressed to produce phenotypes. What do genes encode for? How does that produce a phenotype? (Think about the red hair allele as an example.)
Genes encode for chains of amino acids that make up proteins, which impact the phenotype.
Compare/contrast how transcription factors regulate the transcription rate in prokaryotes and eukaryotes.
In prokaryotes there are fewer transcription factors while in eukaryotes there can be thousands of transcription factors with multiple steps
List and briefly describe the three steps of DNA replication
Initiation: unwinding the DNA double helix and synthesizing RNA primers. Elongation: synthesizing new strands of DNA using each of the parental strands as templates. Termination: DNA synthesis ends.
Describe microRNA. At what level do they regulate gene expression?
MicroRNAs bind to mRNA to block translation or cause premature degradation. miRNA is formed from a double stranded RNA that is cut into small segments. miRNA will combine with proteins to form an RNA-induced silencing complex which inhibits translation or causes degradation of complementary RNAs. This occurs post transcription.
Describe what is meant by the genetic code being degenerate.
Most amino acids have 2-6 codons that encode them
Explain the basic rules of probability. What is the probability of a guaranteed event, an impossible event, or an event with multiple outcomes?
Probability is the predicted ratio is statistically likely, but not guaranteed. A guaranteed event would have a probability equal to 1. An impossible event would have a probability equal to 10. A mixed event would have a probability between 0 and 1.
Why is it much more acceptable for mutations (misplaced nucleotides by RNA polymerase) to occur during transcription when compared to DNA replication?
RNA polymerase has poor proofreading ability, but mistakes are less problematic than in DNA replication because RNA sequences are shorter, RNA errors are not passed to offspring, and many RNAs are synthesized very quickly and have a short lifespan
Describe the three DNA replication hypotheses
Semiconservative replication hypothesis is when each parental strand is a template for a new strand. Conservative replication hypothesis both strands act as a single template and produce one double-stranded daughter molecule. Dispersive replication hypothesis parent molecule is dispersed among two daughter molecules.
What is the difference between spontaneous and induced mutations?
Spontaneous errors are completely spontaneous while induced mutations are caused by mutagens (certain chemicals or radiations) that damages DNA
Describe the discovery made by Rosalind Franklin regarding the shape of DNA.
The double helix structure found through her work in x-ray crystallography
How does genetic information contained in mRNA encode for specific amino acids?
The mRNA contains codons that encode specific amino acids. Codons are 3 letter sequences (AUG, UUG, etc) that chunked together.
Describe what is meant by a transgenic organism
Transferring genes from one organism to another
Describe the termination of DNA replication. Compare/contrast termination when replication forks meet, when the leading strand reaches the end of the chromosome, and when the lagging strand reaches the end. What problem occurs when the lagging strand reaches the end of the chromosome? Why is this an issue?
Two replication forks moving toward each other meet (proteins bind to stop replication). Or a replication fork reaches the end of the chromosome (leading completes the whole strand and lagging cannot be completed (primer is not replaced) and the DNA is shortened).
Explain the concept of "wobble" in reference to codons. What does this allow?
Wobble is the fact that the third base of a codon does not always need to match the anticodon. Allows fewer tRNA variants while avoiding ambiguity.
What is an operon? Explain how the promoter, operator, and structural genes make up an operon. What are the implications of having one promoter/operator for several genes? Think about the effect on transcription and regulation.
a series of genes with a single promoter is called an operon. the regulatory sequence between the promoter and the genes is called the operator it acts as a binding site for the repressor-blocking transcription
What are transcription factors? How do repressors and activators regulate transcription?
regulatory proteins that control gene transritpion which bind to specific dna sequences either increaseing or decreasing rate of transcription
Compare/contrast start and stop codons
1 start codon that begins translation. 3 stop codons that terminate translation
In what ways is mRNA (Pre-mRNA) processed after transcription to create mature mRNA that is ready for translation? What sequences are removed? What is added to each end?
1. Coding regions (exons) are sequences of DNA that are translated into polypeptides. 2. Non-coding regions (introns) are removed from Pre-mRNA and exons are spliced together. Stop codons are added to each end.
What were the two discoveries made that changed the "One gene-one enzyme" hypothesis to the "One gene-one polypeptide" hypothesis?
1. Genes can encode for proteins other than enzymes. 2. Some proteins are made up of multiple polypeptides.
What was the circumstantial evidence that DNA is the molecule of inheritance? List and describe how each piece of evidence was discovered
1. Present in the nucleus of a cell and in chromosomes (discovered by using light microscopy). 2. Doubles during the S phase of the cell cycle (discovered by flow cytometry). 3. Diploid cells have twice as much as haploid cells (discovered using flow cytometry).
Compare/contrast transcription and DNA replication.
1. RNA polymerase doesn't require a primer (sequence of bases to tell where to start [called promoter]). 2. Doesn't copy the whole strand (sequence tells where to stop). 3. Produces single-stranded RNA. 4. Uses rNTPs to add the nucleotides, rather than dNTPs (ribose rather than deoxyribose).
Describe the overall process of gene expression with relation to the processes involved and where these processes occur within a cell
1. Template DNA strand is transcribed inside the nucleus (produces single stranded complementary mRNA). 2. Strand is processed (pre-mRNA to mature to mRNA). 3. mRNA moves out of the nucleus to the cytosol. 4. Translation of mRNA of mRNA into a polypeptide at the ribosome.
Describe the process of RNA splicing. Explain how each of the components (consensus sequences, snRNPs, spliceosome, and the branch site) are involved in the process of removing introns.
1. snRNPs bind near consensus sequences. 2. Spliceosome removes the intron by: a. Cutting the 5' end of the intron and attaching it to the branch site. B. cutting 3' end to release intron. C. splices two exons together.
Compare/contrast sense/missense (stop) codons.
3 stop codons that terminate translation. 61 sense codons that make up the meat of the amino acid chain.
Explain what a Barr body is. How does this relate to the fact that calico/tortoiseshell cats can only be female? In what situation is it possible for a male cat to be calico?
A barr body is one X chromosome condensed and silenced because otherwise female mammals (XX) would express that genes on the X twice as much as males (XY). Calico/tortoiseshell cats is when patches arise from clusters of related cells with the same X being expressed and only females have XX. Males can exhibit this when being aneuploidy (XXY) but it is rare.
Which type of mutation is more likely to be deleterious (harmful): a point mutation or a chromosomal mutation? Why?
A chromosomal mutation is more likely to be harmful. Because many different bases are rearranged or missing which has a larger impact than one single base being different
What is a mutagen? List examples of chemical and radiative mutagens
A mutagen is any agent (e.g., a chemical, radiation) that increases the mutation rate. Chemical mutagens come from consuming, breathing in, and exposure to skin (examples: smoking [accounts for ⅓ of all cancers] and diet [appears to account for another ⅓ of cancers]). Radiation DNA damage comes from radiation (examples: UV radiation [in sunlight can cause skin cancer] and ionizing radiation [ from power plants and bombs]).
What is a Punnett square? What does it allow us to visualize? What do you write on the sides of the square, and what do you write in the intersections in the middle?
A punnett square is how we represent the crossing of different gametes. Visualizes intersections as fertilization. On the side of the square you write one parent's alleles and on the top you write the other parent's alleles.
Describe translational repressors. At what level do they regulate gene expression? What other regulatory proteins are these similar to?
A translational repressors are proteins that bind to mRNAs to prevent translation. This regulates gene expression post transcription. THis is similiar to transcription repressors.
Describe alternative splicing. What is removed from the genes? What is spliced together? How does alternative splicing allow for one gene to create multiple different proteins? At what level does this regulate gene expression?
Alternative splicing is when different combinations of exons are spliced together to create different mRNAs. NOthing is really completely removed from the genes. Different exons are spliced together. Because the exons can be exhibited in multiple proteins in different arrangements there are multiple different proteins formed. This occurs post transcription.
Explain how Archibald Garrod's research involving alkaptonuria led to his hypothesis that genes encode proteins.
Arcchibald Garrod hypothesized that genes encode enzymes. Studied Alkaptonuria (pee turns black when exposed to air) He discovered this was caused by an accumulation of homogentisic acid and it followed a recessive inheritance pattern. His conclusion was that non-functional enzyme for breaking down homogentisic acid must be inherited genetically by those with the disease.
Explain Beadle & Tatum's experiment. How did they knock out the metabolic pathway for the production of arginine? How did this support the idea that genes encode enzymes?
Beadle and Tatum developed a method for studying mutations that "knock out" metabolic pathways (enzyme catalyzed reactions). Worked with bread mold to grow in minimum mediums and whichever ones did not grow when put in arginine bread mold would grow. Concluded that the enzyme responsible for arginine production must have been disrupted by mutations caused by the radiation.
Why can we relate pennies to genotypes and flip outcomes to alleles? Think about the Law of Segregation
Because the physical pennies are associated with genotypes. When flipping a coin, getting heads is like having a dominant allele and getting tails is like getting a recessive allele. Due to allele segregating equally (and being randomly put into gametes) passing on an allele is like a coin flip (but if double sided coins also existed.
Explain how a kitten might have point coloration when that allele is not in the population's gene pool. What type of mutation is this? (Somatic vs Germline, Spontaneous vs Induced, Silent vs loss of function vs gain of function vs conditional) Describe how the mutation that causes point coloration impacts the protein and phenotype.
Because the point coloration mutation is an example of condition mutations (which produce a protein that only functions under certain environmental conditions). In the cat example the enzyme tyrosinase only functions in the cold which places on the body with lower temps (ears etc) led to the fur darkening. Germline. Spontaneous. And gain of function.
Explain the differences between blending inheritance and particulate inheritance. What evidence did Mendel's monohybrid cross uncover that supported particulate inheritance and didn't make sense with blending inheritance?
Blending inheritance is the idea that offspring inherit characteristics that are a blend of those seen in the parents while particulate inheritance determinants (now called genes) are passed to the next generation without blending. HIs experiments with Pea plants and how they inherit genes from their parents was how he discovered the two laws of inheritance.
Compare/contrast somatic and germline mutations. Which type can be passed onto future generations? Which type impacts only an individual?
Both are cell mutations. Somatic mutations occur in somatic (body) cells which may impact an individual, but not passed to offspring. Germline mutations occur in germ line cells (gametes) and are passed to offspring and future generations
What are mutations? And what are some of the general reasons they can occur?
Changes in a DNA sequence as a result of 1. Errors during DNA relocation 2. DNA damage by chemicals or other agents 3. Errors during cell division
Given everything discovered regarding the makeup and shape of DNA, describe its structure. What aspect of its structure allows both strands to contain the same genetic information?
Complementary base pairings
List the chemical components that compose DNA. Compare/contrast purines and pyrimidines.
Consists of Deoxyribose, a phosphate group, and a nitrogen base. Either a Purine (A and G the larger bases) or a pyrimidines (T and C are smaller bases)
How is DNA packaged? (Think about nucleosomes and histones.) Why does it need to be packaged in this way?
DNA is packaged into nucleosomes, which are composed of 8 histone proteins that the DNA is wrapped around. DNA has to be condensed to fit into a cell. Histones have positively charged amino acid tails and the strong attraction bw positive histone tails and negative phosphate groups of DNA.
List and describe each form of chromosomal rearrangement (Deletion, Duplication, Translocation, and Inversion. What situations cause each to occur?
Deletion is when a portion of a chromosome is lost. Occurs when chromosomes break in two locations and regions without middle segments. This results in missing genes that can have severe or fatal consequences. Duplication is when a portion of a chromosome is repeated. Occurs when homologous chromosomes break at different positions when crossing over. Resulting in one chromosome will lack a segment (deletion) and the other will have two copies (a duplication). A translocation is when a portion of a chromosome is in the incorrect location. Occurs when two non-homologous chromosomes break and exchange segments (not always reciprocal). Resulting in chromosomes with sequences belonging to another. An inversion is when a portion of a chromosome is flipped. Occurs when the chromosome breaks twice and rejoins, but the segment is inverted. Can result in loss-of-function mutations.
Methylation is more of a long-term gene-silencing mechanism. This is because methylation can be passed on from parent to daughter DNA molecules. Explain what this process looks like, given your understanding of the semiconservative nature of DNA replication.
Due to semiconservative replication replicated DNA is hemimethylated (methyl is on strand that is copied) and the maintenance methyltransferase catalyzes formation of 5-methylcytosine in the new DNA strand.
Explain why an Rr x rr cross can produce all rr offspring.
Due to the alleles separating Rr and rr are both possibilities
Explain the Law of Segregation. What does it mean? And how does it relate to Mendel's experiments?
During the formation of gametes, alleles separate equally so that each gamete receives only one copy. Basically each gamete gets only one copy of the gene (either A or a version). Which explain medel's monohybrid cross observations (the 3:1 phenotypic ratio and the 1:2:1 genotypic ratio)
Describe how the Meselson-Stahl experiment was performed and how it provided evidence for the semiconservative DNA replication hypothesis.
E coli was grown with N15 (which made DNA more dense) and then transferred to an N14 medium (used for future replication). Used the DNA density ratios to prove DNA replication was semiconservative.
What is epigenetics? In general, how do these modifications regulate transcription?
Epigenetics is the chemical modification of DNA "packing" that influences gene expression. Modifies by making genes accessible (acetylation) or inaccessible (tightly wound nucleosomes).
Explain the differences between introns and exons, and how hybridization experiments discovered introns. Why did a loop form in the DNA during the hybridization of mature mRNA, but not during the hybridization of Pre-mRNA?
Exons kept in, Introns kicked out. Introns were discovered through Hybridization experiments where RNA can hybridize (match up and connect with) complementary DNA. Loops form because mature mRNA will not fully hybridize (loop sequences aren't in the mature mRNA) unlike premRNA and prokaryotic nRNA will fully hybridize with complementary DNA.
Explain the process that Mendel went through to do his monohybrid cross. Explain how he created the Parental generation, and F1 generation, and the F2 generation. What were the phenotypic ratios of each generation?
First he created the parent generation by true breeding (selfing) a line for a while to insure that the same traits were seen as their parents. To create the F1 generation he reciprocally crossed the true breeding plants. To create the F2 generation he allowed the F1 generation to self fertilize. All F1 generations were all purple. The phenotypic ratio of F2 purple:F2 white was always 3:1.
Be able to define and explain the relationship between the terms: genes, alleles, genotype, phenotype, dominant, recessive, homozygous, and heterozygous
Gene=sequence of DNA at a specific locus that performs a particular function. Alleles=different makeup of an individual. Genotypic=allelic makeup of an individual. Phenotype=outward expression of the genotype. Dominant=requires only one copy of that allele in order to be expressed (A). Recessive= requires both copies of that allele in order to be expressed (a). Homozygous= two alleles at a locus are the same (AA or aa). Heterozygous=two alleles at a locus are different (Aa).
Describe the two ways that Mendel controlled the mating of pea plants (involved pollen transfer) so he could know which parents produced specific offspring.
He controlled the mating by removing pollen from stamens and manually placing into pistols of either another plant (cross-fertilization) or the same plant (self-fertilization/selfing)
What patterns do you see when you look at the table of all amino acids? Can multiple codons encode from one amino acid? Can one codon encode multiple amino acids? What can you infer about the code based on these answers?
If two codons both code for the same amino acid then their first two nucleotides are the same. The reverse is not true, however, if the first two nucleotides are the same they either encode the same amino acid or amino acids that are very similar. Multiple codons can encode for the same amino acid. One codon cannot encode multiple amino acids.
Compare/contrast the two ways that bases themselves can be altered in a way that causes them to be paired with the incorrect base
In tautomeric shift the base is slightly altered with the same chemical formula (just different arrangement) while in deamination the case loses an NH2 group (cytosine changes to uracil)
Explain what is meant by the underlying 1:2:1 "potential offspring" ratio that Mendel saw in the F2 generation of his pea plant crosses. How did he find this underlying ratio? Why could some of the purple flowers produce white offspring, while the other purple flowers could not?
In the F3 Generation out of the four flowers produced: 1 was always purple true breeding, 2 were purple not true breeding (could produce purple or white flowers), and 1 was white true breeding.
Describe the Transformation experiment, and how it provided strong evidence that DNA is the molecule of inheritance.
In the experiment they used a deadly S strain which killed the mice and a nondeadly R strain that didn't kill the mice. But when they injected the mic with heat killed S strain and living R strain the mice also died. LAter they test multiple enzymes which led them to discover that adding a DNA-degrading enzyme stopped the transformation (aka the mice lived).
Explain the central dogma of molecular biology. How is genetic information expressed? Describe the flow of the information, how it is transformed, and what processes transform it.
Information flows from DNA -> RNA -> polypeptide (protein). Genetic information is expressed in polypeptides. DNA goes to RNA by translation. RNA goes to a polypeptide by Translation.
Explain the process of translation in detail. What happens during initiation, elongation, and termination? What site do tRNA molecules bind to? What is the site where the growing polypeptide chain is attached? Explain how termination works in translation.
Initiation complex forms when the small subunit binds to mRNA and locates start codon (AUG), then tRNA binds to start codon, then the large subunit joins with tRNA in the P site. Elongation occurs when another tRNA enters the A site and the large subunit catalyzes two reactions (1. Breaks bonds between tRNA in the P site and its amino acid. 2. Forms peptide bond between that amino acid and the amino acid on tRNA in the A site. 3. tRNAs shift into the adjacent site to make space for arrival of the next tRNA. 4. Cycle repeats and the polypeptide chain grows.). Termination (1. Stop codon renters the A site and release factor attaches [No tRNAs match a stop codon]. 2. Protein release factor binds and breaks bond between polypeptide chain and tRNA [polypeptide is released]. 3. Subunits of ribosome separate).
Explain what happens during each step of transcription: initiation, elongation, and termination.
Initiation is when RNA polymerase binds to a promoter: sequence of DNA that tells where to begin transcription (transcription factors bind upstream from the initiation site to regulate gene expression). Elongation is similar to DNA replication, but only one strand with a ribose sugar backbone rather than deoxyribose. Termination is when a particular sequence of bases (termination site) specify stopping point where the specific mechanism for termination differs across genes and organisms (generally involves recognizing the termination site and separating the RNA from the DNA template and RNA polymerase).
Why is it beneficial that multiple ribosomes can translate a single mRNA molecule simultaneously?
It is much more efficient. And it is easy to do because translation only occurs in one direction.
Describe the Hershey-Chase experiment, and how it provided strong evidence that DNA is the molecule of inheritance.
Label DNA or protein of virus with a radioactive isotope (32P vs 35S). 2. Infect bacteria with the virus. 3. Use a blender to detach viruses from bacteria. 4.Centrifuge to Separate viruses and bacteria. 5. Determine where the viral DNA or protein ended up! The results were Viral DNA - found in the pellet with the bacteria, and Viral proteins - found in the supernatant with the virus
Describe all of the major parts of a ribosome: large subunit, small subunit, A site, P site, and E site.
Large subunit has 3 tRNA binding sites (A, P, E). A site is where the tRNA binds to codon of the mRNA. P site is where tRNA adds amino acid to the polypeptide chain. E site is where tRNA waits until released from the ribosome. Small subunit validate the match of mRNA codon to tRNA anticodon (ejects tRNA if it doesn't match).
Explain the process of methylation. Where are methyl groups added? How does this impact the transcription of methylated DNA? (Think about the location on the DNA where methylation occurs.)
Methylation is the addition of methyl groups to cytosine bases in DNA, repressing transcription. Process: 1) DNA methyltransferase catalyzes modification of cytosines into 5-methylcytosine 2) Demethylase catalyzes removal of methyl groups from cytosine. Liske acetylation this process is reversible but it tends to be a long term gene silencing mechanism
How can monozygotic twins be used to study epigenetics?
Monozygotic twins demonstrate how environmental factors (diet, chemical exposure, stress, hormones) impact methylation patterns which influence phenotype.
How do mutations impact cells? List and describe the three types of mutations based on their impacts on the proteins that result. How does each of these impact the phenotype of an organism with these mutations?
Mutations cause a function change in a protein to affect the phenotype. Silent mutations do not affect protein function resulting in the protein functioning normally with no impact on phenotype.. Loss of function mutations that prevent gene transcription or produce non functional proteins has an impact on phenotype. Gain of function mutations leading to a protein with altered function has an impact on phenotype.
Explain how germline mutations help provide the raw material for evolution.
Mutations lead to a new trait which may become common in a population if improved fitness (or at least doesn't hinder it)
What does it mean that the genetic code is universal? What are the implications of this?
Nearly all organism use the same codons to encode the same amino acids
What patterns did Mendel observe in all 7 of his monohybrid crosses? How did the phenotypes present change from generation to generation? What about the phenotypic ratio in the F2 generation?
One trait disappeared in the F1 generation and reapered in the F2. The F2 traits were always in a 2;1 ratio
Describe the three ways that polypeptides can be modified post-translationally. How do each change the polypeptide, and why might each be necessary?
Phosphorylation is the addition of phosphate groups, changing the shape (function). Glycosylation is the addition of carbohydrates, which may have important functions. Proteolysis is the cutting long polypeptides into smaller pieces that have their own function of removal of signal sequences.
Describe how a test cross works. What do these allow you to do?
Plant with dominant phenotype but unknown genotype (A_) is crossed with a plant with a known recessive homozygous genotype (aa). We can learn the unknown allele
Describe the initiation of DNA replication. Explain the function of DNA helicase, topoisomerase, primase, and primers.
Pre-replication complex binds to site(s) or origin (ori). Replication bubbles form at ori with replication forks at each end. DNA helicase moves away from the ori, separating the strands and widening the replication bubble with the help of topoisomerase. DNA helicase is an enzyme that catalyzes the unwinding of a nucleic acid double helix. Topoisomerase is an enzyme that relieves tension for the DNA helicase. Primase is an enzyme that catalyzes the synthesis of a primer for DNA replication. Primers is a strand of nucleic acid, usually RNA, that is the necessary starting material for the synthesis of a new DNA strand, which is synthesized from the 3′ end of the primer.
What is the incorporation error rate? And how is DNA polymerase able to correct itself?
Probability that an incorrect base will be inserted is about 1 in 100,000. Result is a mismatch between complementary strands. Most replication mistakes are repaired as they happen or shortly afterward. DNA polymerase will proofread a strand and recognizes a mismatch, backs up, removes mismatched nucleotide, then recommences synthesis
Describe the discovery made by Erwin Chargaff regarding the ratios of the bases found in DNA. Think about why these ratios help in our understanding of DNA structure and function.
Purine and Pyrimidines have equal ratios which led to us having complementary base pairings
What helps direct polypeptides to different locations in the cell post/during translation?
Signal sequences in the RNA tell the polypeptide where to go. Usually happens post translation, but in the rough endoplasmic reticulum ribosomes travel to the RER during translation.
Describe the end-replication problem. How are we able to overcome this problem?
Single stranded regions of DNA at each end of chromosome are cut off, resulting in a slightly shortened chromosome after each replication. Able to to solve using telomeres and telomerase.
Explain how each type of mutation impacts the chain of amino acids produced: synonymous, missense, nonsense (stop), loss-of-stop, and frame-shift.
Synonymous mutations don't alter the amino acid. Missense mutations change the amino acid sequence (swaps nucleotides). Nonsense mutations produce a premature stop codon. Frameshift mutations change a stop codon to a sense codon (changes all amino acids down the line).
Describe telomerase and how it functions.
Telomerase is a form of DNA polymerase that can increase telomere length. Works by: Telomerase has complementary RNA sequence to the telomere. Acts as template to lengthen the 3' overhang. A new primer is built on the template strand. Then, DNA polymerase builds the complementary strand to the new segment.
Describe what a telomere is and how they work.
Telomeres are repetitive non-coding sequences at the ends of eukaryotic chromosomes to protect coding regions. Like how an aglet on a shoelace works.
What was the goal of Mendel's experiments? What was he trying to understand?
The goal was to understand how traits (forms of character -ex: purple vs white flowers) in pea plants are passed on from parents to offspring. Aka how traits are inherited.
Compare/contrast euchromatin and heterochromatin.
The two types of chromatin are visible during interphase are euchromatin (unmethylated) and heterochromatin (methylated). Euchromatin is diffused and light staining, and the DNA is available from transcription (genes can be expressed) Heterochromatin is condensed and dark staining, and cantiona genes not transcribed (genes are silenced).
Why do codons exist, and how were they discovered?
There are not enough nucleotides (only 4) for them to directly code amino acids (of which there are 20). They were discovered by Nirenberg and Matthaei discovered the first codons through experiments involving synthetic mRNA. Used poly-U and found if they had at least 3 U's in a row radioactive phenylalanine would be produced, if there was only 2 U's they did not see this pattern.
There are 1500+ transcription factors in human cells that can interact with genes to regulate their expression. What does this allow our cells to do? What might be possible if we can understand how specific genes are regulated by specific transcription factors? (Think about the study with mice skin cells.)
This allows different genes to be expressed by cell differentiation. From changing the specific transcription factors we could change the type of cell that is produced (like when researchers manipulated the expression of transcription factors in mice skin cells to change them into neurons). This could also lead to us growing organs from your own cells, less rejection rates.
Describe the relationship between ubiquitin and the proteasome. At what level do these regulate gene expression? Does this level of gene regulation conserve or waste resources/energy compared to regulation during transcription?
Ubiquitin is the protein that identifies other proteins for breakdown by the proteasome (enzyme). This occurs post-translationally. This level of gene regulation wastes energy in that it uses energy to create these proteins just to break them down.
When during gene expression does regulation occur? What stage is the most common, and why?
can occur at any step in the process of gene expression but is most common during transcription
Describe the three main products of transcription and explain how they work together to form polypeptides. What parts does each play in this process? Which one contains the information being expressed?
mRNA (messenger) contains the information being expressed/contains information used to build the polypeptide. rRNA (ribosomal) part of the ribosome that builds the amino acid chain. tRNA (transport) brings the next amino acid to add to the growing chain.
Compare/contrast inducible, repressible, and constitutive genes. Explain an example of each.
not expressed unless needed, vs usually expressed unless not needed, vs always expressed
Compare/contrast negative and positive regulation. What type of transcription factor is involved in each? Where does a repressor bind, and how does that impact transcription? Where does an activator bind, and how does that impact transcription?
repressor negative, activator positive both bind to operator
What are the two major sites on a tRNA molecule, and what is the function of each?
tRNA has an amino acid attachment site (tRNA synthetase binds a specific amino acid to this site) and has an anticodon (nucleotide triplet complementary to the mRNA codon for the attachment amino acid).
Why is gene regulation important? What would happen if all of your cells expressed every gene all of the time?
think of stomach acid in eyes
