Flashcards in Molecular Genetics Deck (148):
Origin of replication
location on the chromosome where replication begins
DNA replication proceeds in both directions simultaneously from the origin
each of the newly formed daughter helices is made up of one old strand paired with one new strand
one strand (the leading strand) is synthesized continuously and the other strand (the lagging strand) is synthesized in Okazaki fragments (i.e., discontinuous)
DNA replication start to finish
DNA replication begins at an origin of replication. Helicase unzips the double-helix. Immediately, single strand binding proteins coat the individual strands and prevent them from re-annealing. Simultaneously both strands are fed through a replication complex that contains all of the proteins necessary for replication. Because DNA polymerase can only add to an existing 3’ OH group, primase (an RNA polymerase) first constructs short RNA primers on both strands. Two DNA polymerase molecules then begin building new complementary DNA strands. In doing so, they must “read” (i.e., move along the strand) in the 3’ to 5’ direction and are therefore building the new strands in the 5’ to 3’ direction. The sliding clamp is a protein that helps keep the DNA polymerase tightly associated with the strand. Because both enzymes must move along the strand in the 3’ to 5’ direction, they will be moving in opposite directions. If this continued indefinitely the two enzymes would move farther and farther apart. Instead, all enzymes and proteins remain closely associated with the replication fork in what is often called the “replication complex.” As a result, the enzyme working on the lagging strand must copy short segments downstream, release from the strand, move upstream, and copy another short segment downstream—and then repeat. This also means that while the leading strand requires only a single primer, the lagging strand requires multiple primers—one for each these short segments called Okasaki fragments. After this initial replication step, the enzyme RNase H removes all RNA primers. DNA polymerase then fills in the gaps. However, DNA polymerase functions only to add nucleotides to existing 3’ OH functional groups. Therefore, although it can add a nucleotide to fill the last missing base pair in a gap, it cannot connect that last nucleotide to its downstream neighbor. This functionality is performed by DNA ligase. DNA ligase creates the last necessary phosphodiester bond creating a completed strand.
How does the lengths of replicated DNA strands compare to the original? Why?
The replicated strand is always slightly shorter. The DNA polymerases require an existing 3’ hydroxyl group to which they can add their first nucleotide—they cannot set down a nucleotide with a free 5’ end. For this reason, an RNA primer must be placed at the 5’ end of any DNA strand. Later in the process all primers are removed and the gaps are filled in by DNA polymerase and DNA ligase. At the 5’ end, however, there will still be no existing 3’ hydroxyl group and so DNA polymerase cannot replace that section of primer. As a result, every time a chromosome is replicated the new daughter strands will be slightly shorter than the parent strands—by an amount exactly equal to the RNA primers that were in place on both ends of the chromosome
What are telomeres and why are they important?
Long sections of repetitive DNA nucleotides found on both ends of chromosomes. Act as a buffer-region of non-coding DNA so that length loss does not affect the coding region. Buffer lasts for about 50 replication cycles
What is telomerase?
enzyme that adds length to the telomeres
Why is telomerase turned off in mature somatic cells?
Built-in destruction clock that helps to prevent uncontrolled cell division
DNA polymerase reads from _ 'to _'
3'--5', meaning creates 5'-3-
What are the different mechanisms for DNA repair?
what is an endonuclease?
enzyme that cleaves the phosphodiester bond of a polynucleotide chain
what are restriction endonucleases
enzymes that cleave at specific nucleotide sequences.
if red+blue, = purple
all of the dominant ie red
both red and blue show up
what trait physically appears as
what traits alleles consist of
what are mutations
mistakes in DNA
where do large scale mutations take place
two genes on same chromosome switch places
gene on one chromosome swapped with one on another
chemical/physical substance/event that can cause genetic mutations
where are reactive oxygen species produced. examples? what effects might they have? what prevents them?
mitochondria. O2-, H202. they can be bad because they can react with DNA and cause damage such as double strand breaks or base modification (bases changed/swapped). antioxidants help prevent oxidative stress (when ROS gets too high)
where do effects of mutation generally appear?
what are the 3 stop codons?
UAG UGA UAA
what are other names for stop codons?
definition of a gene?
The portion of the genome that codes for a protein or an RNA is called a gene.
which way does the ribosomal complex move tRNA?
initiates at P. moves to E as subsequent tRNA comes into A (amino acid on initial fuses with next one as it comes into P site) once amino acid is gone in E site it is released
what are introns?
non-coding regions of pre-mRNA that are spliced out by snRNPs to create functional mRNA
what two traits does the genetic code have?
degenerate (multiple codons code for the same amino acid)
unambiguous (codon only codes for one amino acid)
what are other names for the coding strand?
what are other names for the template strand?
anti-sense, non-coding, transcribed
the presence of lactate will affect lac gene expression how?
lactate will bind with the lac repressor so that it does not bind to the operon, allowing gene transcription
what happens when lactose is absent
lac operon is repressed. (means there is sufficient glucose)
what does wild type refer to?
non-mutated DNA strands (the normal or typical phenotype)
law of segregation
alleles segregate independently of one another when forming gametes
law of independent assortment
(2nd law) genes located on different chromosomes assort independently
if both probabilities must occur then:
multiply probabilities of each event occurring individually
if either event fulfils requirement then:
add probabilities of each event occurring individually
when dealing with the dominant phenotype unless otherwise stated assume that :
homozygous dominant. other cases will be stated
The P1 Generation is the first parental generation in Mendel’s experiments. Both parents in this generation were pure-breeding (i.e., homozygous) for their trait. This would tell us that one was homozygous dominant (TT) and the other homozygous recessive (tt).
The F1 Generation was the offspring from the P1 Generation, which Mendel crossed with each other. Both parents in the F1 generation had to be heterozygotes (Tt)
The F2 Generation was the offspring of the F1 generation. The F2 generation showed the characteristic 3:1 phenotypic ratio and 1:2:1 genotypic ratio.
3:1 phenotypic ratio for F2 generation
A test cross is a cross between a homozygous recessive individual and an individual with a dominant phenotype for whom the genotype is uncertain (could be TT or Tt). If the dominant individual was TT then all offspring of the test cross will show the dominant phenotype (all will be Tt). However, if the dominant individual was a heterozygote then half would have the dominant phenotype (genotype Tt) and half would have the recessive phenotype (genotype tt).
Phenotype refers to the expression of the gene in terms of its visible or observable characteristics
The genotype refers to the specific alleles held by that individual. Note that individuals with different genotypes (TT and Tt) can exhibit the same phenotype (tall and tall).
A gene is a segment of DNA that codes for a protein
An allele is one of various alternative forms of the same gene. For example, if hair color is determined by a single gene at a single locus, that segment of DNA would be the “hair color gene.” One version of that gene (i.e., one allele) might produce blonde hair, while another variation in the sequence at that segment (i.e., a second allele) might produce brown hair, and so forth.
A locus is the specified physical location of a gene on a chromosome.
Malignant refers to tumors that are cancerous—meaning they are currently exhibiting uncontrolled growth, are likely to metastasize, etc
Benign refers to tumors that are still slowly growing, have not invaded other tissues, but could become cancerous later on.
Metastasis is the spreading of a cancer from one tissue or organ to another
Proto-oncogenes are “good” or “normal” genes that can become oncogenes (i.e., cancer-causing genes) if mutated; proto
oncogenes usually regulate cell division, cell cycle, growth, apoptosis, etc. as their normal function. It is therefore logical to see how they could cause cancer when mutated.
Tumor suppressor genes
Tumor suppressor genes are genes that help protect the cell form uncontrolled growth. When function of such a gene is lost the cell is more easily able to become cancerous. Tumor suppressor genes require two recessive alleles to lose function. Oncogenes, however, are generally gain-offunction alleles and therefore having only one bad copy can result in the undesired cancerpromoting protein. Most cancers follow the “two-hit” or “multiple hit” hypothesis. In other words, multiple mutations must accumulate before the cell becomes cancerous. For example, a proto-oncogene could be mutated, but the cell might not become cancerous because of the action of a tumor suppressor gene. If the tumor suppressor gene lost function (the “second hit”) then the cell would become cancerous.
Carcinogens are mutagenic chemicals that cause or promote cancer.
A point mutation is a single base pair substitution
A missense mutation is a mutation that changes the codon such that a different amino acid will be incorporated
A nonsense mutation is a mutation that changes a normal codon into a premature stop codon
A silent mutation is any mutation that does NOT alter the amino acid sequence. This could be because the codon was changed from one codon that codes for an amino acid to one of the other codons that also codes for that same amino acid (i.e., degeneracy/redundancy of the code). Mutations in an intron would also be considered silent mutations
A frameshift mutation is any mutation that changes the reading frame. This would be any insertion or deletion that does not occur in multiples of three
A neutral mutation is any mutation that does not negatively impact the fitness of the individual. Theoretically, any of the above types of mutations could be silent, although it is reasonable to assume that most nonsense or frameshift mutations will cause too much alteration to the protein for it to remain functional
role of rRNA
is the polymer of which ribosomes are constructed. can be considered an enzyme
role of tRNA
Transfer RNA (tRNA) is the molecule that bridges the gap between mature mRNA and the assembled protein. Each tRNA has an anti-codon on one end and on the other end is covalently bonded to the amino acid associated with that anticodon (or more precisely, the codon that is complementary to the anti-codon)
role of mRNA
Messenger RNA (mRNA) is the complementary RNA strand copied from the DNA template strand. The original copy is called pre-mRNA because it contains many non-coding introns and lacks the poly-A tail and 5’ cap. After it is fully processed and ready for translation it is called mature mRNA.
Restriction endonucleases are enzymes that cut DNA at specific pre-determined sequences. They are used in DNA cloning to create the DNA fragments with “sticky ends” that can be hybridized with vector DNA to form recombinant DNA.
The recognition sequence is the specific base sequence recognized by the endonuclease
The “sticky ends” already mentioned are said to be “sticky” because the endonuclease cuts the DNA in a staggered fashion that leaves one side of the helix longer than the other
Because the endonuclease ONLY cuts at one sequence, any fragment cut by that same enzyme will be complementary to any other fragment—and therefore any two fragments can hybridize, or join together to form a single strand.
A vector is a segment of DNA used to transfer a desired sequence into another cell. Often, the vector is a bacterial DNA sequence such as a plasmid.
. Phage is a shortened term for a bacteriophage (a virus that infect bacteria). As an alternative to the use of a bacterial plasmid as just described, the vector can also be inserted into a bacteriophage. Bacteria are then infected with the phage. The phages take over the machinery of the bacteria they infect in order to reproduce large numbers of new phages. This too results in many copies being made of the vector and the target sequence that was inserted into it
The target DNA sequence that researchers desire to multiply is added into the bacterial vector using restriction endonucleases. The vector can then be placed inside of bacteria and the bacteria cultured. Because bacteria reproduce exponentially, a huge number of new copies of the vector (with the target sequence included) can be created in relatively little time.
Gel electrophoresis is a lab technique used to separate molecules by size. A mixture of molecules (usually nucleotide segments or proteins) is loaded onto a plate covered with an agarose gel. A charged field is created across the gel. Because nucleotides are negatively charged (due to the phosphate groups) they will be pulled through the gel toward the positive side of the field. However, the gel acts like a molecular sieve, providing more resistance to the larger molecules. As a result, the smallest of all molecules travels the farthest, with all other molecules traveling a somewhat shorter path along a continuum down to the largest molecule. When a special kind of paper is placed on top of the gel the separated molecules attach to the paper at their respective positions. This paper can then be exposed on a film to create a map of the separated molecules.
what will happen to the lactase gene in the following situations?
a) glucose, no lactose
b) lactose, no glucose
c) no glucose, no lactose
d) lactose and glucose
a) not transcribed (inhibitor bound)
c) not transcribed (inhibitor bound)
d) no transcription (or very little; inhibitor would not be bound, but cAMP levels (the activator) are low when glucose is present)
what is alternative splicing and what is its significance?
Alternative splicing refers to the fact that after introns are removed from the mRNA transcript, the exons can be assembled in any of a number of different orders—each variation resulting in a different protein. This process is often cited as an explanation for how eukaryotes produce an almost unfathomable number of antibodies from relatively few genes
how do you use PCR?
To answer the second question first, to perform PCR one must know ahead of time a specific sequence on the DNA that will be used. Primers are then synthesized that that will anneal with the DNA on either side of the target sequence. Two primers are required, one that is complimentary to the 3’ end of the sense strand and one complimentary to the 3’ end of the antisense strand. The DNA is heated to a temperature sufficiently high to denature the helix (around 95°C). The primers are added along with special DNA polymerases harvested from thermophilic bacteria that live in hot springs (usually Taq Polymerase). The mixture is then cooled to a much lower temperature to allow the primers to anneal (50-65°C). The temperature is then raised again to the optimum temperature range for the thermophilic enzyme (around
72° for Taq Polymerase). The polymerase then copies the DNA, creating two new DNA helices. The temperature is raised again high enough to denature both helices and the entire process is repeated. The number of copies doubles for each cycle.
used to verify the presence/absence of a specific DNA sequence. WIll also indicate the relative size of restriction fragments
nearly identical to southern blot but used on RNA instead of DNA
Same basic procedure as N and S blots; used on protein segments instead of nucleotide segments. Probes used are radiolabeled antibodies rather than nucleotide sequences
similar to western, used to verify post-translational modification. probes used bind to lipids, carbohydrates, or phosphates
where does translation occur?
Translation occurs in the cytoplasm on free-floating ribosomes and on the rough ER. Recall that many proteins bound for certain organelles, the plasma membrane, the ER membrane, the lumen, and for excretion from the cell are translated on the cytosolic side of the rough ER and translocate into the ER membrane or into the ER lumen instead of into the cytoplasm. Some translation also occurs in the mitochondria because they have their own protein-synthesis machinery .
why is it important to distinguish between germ cells and somatic cells?
The MCAT loves this concept, but fortunately it’s pretty straightforward. Germ cells are the only cells passed on to offspring (only one specific gamete to be precise). Therefore, ONLY those mutations that occur in germ cells are heritable. Mutations in somatic cells may harm that particular cell during its lifetime and daughter cells derived from that cell via mitosis, but the next generation will ONLY receive the genetic information found in the sperm or egg cell they receive from each respective parent.
why is hemophilia more common in maes?
Hemophilia is more common in males because all X-linked recessive genetic disorders are easier for males to contract. This is seen rather simply by considering that males only need to receive a single “bad X” chromosome to be affected. This is because all males, by definition, will have a Y rather than another X. A Y chromosome does not mask a recessive allele as would another wildtype X. In females, however, to “bad X” chromosomes are required in order for the female to be affected. As a result, there is no such thing as a male carrier for an X-linked condition. If they have one copy they ARE affected, and it is impossible for them to have two copies.
where various individuals all have identical genotypes and yet some get the disease phenotype and others do not
Limited Expressivity is the case in which various individuals all have the same genotype AND all of them have the disease phenotype (i.e., 100% penetrance), but individuals are impacted in varying degrees.
Polygenic is a case where many genes contribute toward one phenotypic trait
Pleiotropy is the case where one single gene contributes to multiple phenotypic traits
Mosaicism is the case in which different cells within the same individual contain non-identical genotypes (NOT different alleles for the same gene, but different genotypes. Normally, all cells have the same genotype: Tt, Rr, etc. In this case one cell line may be TT and the other Tt).
Genetic Imprinting (a.k.a. Genomic Imprinting) is a case in which one specific gene is expressed differently depending on which parent it originated from
Epigenetic refers to any heritable phenotype resulting from any process other than a change in the DNA sequence itself. You could think of this as any genetic influence that is “outside” of the DNA sequence itself just as Epi-dermis is on the “outside” of the body (The prefix epi- translates in Greek to mean above, beyond, outside, on, at or near
when there is variance from expected ratios or random assortment it suggests:
what is linkage and how does distance between genes on chromosomes play a role?
When we say that two genes are linked we mean that they are not assorted independently. In other words, inheriting one gene changes the probability of inheriting the other. When you look at chromosomes and consider that they contain many, many genes, and yet are inherited as a single, whole chromosome, we would expect that all of the genes on a chromosome would be linked. This is not the case due to crossing over. Crossing over between chromosomes during Prophase I of Meiosis happens to such a large extent that it is as if all of the genes were not riding together on chromosomes, but were individual little segments assorted independently and each having an equal and independent probability of landing in one cell or the other. Linkage does occur, however, when two genes are very, very close to each other on the same chromosome because at certain proximity it become unlikely that a crossing over event will occur exactly between them.
The gene pool is the complete set of genes and/or alleles in a population.
Evolution is defined as any change in the gene pool across generations.
Polymorphisms are random variations in genetic sequence among individuals that create variable forms. Polymorphisms are random,
usually due to mutation, and may or may not be increasingly represented in future generations depending on whether or not that particular variation in form provides an evolutionary fitness advantage
A niche is the very specific status or role an organism plays in its ecosystem. It can also refer to a specific habitat occupied by one organism with its ecological community.
survival of the fittest
Survival of the fittest is a term meaning that the individual best suited to its environment will be most likely to survive and pass on its genetic information to future generations.
Natural selection is the more precise term for the concept described by “Survival of the fittest.” For the MCAT you could consider them to be synonyms. A careful definition of natural selection would be something like: the process by which individuals with genetic traits that provide them with an advantage in terms of interacting with their environment differentially produce more offspring and therefore those traits become more prevalent in subsequent generations.
Speciation simply means the formation of new species from existing ones.
Adaptive radiation is the rapid formation of a variety of species from one ancestral species—usually characterized by a strong environment-species connection. In other words, if one species of turtle immigrated to five different environments and rapidly formed five different species based on natural selection driven by the unique characteristics of each environment.
An evolutionary bottleneck is a sudden decrease in the number of individuals in a population
Genetic drift is a change in the allele frequency within a population due to random, non-genetic, non-selective factors. A bottleneck would be an example of genetic drift because there is no “fitness advantage” or other factor responsible for the change in allele frequency. For example, if a meteorite struck the earth the question of who survived and who did not would not be a question of fitness, it would be a random result of who happened to be in the meteors path
Carrying capacity is the maximum number of individuals an ecosystem or environment can sustain.
in order for natural selection to occur:
1) one individual must have a polymorphism that provides an evolutionary fitness advantage
2) that advantage must result in the individual differentially producing more offspring
What are the H-W assumptions?
1) large population
2) no mutation
3) no immigration or emigration
4) random mating
5) no natural selection
What are the H-W equations?
p^2 + 2pq + q^2 = 1
what is the order of classification largest o smallest
what is the species distinction?
organisms classified as different species should not be able to mate with one another and produce viable, fertile offspring
what are different tools for scientists to determine taxanomical classifications?
embryology, phylogeny, anatomy, DNA sequencing, fossil records
distinct features of animals
multicellular, motile, heteretrophic eukaryotes, don't have cell walls
distinct features of chordates
have notochord, dorsal hollow nerve cord, pharyngeal gills and post-anal tail at some point during development
distinct features of mammals
distinct features of primates
opposable thumbs, fingernails, enlarged cerebral cortex
oxidize organic or inorganic compounds to harvest energy
capture their own energy directly from the sun via photosynthesis
capable of fixing CO2 and can use CO2 as carbon source for synthesizing organic molecules
must ingest organic molecules such as carbohydrates as their carbon source
both participants benefit equally
one participant benefits at the expense of the other
one participant benefits and the other participant's experience is neutral
distinct characteristics of a virus
viruses are acellular and cannot survive, grow or reproduce on their own. They require a host to accomplish most if not all of the functions we normally associate with “living things.”
what are the components of all viruses?
Viruses always contain some form of nucleic acid (DNA or RNA, but never both) plus proteins. Bacteriophages (viruses that infect bacteria) have a more specific structure, with a capsid head, a tail, tail fibers, etc. (see below). Enveloped viruses such as the cold virus, HIV, etc. are small circular membranes surrounding a protein capsid and the nucleic acid (see below). If the virus is known to be a retrovirus then we know that it must contain a specific enzyme called reverse transcriptase that can translate its RNA nucleotide sequence into DNA (because RNA could not be incorporated into the host’s genome).
funghi have ___ made of ___
fungi spend majority of life as ____
fungi reproduce sexually when____ and asexually when___
life is hard (stress, little food, -->goal to have offspring better adapted)
life is good (no need for adaptation)
What is lichen
symbiosis between fungi and algae
what is mycorrhizae
symbiosis between fungi and plant roots
how do bacteria increase genetic variability?
conjugation-F+ plasmid forms pilus with F- plasmid bacteria and transfers gene into bacteria
transformation-bacteria pick up DNA from the environment via surface proteins
transduction-viruses accidentally incorporate host genetic material into their nucleic acids and inject into other cells
how do bacteria reproduce?
via binary fission. extrachromosomal DNA ie plasmid distribution is random.
what are the major differences between mitosis and binary fission?
Mitosis is a complex process coordinated and heavily regulated by a large number of genes and involving intricate interactions between centrioles, spindle fibers (microtubules), centromeres, chromosomes, etc. Absent any errors, mitosis delivers an exact and equal amount of DNA to each new daughter cell. Binary fission is the method employed by prokaryotes and involves none of the items listed above, except for DNA. In binary fission the circular DNA is copied and attached to the membrane. The cell splits, pulling the two copies apart and each daughter cell gets one copy of the chromosome. An important caveat, however, is that prokaryotes contain
extrachromosomal DNA (usually circular plasmids). There is no system for segregating this DNA, so each daughter cell may or may not get certain plasmids based solely on random chance
primary differences between prokaryotes and eukaryotes?
Prokaryotes have no nucleus, no complex, membrane-bound organelles, circular DNA, no histones or chromosome structure, and 70S (50S & 30S) ribosomes. Eukaryotes have a true nucleus, complex, membrane-bound organelles, linear DNA with histones and chromosome structure, and 80S (60S & 40S) ribosomes. Explain to students that the ribosome measures do not add up (i.e., 50S + 30S ≠ 70S) because they are not directly related to mass or volume, but are sedimentation coefficients derived from the result of centrifuging the ribosomes
gram positive bacteria:
very thick cell wall
single cell membrane
gram negative bacteria:
relatively thin cell wall
do not form endospores
contain 2 cell membranes sandwiching wall
The lytic cycle of a virus is the period during which viral genes are actively being transcribed and new viruses are being assembled. During this phase infected cells eventually burst to release large numbers of new viruses. Examples would be an active cold sore (herpes virus) or AIDS
The lysogenic cycle is the dormant cycle of the virus during which time viral DNA is incorporated into the host’s genome but new viruses are not being assembled. This would be equivalent to HIV infection without AIDS symptoms, or to the presence of the herpes virus in the DNA of the host without any present cold sores or other symptoms.
what is a vaccine and how does it work?
A vaccine is an inactivate virus or portion of a virus delivered to a person so that their immune system can develop antibodies against the virus without actually being infected. Upon exposure to the viral proteins, the immune system will create memory B-cells with antibodies that match the viral proteins. If this host is later infected with that virus these B-cells will differentiate into plasma cells that rapidly produce and release antibodies for the virus. Vaccines tend to lose effectiveness over time because viruses mutate at a rate that is faster than any known living thing
disulfide bonds are found where?
viruses contain organelles (true/false?)
viruses are faster at evolving than bacteria (true/false)?
true. due to lack of proof-reading mechanism during replication. viruses have highest baseline mutation rate of any known system, leading to rapid evolution
do prokaryotes have organelles?
they do not have complex organelles, but they DO have simple organelles such as ribosomes
3 phenotypes of an increasing/decreasing degree indicates__
generally indicates example of incomplete dominance
what base pairs would you expect to find at origins of replication and why?
AT pairs (require only 2H bonds) so it is easier (less energy) to open these sites