Genes Flashcards

Question

tRNA

Answer 1

Transfer RNA. Collect amino acids in the cytosol, and transfers them to the ribosomes for incorporation into a protein.

Answer 2

All RNA is manufactured from a DNA template in a process called transcription. Eukaryotic transcription takes place in the nucleus and mitochondrial matrix, since DNA cannot leave those two spots. Transcription starts with initiation. Only the template strand of the DNA double helix is transcribed. The sequence of the coding strand resembles the sequence of the newly synthesized mRNA.

Answer 3

The beginning of transcription is called initiation. A group of proteins find a promoter on the DNA strand and assemble a transcription initiation complex, which includes RNA polymerase. Prokaryotes have one type of RNA polymerase. Eukaryotes, except plants, have three: one each for mRNA and snRNA, tRNA, and rRNA.

Answer 4

A promoter is a sequence of DNA nucleotides that designates a beginning point for transcription. The promoter and prokaryotes is located at the beginning of the gene, "upstream". The transcription start point is part of the promoter. The first base pair at the transcription start point is designated +1, base pairs located before the +1 transcription site are designated by negative numbers.

Answer 5

After binding to the promoter, RNA polymerase unzips the DNA double helix creating a transcription bubble. Next the complex switches to to elongation mode. In elongation, RNA polymerase transcribes only one strand of DNA nucleotide sequence into a complementary RNA nucleotide sequence. Only one strand in a molecule of double-stranded DNA is transcribed, the template strand. The other strand, coding strand, protects its partner against degradation.

Answer 6

RNA polymerase is included in the transcription initiation complex. After binding to the promoter, it unzips the DNA double helix, creating a transcription bubble. Like DNA polymerase, RNA polymerase moves along the DNA strand in the 3' to 5' direction, building the new RNA strand in the 5' to 3' direction. Note that RNA polymerase does not have a proofreading mechanism, so the rate of errors for transcription is higher than for replication.

Answer 7

The end of transcription is called termination. This requires a special termination sequence and special proteins to dissociate RNA polymerase from DNA.

Answer 8

Replication makes no distinction between genes. Instead, genes are activated or deactivated at the level of transcription. Most regulation occurs via proteins called activators and repressors. These bind to DNA close to the promoter, and activate or repress the activity of RNA polymerase. They are allosterically regulated by small molecules like cAMP. The amount of a given type of protein within a cell is likely to be related to how much of it's mRNA is transcribed.

Answer 9

An operon is a sequence of bacterial DNA containing an operator, a promoter, and related genes. The genes of an operon are transcribed on one mRNA. Genes outside the operon may code for activators and repressors. The lac operon codes for enzymes that allow E. coli to import and metabolize lactose when glucose is not present in sufficient quantities. Low glucose levels lead to high cAMP levels. cAMP binds to and activates CAP. Activated CAP to a CAP site, activating the promoter, allowing the formation of an initiation complex and the subsequent transcription and translation of three proteins. The operator, located adjacent and downstream of the promoter, provides a binding site for a repressor protein. The repressor protein is inactivated by the presence of lactose in the cell. It will bind to the operator unless lactose binds to the repressor protein. The binding of the lac repressor to the operator in the absence of lactose prevents the transcription of the lac genes. Lactose can induce the transcription of the operon only when glucose is not present.

Answer 10

The addition of the 5' cap to eukaryotic mRNA, which serves as an attachment site in protein synthesis and as a protection against degradation by exonucleases. The polyadenylation of the 3' end of mRNA with a poly-A tail, also protecting it from exonucleases. The splicing of introns from the primary transcript.

Answer 11

The initial mRNA nucleotide sequence arrived at through transcription is called the primary transcript. The primary transcript is processed in three ways: by the addition of nucleotides, deletion of nucleotides, and modification of nitrogenous bases.

Answer 12

The primary transcript is much longer than the mRNA that will be translated into a protein. Before leaving the nucleus, the primary transcript is cleaved into introns and exons. Enzyme-RNA complexes called small nuclear ribonucleoproteins (snRNPs) recognize nucleotide sequences at the end of the introns. Several snRNPs associate with proteins to form the spliceosome. Inside the spliceosome, the introns are looped bringing the exons together. The introns are then excised by the splicesome and the exons are spliced together to form the single mRNA strand that ultimately codes for a polypeptide. Intron's do not code for protein and integrated within the nucleus. Although there are only an estimated 20 to 25,000 protein coding genes in the human genome, there are about 120,000 proteins made possible by differential splicing of exons. Introns represent about 24% of the genome. Exons represent about 1.1%.

Answer 13

When heated or immersed in high concentrations salt solution or high pH solution, the hydrogen bonds connecting the two strands in a double-stranded DNA molecule are disrupted and the strands separate. The temperature needed to separate the DNA strands is called the melting temperature. DNA with more GC base pairs has a greater melting temperature, since guanine and cytosine make three hydrogen bonds. Heating two 95°C is generally sufficient to denature any DNA sequence. Denatured DNA is less viscous, denser, and more able to absorb UV light. Separated strands will spontaneously associate with their original partner or any other complementary nucleotide sequence.

Answer 14

Separated strands will spontaneously associate with their original partner or any other complementary nucleotide sequence. Thus different double-stranded combinations can be formed through hybridization- DNA and DNA, DNA and RNA, and RNA and RNA. Hybridization techniques allows scientists to identify nucleotide sequences by binding unknown sequence with an unknown sequence.

Answer 15

One method bacteria use to defend themselves from viruses is to cut the viral DNA into fragments with restriction enzymes. These bacteria protect their own DNA from enzymes by methylation. Methylation is usually associated with inactivated genes. Also called restriction endonucleases, these digest, or cut, nucleic acids only at certain nucleotide sequences along the chain called restriction sites. Most restriction enzymes cleave the DNA strand unevenly, leaving complementary single-stranded ends which can reconnect through hybridization called sticky ends. Once paired, the phosphodiester bonds of the fragments can be joined by DNA ligase. There are hundreds of restriction endonucleases known, each attacking a different restriction site. Two DNA fragments cleaved by the same endonuclease can be joined together regardless of the origin of the DNA.

Answer 16

To DNA fragments cleaved by the same endonuclease can be joined regardless of the origin of the DNA. When DNA is artificially recombined like this, it is called recombinant DNA.

Answer 17

Recombinant DNA can be made long enough for bacteria to replicate and then placed within the bacteria using a vector, typically a plasmid or a virus. The bacteria can then be grown in large quantity.

Answer 18

When recombinant DNA is placed within bacteria, and then grown in large quantity, it forms a clone of cells containing the factor with the recombinant DNA fragment. These clones can be saved separately producing a clone library.

Answer 19

To make a DNA library, take a DNA fragment, use a vector to insert it into a bacterium, and reproduce that bacterium like crazy. Now you have clones of bacteria with your DNA fragment. Because the cloning process isn't perfect, some bacteria in a library don't have the vector and some vectors don't have the DNA fragment. To screen out these undesirable elements, include the gene of interest and an antibiotic resistant gene when you prepare your clone. Also when preparing your clone, use an endonuclease that will insert your DNA fragment into the middle of the gene of interest and inactivate it.

Answer 20

The radioactively labeled complementary sequence of the desired DNA fragment, which is used to search the library.

Answer 21

cDNA. This is DNA reverse transcribed from mRNA. It lacks the introns that would normally be found in eukaryotic DNA. This is used because bacteria have no mechanism for removing introns, so it is useful to clone DNA with no introns.

Answer 22

Polymerase chain reaction is a much faster method of cloning, which uses a specialized polymerase enzyme found in a series of bacterium adapted to life in nearly boiling waters. In PCR, the double-stranded DNA to be cloned (amplified) is placed in a mixture with many copies of two DNA primers, one for each strand. The mixture is heated to 95°C to denature the DNA. The mixture is then cool to 60°C, where the primers hybridize, or ANNEAL, to their complementary ends of the DNA strands. Next, the heat resistant polymerase is added with a supply of nucleotides, and the mixture is heated to 72°C to activate the polymerase. The polymerase amplifies the complementary strands, doubling the amount of DNA. This procedure can be repeated many times without adding more polymerase because it is heat resistance. The result is an exponential increase in the amount of DNA. Starting with the single fragment, 20 cycles produces over 1 million copies.

Answer 23

Southern blotting is used to identify target fragments of known DNA sequence in a large population of DNA. It can be used to map the structure of particular genes. Chop up DNA, use electrophoresis to spread out pieces according to size. Blot it onto a membrane. Add a radioactive probe made from DNA or RNA. Visualize with radiographic film. A northern blot uses the same techniques to identify specific sequences of RNA.

Answer 24

A Western blot can detect a particular protein in a mixture of proteins. It detects a protein using anti-bodies. The reaction catalyzed by the enzyme attached to the anti-body produces a reaction product which can be visualized with x-ray film.

Answer 25

Identifies individuals, as opposed to identifying specific genes. The DNA of different individuals possesses different restriction sites and varying distances between restriction sites. The population of humans is polymorphic for restriction sites. RFLP's are the DNA fingerprints used to identify criminals in court cases. They fragment the DNA sample with endonucleases, and reveal a band pattern unique to an individual on radiographic film, via southern blotting techniques.

Answer 26

mRNA nucleotides are strung together to form a genetic code which translates the DNA nucleotide sequence into an amino acid sequence and ultimately into a protein. There are four different nucleotides in RNA that together must form an unambiguous code for the 20 common amino acids. The code is a combination of three nucleotides. Because more than one series of three nucleotides may code for any amino acid, the code is degenerative. But any single series of three nucleotides will code for one and only one amino acid, thus, the code is unambiguous. In addition, the code is almost universal, nearly every living organism uses the same code. The start codon is AUG (codes for methionine). The stop codons are UAA, caps UAG, and UGA. To figure out how many possible codons exist, take the number of possible nucleotides and raise it to the number of positions.

Answer 27

Three consecutive nucleotides on the strand of mRNA represent a codon. All but three possible codons code for amino acids. The remaining codons are stop codons.

Answer 28

Stop codons are also called termination codons. Stop codons signal an end to protein synthesis. The stop codons are UAA, UGA, and UAG.

Answer 29

Translation is the process of protein synthesis directed by mRNA. Each of the three major types of RNA plays a unique role in translation. mRNA carries the genetic code from the nucleus to the cytosol in the form of codons. tRNA contains a set of nucleotides that is complementary to the codon, called the anti-codon. tRNA sequesters the amino acid that corresponds to its anticodon. rRNA with protein makes up the ribosome, which provides the site for translation to take place. Translation may take place on a free-floating ribosomes in the cytosol, producing proteins that function in the cytosol. Otherwise, a ribosome may attach itself to the rough ER during translation and inject proteins into the ER lumen. Proteins injected into the ER lumen are destined to become membrane bound to proteins of the nuclear envelope, ER, Golgi, lysosomes, plasma membrane, or bound for secretion.

Answer 30

The ribosome is composed of a small subunit and a large subunit made from rRNA and many separate proteins. The ribosome and its subunits are measured in sedimentation coefficients given in Svedberg units. The sedimentation coefficient gives the speed of a particle in a centrifuge, and is proportional to mass and related to shape and density. Prokaryotic ribosomes are smaller than eukaryotic ribosomes. The ribosome is assembled in the nucleolus, and the small and large subunits are exported separately to the cytoplasm.

Answer 31

The complex structure of ribosomes requires a special organelle called the nucleolus in which to manufacture them. Prokaryotes do not possess a nucleosis, but synthesis of prokaryotic ribosomes is similar to eukaryotic ribosomes. Although the ribosome is assembled in the nucleosis, the small and large subunits are exported separately to the cytoplasm.

Answer 32

After post transcriptional processing in a eukaryote, mRNA leaves the nucleus through the nuclear pores and enters the cytosol. With the help of protein initiation factors, the 5' end and attaches to the small subunit of a ribosome. A tRNA possessing the 5'-CAU-3' anticodon sequesters the amino acid methionine and settles in at the P site, peptidyl site. This is the signal for the large subunit to join and form the initiation complex. This process is termed initiation.

Answer 33

After initiation, elongation of the polypeptide begins. A tRNA with its corresponding amino acid attaches to the A site (aminoacyl site) at the expense of two GTP's. The C terminus of the methionine attaches to the N terminus of the amino acid at the A site in a dehydration reaction. In an elongation step called translocation, the ribosome shifts three nucleotides along the mRNA toward the 3' end. The tRNA that carried methionine moves to the E site where it can set the ribosome. The tRNA carrying the nascent dipeptide moves to the P site, clearing the a site for the next tRNA. Translocation requires the expenditure of another GTP. The location process continues and repeats until a stop codon reaches the P site.

Answer 34

Translocation is the shifting of the ribosome three nucleotides along the mRNA toward the 3' end. It requires the expenditure of a molecule of GTP.

Answer 35

Translation ends when a stop codon is reached in a step called termination. When a stop or nonsense codon reaches the A site, proteins known as release factors bind to the A site allowing a water molecule to end the polypeptide chain. The polypeptide is freed from the tRNA and ribosome, and the ribosome breaks up into its subunits to be used again for another round of protein synthesis later.

Answer 36

Even as the polypeptide is being translated, it begins folding. The amino acid sequence determines the folding confirmation and the folding process is assisted by proteins called chaperones. Post translational modifications include the addition of sugars, lipids, or phosphate groups two amino acids. The polypeptide may be cleaved in one or more places. Separate polypeptides may join to form the quaternary structure of a protein.

Answer 37

Translation begins on a free-floating ribosome. A signal peptide at the beginning of the translated polypeptide may direct the ribosome to attach to the ER, in which case the polypeptide is injected into the ER lumen. Polypeptides injected into the lumen maybe secreted from the cell via the Golgi or may remain partially attached to the membrane. The signal peptide is recognized by protein-RNA signal recognition particle that carries the entire ribosome complex to receptor protein on the ER.

Answer 38

Any alteration in the genome that is not genetic recombination is called a mutation. Mutations may occur at the chromosome level or on the nucleotide level. In multicellular organisms, a mutation and a somatic cell is called a somatic mutation. A somatic mutation of a single cell may have very little effect on an organism with millions of cells. A mutation in a germ cell, from which all other cells arise, can be very serious for the offspring. Only about one of every million gametes will carry mutation for a given gene. Mutations can be spontaneous or induced. Induced mutations are due to physical or chemical agents called mutagens. Mutagens that cause cancer are called carcinogens.

Answer 39

A gene mutation is the alteration in the sequence of DNA nucleotides in a single gene.

Answer 40

A chromosomal mutation occurs when the structure of a chromosome is changed.

Answer 41

Mutagens are the physical or chemical agents which cause induced mutations. They increase the frequency of mutation above the frequency of spontaneous mutations.

Answer 42

If the mutation changes a single base pair of nucleotides in a double strand of DNA, that mutation is called a point mutation.

Answer 43

A type of point mutation in which one base pair is replaced by another. When one purine is exchanged for the other (A for G), or one pyrimidine is exchanged for the other (C for T), it is called the transition mutation. Changing a purine for a pyrimidine is called a transversion mutation.

Answer 44

A base pair mutation that occurs in the amino acid coding sequence of the gene. May or may not alter the amino acid sequence of the protein. The alteration of a single amino acid may or may not have serious effects on the function of the protein. If there is no change in protein function, the mutation is called a neutral mutation. If the amino acid is not changed, it is called the silent mutation. Even a silent mutation may be significant because it may change the rate of transcription.

Answer 45

And insertion or deletion of a base pair may result in a frameshift mutation. This results when the deletions or insertions occur in multiples other than three. Frameshift mutations often result in a completely nonfunctional protein, whereas non-frameshift mutations may still result in a partially or even completely active protein. If a base pair substitution or insertion or deletion mutation creates a stop codon, a nonsense mutation results. Nonsense mutations are usually very serious because they prevent the translation of a functional protein.

Answer 46

Structural changes may occur to a chromosome in the form of deletions, duplications, translocations, and inversions. Chromosomal deletions occur when a portion of the chromosome breaks off, or is lost during homologous recombination and/or crossing over. Duplications occur when a DNA fragment breaks free of one chromosome and incorporates into a homologous chromosome. Deletion or duplication can occur with entire chromosomes, aneuploidy, or even entire sets of chromosomes, polyploidy.

Answer 47

When a segment of DNA from one chromosome is exchanged for a segment of DNA on another chromosome, the resulting mutation is called a reciprocal translocation. In inversion, the orientation of the section of DNA is reversed on chromosome. Translocation and inversion can be caused by transposition. Trends position takes place in both prokaryotic and eukaryotic cells. The DNA segments called transposable elements or transposons can excise themselves from a chromosome and reinsert themselves at another location. when moving, the transposon may excise itself from the chromosome and move, copy itself and move, or copy itself and stay, moving the copy. Transfer position as one mechanism by which a somatic cell of a multicellular organism can alter its genetic makeup without meiosis.

Answer 48

A mutation can be forward or backward. The mutation in the forward direction changes the organism even more from its original state. The mutation in the backward direction reverts the organism back to its original state, called the wild type.

Answer 49

Certain genes that simulate normal growth in humans are called proto-oncogenes. Proto-oncogenes can be converted to oncogenes, genes that cause cancer, by mutations such as UV radiation, chemicals, or random mutations. Mutations that cause cancer called carcinogens.

Answer 50

Since the nucleus is much smaller than the 5 feet of unwrapped DNA it contains, the sections of DNA that are not in use are wrapped tightly around globular proteins called histones. Eight histones wrapped in DNA form y a nucleosome. Nucleosomes wrap into coils called solenoids, which wrap into supercoils. The entire DNA/protein is called chromatin. Chromatin is one third DNA, two thirds protein, and a small amount of RNA. Chromatin received its name because it absorbs basic dyes due to the large basic amino acid content and histones. The basicity of histones gives them a net positive charge at the normal pH of the cell. Chromatin condensed in the manner above is called heterochromatin. Some chromatin is permanently coiled. When transcribed, chromatin must be uncoiled. Chromatin that can be uncoiled then transcribed is called euchromatin. Euchromatin is only coiled during nuclear division.

Answer 51

Inside the nucleus of the human somatic cell, there are 46 double-stranded DNA molecules. The chromatin associated with each one of these molecules is called the chromosome. Each chromosome contains hundreds or thousands of genes. In human cells, each chromosome possesses a partner that codes for the same traits as itself. Two such chromosomes are called homologues. Humans possess 23 homologous pairs of chromosomes. Although the traits of the same, the actual genes might be different. Different forms of the same gene are called alleles. Any cell containing Homologous pairs is said to be diploid. Any cell that does not contain homologs is said to be haploid.

Answer 52

G1, S, and G2 collectively are called interphase

Answer 53

In G1, the cell has just split, and begins to grow in size producing new organelles and proteins. Regions of heterochromatin have been on wound and decondensed into euchromatin. RNA synthesis and protein synthesis are very active. The cell must reach a certain size, and synthesize sufficient protein in order to continue to the next stage. So growth is assessed at the G1 checkpoint near the end of G1. If conditions are favorable for division the cell enters S-phase, otherwise the cell enters G0 phase. The main factor in triggering the beginning of S is cell size based on the ratio of cytoplasm to DNA. G1 is normally the longest stage.

Answer 54

A non-growing state distinct from interface. Allows for the differences in length of the cell cycle. In humans, enterocytes of the intestine divide more than twice per day, while liver cells spend a great deal of time and G0 dividing less than once per year. Mature neutrons and muscle cells remain in G0 permanently.

Answer 55

The cell prepares to divide. Cellular organelles continue to duplicate. RNA and protein are actively synthesized. G2 occupies about 10 to 20% of the cell lifecycle. Need the end is the G2 checkpoint. This checks for mitosis promoting factor, when MPF is high enough, mitosis is triggered.

Answer 56

The cell devotes most of its energy to replicating DNA. Organelles and proteins are produced more slowly. Each chromosome is exactly duplicated, but the cell is still considered to have the same number of chromosomes, only now each chromosome is made of two identical sister chromatids. This is a convention.

Answer 57

Nuclear division without the genetic change. Four stages: prophase, metaphase, anaphase, telophase PMAT). Mitosis results in genetically identical daughter cells.

Answer 58

Characterized by the condensation of chromatin into chromosomes. Centrioles located in the centrosomes move to opposite ends of the cell. First the nucleolus and then the nucleus disappear. The spindle apparatus begins to form consisting of aster, (microtubules radiating from the centrioles), kinetochore microtubules growing from the centromeres, and spindle microtubules connecting the two centrioles.

Answer 59

A group of proteins located toward the center of the chromosome, part of the spindle apparatus.

Answer 60

Connect the two centrioles in prophase

Answer 61

A structure of protein and DNA located at the centromere of the joined chromatids of each chromosome

Answer 62

Chromosomes align along the equator of the cell

Answer 63

Begins when sister chromatids split at their attaching centromeres, and move to an opposite ends of the cell. The split is termed disjunction. Cytokinesis, the actual separation of the cellular cytoplasm due to construction of microfilaments about the center of the cell, make amends to the end of this phase.

Answer 64

The nuclear membrane reforms, followed by the reformation of the nucleolus. Chromosomes deco dense and become difficult to see under the light microscope. cytokinesis continues.

Answer 65

A double nuclear division which produces four haploid gametes, also called germ cells. In humans, only the spermatogonium and the oogonium undergo meiosis. All other cells are somatic cells and undergo mitosis only. Meiosis is like mitosis except that in meiosis, there are two rounds, the daughter cells are haploid, and genetic recombination occurs. Recognize that, under the light microscope, metaphase in mitosis would appear like metaphase II in meiosis and not like metaphase I. Meiosis I is reduction division. Meiosis II creates four haploid gametes, each with 23 chromosomes.

Answer 66

After replication occurs NES phase of interphase, the cell is called the primary spermatocyte or primary oocyte. In the human female, replication takes place before birth, and the lifecycle of all germ cells are rested at the primary oocyte stage until puberty. Just before ovulation, a primary oocyte undergoes the first meiotic division to become a secondary oocyte. The secondary to say is released upon ovulation, and the penetration of the secondary oocyte by the sperm stimulates anaphase II the second meiotic division in the oocyte.

Answer 67

Homologous chromosomes line up alongside each other, matching up genes exactly. At this time, they may exchange sequences of DNA nucleotides in a process called crossing over. Genetic recombination in eukaryotes occurs during crossing over. Since each duplicated chromosome in prophase I appears as an x, the side-by-side homologs exhibit a total of four chromatids, and are called tetrads. If crossing over does occur, the two chromosomes are zipped along each other where nucleotides are exchanged. This forms a complex which, under the light microscope, appears as a single point where the two chromosomes are attached, creating an x shape called a chiasma. Genes located close together on a chromosome are more likely to cross over together, and are said to be linked.

Answer 68

The homologues remain attached, and move to the metaphase plate. Rather than single chromosomes aligned along the plate as in mitosis, tetrads align in meiosis.

Answer 69

A nuclear membrane may or may not form. Cytokinesis may or may not occur. In humans both of these events occur. The new cells are haploid with 23 replicated chromosomes, and are called secondary spermatocytes or secondary oocytes. In the case of the female, one of the oocytes, called the first polar body, is much smaller and degenerates. This occurs in order to conserve cytoplasm, which is contributed only by the ovum. The first polar body may or may not go through meiosis II, producing two polar bodies.

Answer 70

The final products are haploid gametes each with 23 chromosomes. In the case of the spermatocyte, four sperm cells are formed. In the case of the oocyte, a single ovum is formed. In the female, telophase II produces one gamete and a second polar body.

Answer 71

If during anaphase I or II the centromere of any chromosome does not split. In the case of primary nondisjunction, one of the cells will have to extra chromatids, a complete extra chromosome. The other will be missing a chromosome. The extra chromosome will typically lined up along the metaphase plate and behave normally in meiosis II. Nondisjunction in anaphase II will result in one cell having one extra chromatid and one cell lacking one chromatid. Nondisjunction can also occur in mitosis, but the ramifications are less severe since the genetic information in the new cells is not passed on to every cell in the body. Destruction of chromosome 21 causes Down's syndrome. An abnormal gamete with two chromosome 21s may combine with a normal gamete, and the resulting zygote will have three copies of chromosome 21. This is sometimes referred to as trisomy 21.