Biochem Exam 2 - Quan Flashcards

Question

What is lethal allele?

Answer 1

expression or lack of expression of certain genes can affect the survival of an organism. (ex: agouti and yellow mice, pure yellow genotype will kill the mouse).

Answer 2

the gene that determines a specific character is location on a sex chromosome. Not going to distribute evenly in both sexes since one is XX and one is XY.

Answer 3

during meiosis a limited number of crossover events occur randomly between homologous chromosomes, the closer the two loci reside on the axis of the chromosomes the less likely it is that any crossover event will occur between them. The further the genetic distance the HIGHER the chance of crossing over.

Answer 4

a genetic disorder is the proportion of individuals with the at-risk genotype who actually express the trait, complete penetrance means the trait is expressed in 100% of persons with that genotype (ex: Huntington's disease)

Answer 5

enzymes that cut the DNA sequence in specific locations.

Answer 6

can allow joining of different DNA, blunt ends cut. The end of a DNA fragment resulting from the breaking of DNA molecule in which there are no unpaired bases, so both strands are of the same length.

Answer 7

jagged ends left after restriction enzymes cut them. Has has protruding single-stranded strands with unpaired nucleotides called overhangs, each overhang can anneal with another complementary one to form base pairs.

Answer 8

labels the 5 prime end with phosphate. useful for visualizing DNA

Answer 9

uses labeled complementary DNA or RNA probe to localize a specific DNA or RNA sequence in a portion of.a tissue and also locates specific genes on the chromosomes.

Answer 10

A circular double stranded plasmid DNA (cloning vector) undergoes cleavage with a restriction nuclease, addition of the DNA fragment to be cloned which undergoes covalent linkage by DNA ligase resulting in recombinant DNA.

Answer 11

a virus that can live in bacteria

Answer 12

an enzyme that can catalyze the joining of two large molecules by forming a new chemical bond, usually with accompanying hydrolysis.

Answer 13

Is is collection of the total genomic DNA from a single organism. It is a human double stranded DNA and to do this the DNA is cleaved with restriction nuclease, now has millions of genomic DNA fragments, those DNA fragments are inserted into plasmids, and now you have recombinant DNA molecules.

Answer 14

cDNA refers to complementary DNA. It is known to be synthesized from mRNA (messenger RNA - a large family of RNA molecules that deliver genetic information to ribosome from DNA to make the amino acid sequence for protein synthesis during translation). cDNA is made in a run that is catalyzed by the reverse transcriptase and DNA polymerase enzymes. cDNA is used to clone eukaryotic genes in prokaryotes. Scientists use it when they want to express a protein in a cell that doesn't normally express that protein.

Answer 15

1) lyse (disintegration) cells and purify mRNA 2) hybridize (crossbreed or mix) with poly T primer ( a single sequenced primer used for priming reaction catalyzed by reverse transcriptase). 3) make DNA copy with reverse transcriptase 4) degrade RNA with RNase 5) synthesize a complementary DNA strand using DNA polymerase (makes DNA from nucleotides) 6) RNA fragments act as a primer 7) double stranded cDNA copy of original mRNA

Answer 16

Genomic DNA has introns (introns are non-coding regions or "junk" DNA because they give you no information about protein coding so during RNA splicing, introns are removed and exons are joined together to form a contiguous coding sequence) whereas the mRNA that made the cDNA didn't have any (probably because the introns were spliced before cDNA was made).

Answer 17

It's a method used to determine the exact DNA sequence to which a particular DNA-binding protein binds.

Answer 18

1) region of DNA protected by DNA binding protein 2) random cleavage by nuclease or chemical followed by removal of the protein and separation of the DNA strands. 3) family of single-stranded DNA molecules labeled at the 5' end 4) separation by gel electrophoresis 5) foot print is where no cleavage is observed.

Answer 19

it is an in vitro method used to make specific and intentional changes to the DNA sequence of a gene or any gene products. It's a great way to create a specific mutation/introduce a mutation into the DNA sequence to see what happens.

Answer 20

1) plasmid cloning vector and inserted gene 2) strand separation 3) synthetic oligonucleotide primer containing desired mutated sequence 4) strand completion by DNA polymerase and DNA ligase 5) introduction into cells followed by replication and segregation into daughter cells.

Answer 21

Gene targeting is a genetic technique that uses homologous recombination to change an endogenous gene (gene that originated from within an organism, tissue, or cell). The method can be used to delete a gene, remove exons, add a gene, and introduce point mutations. Gene targeting can be permanent or conditional (it can be controlled).

Answer 22

1) embryonic stem cells growing in tissue culture 2) introduce a DNA fragment containing altered gene into many cells 3) let each cell grow to form a colony 4) test for rare colony in which the DNA fragments has replaced one copy of the normal gene. 5) inject ES cells into early embryo

Answer 23

Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA (especially mRNA) by the enzyme RNA polymerase.

Answer 24

Initiation (start): RNA polymerase binds to DNA at a specific sequence of nucleotides called the promoter. The promoter contains an initiation site where transcription of the gene begins. RNA polymerase than unwinds DNA at the beginning of the gene.

Answer 25

Elongation (make): Only one of the DNA strands acts as a template for the RNA synthesis. RNA polymerase can only add nucleotids to the 3' end of the strand so like DNA, RNA must be synthesized in the 5' to 3' direction. Free ribonucleotides triphosphates from the cytoplasm are paired up with their commplementary base on the exposed DNA template. RNA polymerase joins the ribonucleoside triphosphates to form an mRNA strand. As RNA polymerase advances, the process continues. The DNA that has been transcribed, re-winds to form a double helix.

Answer 26

Elongation (stop): RNA polymerase continues to elongate until it reaches the terminator, a specific sequence of nucleotides that signals the end of transcription. Transcription stops and mRNA polymerase and the new mRNA transcript are released from DNA. The DNA double helix reforms. The termination sequence usually consists of a series of adjancent adenines preceded by a nucleotide palindrome. This gives an RNA molecule that assumes a stem-and loop configuration. This configuration stops RNA polymerase from transcribing any further.

Answer 27

A DNA sequence that determines the site of transcription initiation for an RNA polymerase: it is noncoding, asymmetric so therefore polymerase will always bind in the proper orientation and can only synthesis 5' -> 3' direction.

Answer 28

The RNA sequence is complementary to the template strand, and identical to the coding strand. Either DNA strand may serve as the template. DNA is listed as coding strand in a genome with introns.

Answer 29

This is important for the initiation phase. Different Sigmar factors recognize and bind to different consensus promoter specific sequences near the 10 to -35 positions of the promoter. They basically direct transcription initiation in the right direction and is something that enables specific binding of RNA polymerase to gene promoters.

Answer 30

It is when different sigma factors recognize different consensus promoter sequences.

Answer 31

The stem loop formation terminates transcription. Another term is the hair-pin loop so basically the RNA polymerase just comes off of the sequence so it can't transcribe anymore.

Answer 32

is a an operon composed of genes that are transcribed as single mRNA, all 5 genes code for enzymes necessary for tryptophan synthesis. DNA has one promoter and 5 genes. RNA transcribes one RNA. The protein translates 5 proteins.

Answer 33

This occurs in eukaryotes. 1 gene controls the production of one protein and the control regions are a lot longer.

Answer 34

adjacent genes transcribed as a single mRNA.

Answer 35

They bind to DNA sequences called operators, which overlaps the promoter region. A bound repressor interferes with binding of RNA polymerase and transcription initiation.

Answer 36

a segment of DNA to which a transcription factor (activator or repressor) binds to regulate gene expression.

Answer 37

this is under both negative (repressor) and positive (by CAP protein - activates transcription of lac operon by RNA polymerase) transitional controls. * when you have + glucose and + lactose = operon is turned off because CAP is not bound to the promoter. * +glucose, -lactose = operon off b/c lac repressor is bound and CAP is not bound * - glucose, -lactose = operator off b/c lac repressor is bound * - glucose, + lactose = operon on TRY TO KNOW MORE ABOUT THIS ON YOUR OWN

Answer 38

DNA is wrapped around protein, DNA, exons, introns, regulatory sequences, junk, and proteins (histone).

Answer 39

densely packed, cluster near the nucleolus and nuclear member; transcriptionally silent - doesn't undergo transcription because it's so tightly packed.

Answer 40

loosely packed - transcriptionally active - so undergoes transcription because it's "open"

Answer 41

modifications of histone tails can tight or loosen the nucleosome.

Answer 42

this is when lysine residues in N -terminals sticking out of histones of the nucleosome are acetylated (an acetyl group is attached to the histone tails of nucleosomes). This affects gene expression because this loosens up nucleosome so the DNA in there is readily available for to be transcribed. It basically unwinds/activates the chromatin from a tight ball so it can be transcribed.

Answer 43

Methyl groups are transferred to the chromatin to actually have the DNA wound back up - so it tightens/deactivated the chromatin so the DNA inside of it won't be transcribed. Methyl groups are kind of big so think that if something big is there, then it's going to be hard for the DNA to be transcribed because the methyl group is in the way.

Answer 44

polymerase II

Answer 45

factors that bind to all genes, there are needed to bind Polymerase II to the promoter. Once the TATA-binding protein (TBP), a general transcription factor, binds to a DNA sequence called the TATA box, than a bunch of other transcription factors start attacking which initiated transcription.

Answer 46

DNA sequences outside that are in front or behind the gene, can work upstream, downstream, or in reverse orientation.

Answer 47

an enhancer is a short region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur. These proteins are usually referred to as transcription factors

Answer 48

It activates/looses chromatin - I think

Answer 49

it limits the distance that enhancers operate. There are DNA sequences that bind specialized proteins. These proteins buffer the gene from outside effects, prevent the control region from acting outside the domain, prevent the spread of heterochromatin.

Answer 50

This can be classified into numerous structural types including zinc finger proteins (Zinc finger proteins are among the most abundant proteins in eukaryotic genomes. Their functions are extraordinarily diverse and include DNA recognition, RNA packaging, transcriptional activation, regulation of apoptosis, protein folding and assembly, and lipid binding.) and leucine zipper proteins (The leucine zipper is a common three-dimensional structural motif in proteins and it has that name because leucines occur every seven amino acids in the dimerization domain. The localization of the leucines are critical for the DNA binding to the proteins.). DNA-binding proteins include transcription factors which modulate the process of transcription, various polymerases, nucleases which cleave DNA molecules, and histones which are involved in chromosome packaging and transcription in the cell nucleus.

Answer 51

1) 5-cap prevents the degradation of the sequence 2) poly A tail enzyme adds the tail, no A's in DNA they are on the RNA 3) splicing cuts out introns to give mRNA, there is a specific sequence at the end of the intron that allows the spliceosome to recognize that area to cut it.

Answer 52

cutting a single gene to two so it can code for more than one protein. Must be able to be divided by 3.

Answer 53

Poly A's are not in DNA, the multiple A's in RNa are not copied from DNA, these come and attach onto the RNA at a later time. The poly A site is a specific sequence that an enzyme can recognize and add a bunch of A's on the RNA.

Answer 54

how cells communicate with each other

Answer 55

signaling occurring inside the cell

Answer 56

1) extracellular signal binds to receptor protein 2) the receptor gives off three signaling proteins 3) each signal proteins reach their target protein by appropriate protein (metabolic enzyme, gene regulatory protein and cytoskeletal protein) - all of these will alter the metabolism, gene expression and cell shape/movement.

Answer 57

cell surface receptors (which are large hydrophilic molecules that bind to the receptor) and intracellular receptors (small hydrophobic molecules that go into the cell)

Answer 58

1) contact-dependent (when cells touch) 2) paracrine (cell sends signals to neighboring cells) 3) synaptic (neurotransmitter from an axon to a cell - very precise) 4) endocrine: hormones into the blood and target cells (generalized signal) 5) Autocrine: (one cell is signaling itself, it's week but multiple autocrine signaling is strong) 6) gap signaling: (cardiac cells so everything contracts together - everything is being signaled at the same time so the heart can contract)

Answer 59

YASSSSS. Acetylcholine in the muscle causes the muscle to contract, whereas in the cardiac muscles it causes it to relax and decreases HR and in the salivary glands it helps you secrete saliva.

Answer 60

1) receptor protein - receives chemical signals from outside of the cell 2) scaffold protein (can have preassembled scaffold: relay proteins already attached to scaffold protein, you can also have assembling as activation occurs) - either hold protein kinases in a latent state close to their activating cell-surface receptors, or facilitate flow of activation from one kinase to the next kinase in a signaling cascade. 3) relay protein: pass the message to the next signaling component in the chain without otherwise participating. 4 ) adaptor protein: link the components of signaling pathways by acting as accessories to the chief proteins in a signal transduction pathway. 5) bifurcation protein: spread the signal from one signaling pathway to others. 6) amplifier protein: are usually either enzymes or ion channels. Amplifiers increase the received signal by producing large amounts of small intracellular second messengers or by activating large numbers of downstream intracellular signaling proteins. 7) small intracellular mediator (aka second messengers): they pass the signal on by binding to and altering the behavior of selected signaling proteins or target proteins. 8) integrator protein: integrate signals from two or more signaling pathways and relay the signal onward along a single pathway. 9) anchoring protein: provide a molecular framework that orients these enzymes towards selected substrates. 10) messenger proteins: carry the signal from one part of the cell to another. For example, messengers often carry signals from the cytosol to the nucleus. 11) target protein: control the action and the kinetic behavior of drugs within the organism

Answer 61

steroid hormones (estrogen, progesterone, testosterone, aldosterone, glucocorticoids, DHEA) hydrophobic can penetrate the membrane easily. DNA bind domain, ligand binding domain and transcription-activation domain and an inhibitory protein. When the hormone comes in it binds to an intracellular receptor and activates transcription.

Answer 62

extracellular, these are receptors that can serve as an ion channels. Ex) nicotinic AChR: binding of the receptor allows the opening of the channel.

Answer 63

are indirectly linked with ion channels on the plasma membrane of the cell through signal transduction mechanisms, often G proteins. also called G-protein linked receptors. Ex) muscarine acetylcholine receptor

Answer 64

1) receptor sequestration: taking a receptor off the extracellular surface and bring it in so it can no longer function 2) receptor down regulation: a receptors gets eaten up by a lysosome 3) receptor inactivation: receptor remains on the extracellular surface and just gets deactivation. 4) product can also go back and inactivate a receptor.

Answer 65

1) alpha S - stimulate adenylate cyclase (an enzyme with key regulatory roles in essentially all cells) 2) alpha I - inhibit adenylate cyclase 3) alpha Q - activation Phospholipase C (PLC - a class of membrane-associated enzymes that cleave phospholipids just before the phosphate group) -- PLC connects to IP3 (is a secondary messenger molecule used in signal transduction and lipid signaling in biological cells.) pathway.

Answer 66

The g-protein will dissociate when it is activated. It dissociates into beta and alpha subunits. The alpha subunit has a GDP attached to it so once it is activated, it gets phosphorylated to GTP.

Answer 67

1) beta receptors gets activated by NE 2) this activates a G protein 3) the G protein activates adenylate cyclase 4) adenylate cyclase then converts ATP to cAMP (second messenger) 5) cAMP then activates PKA (is a family of enzymes whose activity is dependent on cellular levels of cyclic AMP)

Answer 68

adds a kinase to a molecule to activate it. protein phosphatase 1 strips the phosphate off the molecule and then inactivates it (not always the case) -PKA dissociates the regulatory element when activated by cAMP.

Answer 69

1) AcH activates the beta receptor 2) which activates a Gq protein 3) the Gq protein activates PLC which cuts a lipid molecule into a IP and DAG (second messengers) 4) IP then binds to another receptor that opens an intracellular calcium channel on the ER, increasing intracellular calcium 5) calcium then bind to open up a coloring channel. Sodium follows the chloride and so does water.

Answer 70

tyrosine kinase receptors, no G proteins involved. These are involved in growth factors. 1) the ligand connects bringing two tyrosine kinase domains together that then auto-phosphorylate each other (dimerization).

Answer 71

It is similar to G protein. When it is inactive it has a GDP bound to it. And when it is activated it is bound to a GTP. Then it can go on to phosphorylate other molecules.

Answer 72

One phosphorylates another. Can't go in reverse. There are protein specific molecules? 1) changes protein activity 2) changes in gene expression

Answer 73

- is a protein complex that controls transcription of DNA, cytokine production and cell survival. 1) a ligand binds to 3 receptors and causes trimerization 2) normally in the cytosol NFKB is inactive by IKB 3) activation triggers degradation of IKB so NFKB is active and free 4) NFKB then translocates to the nucleus and activates gene transcription

Answer 74

Methionine (AUG), more then one codon can code for the same amino acid

Answer 75

3 digit codes that can be read in 3 different ways. You change the reading frame by shifting where you begin. BUUTTTTT there is only 1 open reading frame because you have to begin with AUG and the stop codon needs to be in that same reading Fram.

Answer 76

- 3 loops: clover leaf design | Anticodon loop: matches the codon in a complementary way. Most important are D loop and T loop.

Answer 77

In some genes the protein-coding sections of the DNA ("exons") are interrupted by non-coding regions ("introns"). RNA splicing removes the introns from pre mRNA to produce the final set of instructions for the protein.

Answer 78

Opens ions channels for chloride in salivary glands - to produce saliva

Answer 79

The principle underlying signal transduction by a tyrosine kinase receptor is that ligand binding to the extracellular domain triggers dimerization. This causes a conformational change in the cytoplasmic domain that activates the tyrosine kinase catalytic activity. - basically activates receptors.

Answer 80

amino acid that is added to the tRNA by an ester bond on the 3 prime end.

Answer 81

starts by zipping along the mRNA until it finds the start codon, poly A tail helps fix the ribosome in a right way. - E site: exit - P site: peptide-tRNA binds - A site: aminoacyl-tRNA binds

Answer 82

UAA (U Ain't going Anywhere) UAG UGA

Answer 83

N-terminus is made first and C-terminus is made last. If it is folded wrong, you must trash the protein. Chaperones can help fold it correctly. If it continues to fail, the proteasome can degrade it. Can cause disease and other illnesses if folded wrongly.

Answer 84

the garbage disposal of misfolded proteins.

Answer 85

it's important in getting ride of proteins we don't want. 1) E1: ubiquitin activating enzyme: with help of ATP it gets activated 2) E2 and E3: ubiquitin ligase: E1 activates E2 and E3 3) complex then searches for a protein that is misfolded. 4) misfolded protein binds to the complex, and E1 starts adding a bund of ubiquitin to the protein and signals it to be degraded by the proteasome. Main point is put ubiquitin on the misfiled protein so the proteasome can recognize it.