Molecular Genetics 2 Flashcards

Terms Definitions
Pseudogenes
genes which become nonfunctional
What are introns?
Noncoding sequences
MeCP
methyl-CpG binding protien. binds methylated DNA. includes histone deacetylases. promotes condensation so repression
How does Guanine look like?
Where are Fis sites located?
-60-->-150
genome
the complete instructions for making an organism, consisting of all the genetic material in that organism's chromosomes
sir2p
an NAD dependent histone deacetylase. removes acetyl groups from histones, preferentially at lysine 16 of histone H4. Sir2-like proteins are consereved from bacteria to mammals. Has additional roles in cellular aging
satellite viruses
-satellite viruses are molecular parasites on plant viruses; code for their own coat protein but nothing else and are dependent upon their helper virus
Sigma factor for housekeeping genes
-sigma 70
How does Autoradiography/phosphorimaging work?
1.Electrophoresis with radioactive tags, gel becomes radioactive. 2. Expose to film on the gel for a period of time3. develop film
Do they require energy?
All three do
deoxyribose
any of certain carbohydrates derived from ribose by the replacement of a hydroxyl group with a hydrogen atom.
Proteins
Made from amino acids
each has a specific sequence
unique shape
If one amino acid is missing or different, it is different protein with a different shape and a different function
sas2p and Gcn5p
histone acetyltransferaces believed to counteract sir2p function
constitutive heterochromatin
permanent feature of cells and represents DNA that contains no genes and so can always be retained in a compact organization--found in the centromere and telomere
Organellar genomes
-usually circular but some linear-many copies per organelle, and many organelles per cell so you can have thousands of copies per cell
enhancer
-also bind activators to help the complex assembly-due to DNA bend, enhancers can be located quite a distance away from TATA box
N-formylmethione
-formylation is making sure the N terminus become muted and the C terminus is connected to the second AA
If the bacteria contain plasmid w/o YGI the colonies will be...
BLUE
Affinity Chromatography is a similar method as in creating what?
Fusion proteins!!!
What is this known as?
A silent mutation
What is telomerase?
Telomerase is a ribonucleoprotein complex (RNA + protein) with reverse transcriptase activity (hTERT): it synthesizes DNA using its RNA subunit as the template.

It adds short DNA repeats to the 3'-ends of linear chromosomes. This extension allows room for a primer to bind and initiate lagging-strand synthesis on the other strand, maintaining an appropriate length of chromosome ends and preventing the loss of coding sequences.

Telomerase has been Implicated in cell aging and cancer.
Most somatic cells do not express telomerase but
in cancers, telomerase is re-activated, allowing indefinite cell division and cancer progression.

Telomerase inhibitors can limit cancer cell proliferation.

Dyskeratosis congenita is caused by reduced telomerase activity and effects highly proliferative tissues like hair follicles,gut, skin, bone marrow.
ribosome
tiny organelle occurring in the cell cytoplasm, functioning as the site of protein manufacture
telomeres
Repeated DNA sequences at the ends of eukaryotic chromosomes
swi6
required to keep the mating type genes repressed. localized to the heterochromatic region. binds to the histone H3 tail only when the tail is methylated at lysine 9. H3 lys 9 is localized to the exact same chromomal region as swi6. Contains a chromodomain, which is a protein domain that binds to methylated lysines.
microsatellites
-usually less than 150 BP and repeat unit is usually 13 bp or less-great heterzygosity in terms of the length of the microsatellite array; slipping in the matching up in meiosis-unequal distribution of the array
operon
group of genes involved in a singled biochemical pathway and expressed in conjunction with one another-not all genes of an operon are related
Leucine zipper
two separate proteins unlike the zink finers-have several fingers all connected to each other-leucines are nonpolar, they hate water and gather together to be as interior as they can
Release factor
-a protein that is responsible for termination of translation-prokaryotes have 3, eukaryotes 2-mimics tRNA
How does qPCR work?
during amplification the separated strands anneal to a reporter probe and then the fluorescent tag is released emitting light as DNA polymerase eats away at that bond
What is this template known as?
The antisense strand
Non-Structural Proteins
- The virions (packages) of some viruses contain small amounts of other proteins, including RNA-dependent RNA polymerase (to produce viral mRNA), reverse transcriptase, integrases to help stick retroviral DNA into host genome, transcription factors, and proteases that process viral proteins and inhibit translation of host proteins.
What is a CTD?
C-terminal domain.

Just after RNA transcription initiation (~25 bases) the C-terminal domain (CTD) is phosphorylated.

It recruits the enzymes responsible for mRNA 5’ capping, splicing, and poly(A) addition.
Transduction and Transformation
- General Transduction: Segment of bacterial genome is erroneously packaged in a phage instead of the phage genome. Any section of the bacterial genome can be packaged and transferred to another bacteria in this way.
- Specialized Transduction: the prophage imperfectly excises itself from the bacterial chromosome, carrying some flanking DNA with it. The frequency of genes co-traveling is a measure of their proximity to the phage's insertion site, and can be used to develop a map of the bacterial genome.
- Transformation: Direct uptake of free DNa. This is inefficient and only occurs at certain parts of the cell's replicative cycle. The double-stranded DNA is cleaved at the membrane, one enters the cell, and displaces its homolog in the bacterial chromosome.
restriction enzymes
The proteins used to cut DNA molecules at specilic places so that scientists can isolate pieces with the desired genes.
Heterochromatic gene silencing
differs from simple repression in that larger regions of a chromosome, not just an individual promoter are repressed.
three eukaryotic RNA polymerases
-RNA poly1: rRNA-RNA poly2: mRNA, snRNA, miRNA-RNA poly3: tRNA, snRNA, snoRNA
Difference between DNA and RNA?
Difference in sugar:
 
(ribose for RNA and deoxyribose for DNA)
 
 
Uracil ( RNA) and thymine (DNA)
What are affinity tags (fusion proteins) great for?
Purification/isolation, detection and localization
Shorthand of Sanger Chain Termination Method
1.DNA Template 2.Complementary Oligo3.DNA Polymerase4.Radioactive Label5.Excess of normal DNA6. Chain TerminatorsCTM: DCDREC
What is translation?
The process whereby mRNA codons are transplated into a sequence of amino acids
What does this permit?
It permits viral replication without killing the host cell
Two-Hit Hypothesis
- Suggested by the 10k increase in incidence of familial form of a particular cancer.
- According to the two-hit hypothesis of cancer, both alleles need to be knocked out for tumor initiation. In the familial form, offspring start off life with one hit. There is a 10k higher chance of getting just one hit in a certain gene than two.
How is translation initiated?
eIF = eukaryotic initiation factor.

eIF 2 binds to the tRNA and eIF 4e/4g to the 5' end of the mRNA displacing the CBP cap.

Movement along the mRNA in search of the first AUG is facilitated by other initiation factors, which are powered by ATP hydrolysis.

When the AUG is found, eIF 2 and other initiation factors dissociate and the first aminoacyl tRNA binds.

The first peptide bond forms between methionine and the amino acid.

Elongation begins.
DNA Repair Strategies
- Direct repair: Thymine dimers are fixed with white light, alkyltransferase de-alkylates guanine.
- Base excision repair: Chemically modified base is cut off.
- Nucleotide excision repair: Entire mispaired nucleotide is removed. If this occurs during DNA replication, the template strand is always preferred for mismatch repair because it's already methylated.
- Homologous recombination with another duplex (including the other daughter strand) can somehow correct errors.
histone
any of a group of five small basic proteins, occurring in the nucleus of eukaryotic cells, that organize DNA strands into nucleosomes by forming molecular complexes around which the DNA winds.
Watson and Crick
Were given credit for the structure of DNA
lateral or horizontal gene flow
transfer of genes between species, even between highly unrelated species-happens by means of conjugation, transduction, and transformation
Where do the bonds occur in AT and GC pairs?
What is transformation in eukaryotes?
conversion from normal to cancerous cell
What is a southern blot?
Method to identify specific DNA fragments
How long does transcription and translation occur?
Until the corepressor is synthesized
How does termination work?
It terminates when one of three special mRNA termination codons (UAA, UAG, UGA) arrives in the A site
What is an example of a single base-pair substitution?
Sickle cell anemia
How does elongation work?
Hydrogen bonds form between the mRNA codon in the A site and its complementary anticodon on the incoming aminoacyl-tRNA complex
Types of Genetic Heterogeneity
- Allelic: Most disease genes have large numbers of disease-producing mutations. This produces a spectrum of functional consequences in the protein product of the gene, from variants with variants with zero function to those functional conditionally, to silent mutations. This contributes to the individuality of each patient.
- Locus: One phenotype can be caused by mutations in many different genes. The study of locus heterogeneity for a disease can give us insight into the number of gene products required for a particular system to function normally.
What are the pathways for DNA repair?
Mismatch repair
Base excision repair
Nucleotide excision repair
Transcription factors account for only part of the required molecules for gene regulation in eukaryotes. What else plays a major role?
Enhancer sequences and their activators exert significant control over expression levels.
General Features Distinguishing Prokaryotes from Eukaryotes
- No nuclear membrane
- Usually a single circular chromosome
- Genes uninterrupted by introns
- Ribosome 70S, not 80S
- Cell walls contain muramic acid
- No mitochondria or membrane-bound vesicles
- No cytoskeleton or endocytotic vesicles
- Movement by flagellar rotation
- Cell envelope of 1 or 2 membranes plus peptidoglycan wall
- Glycocalyx or capsule: slimy layer of polysaccharides
Size of the human genome
-3200 MBP-many animals such as mice, locusts, wheat, peas and fritillary all have larger genomes
What can plasmids pick up?
A piece of foreign DNA without ORi
What makes a recombinant protein?
Expression of a foreign gene in bacteria.
What are 2 types of Nucleic Acid Hybridizations?
Southern and Northern Blots
What are corepressors often?
They are often the end-products of the biosynthetic pathways they control
How does it enter the host cell?
Via a variety of mechanisms
What is the rate of replication?
It occurs at approximately 500 nucleotide additions per second
Antigenic Drift and Shift
- Antigenic drift refers to the slow emergence of new antigenic variants as a result of mutation and selection. Though this year's antibodies won't be perfect against next year's virus, they will probably provide some protection.
- Antigenic shift is the result of recombination, usually between a human strain (with RNA capable of multiplying in human cells) with a previously animal-only strain (with HA and NA that our bodies aren't used to). Antigenic shift produces recombinants with a huge selective advantage in human populations, and is the reason we see occasional epidemics or pandemics in the human population. Reintroducing a variant that has not been seen for variations will produce the same basic results.
Do prokaryotes preform RNA splicing?
No, it is unique to eukaryotes.

It allows for mutations to occur with less chance of a detrimental effect (the majority of most genes is intronic)

It also allows for more complex proteins to be created.
What is epigenetics?
The study of DNA changes that do not alter the actual DNA sequence.
eg. DNA methylation

Can be influenced by environmental exposures (chemicals, diet, etc.)

Changes can be transmitted from parent to offspring which we can't fully explain yet. Basically this means you can be obese because of something your grandmother ate.
when does Beta globin take over in humans
about 10 weeks after birth
What does IPTG do ?
A lactose analouge that can induce the lacZ gene, this INDUCES (INDUCER) the gene expression
What are some advantages for using a fusion protein?
.Easy purification of recombinant Protein Use the Tag as a handle on something and using that tag to move it. Affinity tag is a way to isolate YPI based on the presence of the tag 2. Increase expression levels and/or solubility of recombinant protein a. You don’t want your protein to precipitation out of solution
What is a specific type of UCF?
Sucrose Gradient UCF and Equilibrium Density UCF
What happens following peptide bond formation?
A ribosome carries uncharged tRNA in the P site and peptidyl-tRNA in the A site
What does the enzyme peptidyl transferase do?
It catalyzes the formation of a peptide bond between the amino acid attached to the tRNA in the A site and the met attached to the tRNA in the P site
DNA Microarrays and ChIP Technology
- Isolate mRNA from one or several cells of interest.
- Use that mRNA to make labeled target/probe (terminology changes from one source to the next) cDNA.
* If you wanted to compare cancerous and healthy cells, for example, you could label one type green and one type red.
- Obtain microarray with genes of interest or the entire genome, broken up into fragments and stuck into individual wells.
- Wash your aray with both sets of target/probes, then compare fluorescence to see which mRNA are expressed in both cells and which are only in one or the other.
- All you can tell by this method is which genes are or are not being transcribed, since you're looking at mRNA.
- ChIP is used to identify where on DNA a particular protein binds. "Fix" chromatin (DNA plus the protein of interest) tightly together, then use antibodies for the protein of interest (stuck to a bead), shake your DNA to break it into chunks, wash out all DNA not bound to proteins (bound to antibodies, bound to beads), and then use that DNA to probe a DNA microarray to identify the sequences your protein of interest targets.
A human karyotype consists of...
22 pairs of autosomes
1 pair of sex chromosomes
State at least two structural differences between DNA and RNA
1. sugar in RNA contains an extra hydroxyl group
2. DNA has the nucleotide base, thymine, RNA has the base uracil
3. RNA is single stranded, and DNA is double stranded
What is a method to prevent religation of a vector?
Use alkaline phosphotase to remove phosphate groups under alkaline conditions
Where did they find the radioactive label?
n beta subunit (implying where active site is) b/c that’s where the label is retained
What happens in the lytic cycle?
The phage DNA takes control of the bacterium’s genetic machinery and manufactures numerous progeny
What does this base-pairing form?
It forms rungs on the interior of the double helix that link the two polynucleotide chains together
What is a silent mutation?
One in which there is a DNA change, but no amino acid change.

The codon is different but still codes for the same amino acid.
eg. TAT and TAC both code for tyrosine so a change from T to C does not change the protein.
Identify what kind of mutation it is, and whether the mutation is harmful or not. Explain your answer.
 
original strand: AUG AAC CCC ACA UAA
mutation       :  AUG AAC CCC ACU UAA
It's silent mutation, and it's not harmful to body, because this mutation does not result in a change in the amino acid coded for.
In S. blots how are specific bands identified?
labeled probes that are based on hybridzation/complentarity b/w DNA strands
How many tight binding sites compared to loose are there on the promoters?
Only 8 tight binding sites and 1300 Loose sites
What happens to the empty A site?
It is ready for entry of the aminoacyl-tRNA corresponding to the next codon
How do we genotype with microsatellite markers?
We compare two sequences that we know a specific location for and look for a length difference that will identify a different allele.
What 4 things do you need to make a recombinant protein?
cDNA of eukaryotic gene Expression vectorsInducible promotersExpression systems (prokayotic vs. Eukaryotic [higher cost and more effort, low yield ])
What kind of FRET is most useful for our purposes? Which one does not distinguish b/w dissociation or no dissociation of sigma?
Leading Edge fret is useful. Trailing edge FRET does not distinguish b/w dissociation or no dissociation of sigma
How does a change in the level of gene transcription ultimately effect the amount of translated protein?
There are multiple other factors invloved but generally more mRNA means more protein.
What does the addition or loss of a nucleotide cause?
It changes the reading frame of the mRNA
Good Luck
Good Luck
the 5 end
guanine cap
sight of protien synthesis
ribosomes
retrovirus
contains reverse transcriptase which transcribes it RNA to DNA to be incorporated into host DNA
DNA
deoxyribonucleic acid, the material that contains the information that determines inherited characteristics
Corepressor
Ex. tryptophan. Molecule that cooperates with the repressor to switch the operon off
Sequence of splice branch site
A
exact copy of an organism
cloning
E site
where the chain leaves from
Meristems
Where embryonic cells are in plants.
Genetic Pollution
Transgenic organisms hybridize with wild forms of the same species or related species, so the newly acquired gene escapes into the wild. Ex. GM grain crops (like wheat, rye, etc) with a gene for herbicide resistance could hybridize with wild grasses to produce "superweeds" that cannot be controlled with herbicides.
Telomere
Repeating, non-coding sequences at the end of chromosomes, a protective cap since a little DNA is lost with each replication
Bacterial defenses against phages
Evolution, restriction enzymes,lysogeny (can coexist)
polymerase
adds nucleotides to an existing strand
What enzyme joins nucleotide components to one another, forming a long strand of nucleotides?
DNA polymerase
rRNA
combines with proteins to form ribosomes- globular
Genetic Code
provides the "decoding" for each codon, and it identifies the amino acid specified y each o the possible 64 codon combinations
What does DNA stand for?
deoxyribonucleic acid
Four nitrogen bases
adenine guanine cytosine thymine
Frameshift Mutation
Inserting an extra nucleotide and shifts the "reading frame" of the genetic message
conjugation
transfer of DNA between two bacteria cells connected by appendages called sex pili
What is the expected phenotypic ratio of the following cross: AaBb * AaBb? In this example A is dominant to a and B is dominant to b.
9:3:3:1.
tRNA
Delivers amino acids to a ribosomes for their addition into a growing polypeptide chain. Has a clover leaf shape.
Initiation (Translation)
The mRNA strand becomes associated with ribosome before protein formation begins.
Specific tRNAs picks up specific amino acids and bring them to the mRNA/ribosome complex. The first amino acid is always methionine, which is what the "start codon" (AUG) codes for.
transcription
process in which part of the nucleotide sequence of DNA is copied into a complementary sequence in RNA
lytic cycle
A phage reproduction cycle that culminates in death of the host cell.
viroid
Very small circular RNA molecules that infect plants. They do not encode proteins but can replicate in host plant cells, apparently by the use of host cell enzymes. Ex. cadang-cadang
operons
genes in bacteria that are clustered into units
What pyrimidine does RNA contain rather than thymine in its DNA counterpart?
uracil (U)
proof-reads
what the DNA polymerase does in bacteria
Okazaki Segments
short segments of complementary DNA that develop along the 5'->3' template strand
Function of RNA polymerase II
transcribes mRNA, snRNA
DNA sequence resulting from the combininig of two differnet DNA sorces
recombinant DNA
DNA Replication
The double helix unwinds, the DNA opens and hydrogen bonds break, Complimentary Nucleotides match up (assisted by polymerase), 2 DNA strands form; Each double strand reforms a helix again; each DNA strand also acts as a template to produce 2 new complimentary strands; it occurs before cell diviision
semiconservative
DNA unzips; one strand given to each daughter
Termination (Transcription)
This occurs when the RNA polymerase reaches a special sequence of nucleotides that serve as a termination point.
Globin Family
The beta-globin gene family located on chromosome 11 is shown in the figure below and consists of five functional genes (blue boxes) and two pseudogenes (diagonal lines). All of the hemoglobins encoded by these different genes function to carry oxygen in the blood; however, each gene exhibits specific variations in function. For example, the epsilon globin gene is normally expressed in the embryonic yolk sac while the Ag and Gg genes are expressed only during fetal development. These hemoglobin proteins have a higher binding affinity for oxygen than the adult hemoglobins encoded by the b and d genes. This increased binding allows the fetus to successfully extract oxygen from the mother's supply. Adult hemoglobin has a lower oxygen affinity allowing better release of oxygen to tissue, especially muscle.
Pattern Formation
Refers to the pattern of development of organs and tissues in animals
Involves chemical cues that provide positional information (orientation of cells with respect to other cells)
protein synthesis
the formation of proteins by using information contained in DNA and carried by mRNA
TaTa box
A promoter DNA sequence crucial in forming the transcription initiation complex.
recombinant DNA
DNA molecules formed when segments of DNA from two different sources, often different species, are combined in vitro.
Eukaryotic regulation: Transcription initiation
Enhancer and formation of transcription initiation complex
Origin of replication
Where replication begins, a short stretch of DNA with a specific sequence
ribozyme
RNA molecule that acts as an enzyme and plays a catalytic role.
What is mRNA?
Messenger RNA (ribonucleic acid): the RNA molecules that receive the genetic code in the DNA and carry the code in the DNA into the cytoplasm where protein synthesis takes place.
DNA polymerase
moves in the 3'-> 5' direction along each template strand and the new complement strand grows in the antiparallel 5' -> 3' direction
binary fission
reproduction of a bacterial cell- the chromsome replicates and the cell divides into two cells, each one bearing one chromosome. There are no spindle apparatus, microtubules, nor centrioles
Sequence that's 25bp upstream of a gene start site (G-methyl-7) that recruits proteins for transcription.
TATA box
What are nucleic acids?
Large molecules comprised of nucleotides.
Nitrogen bases in RNA
Adenine Guanine Cytosine Uracil( replaces thymine)
Lysogenic Cycle
virus is dormant once its DNA has incorporated with host DNA and is transcribed through normal transcription
In a cross AaBbCc * AaBbCc, what is the probability of producing the genotype AABBCC?
1/64
RNA Interference
Short RNA's can lead to destruction of specific mRNA and/or silencing the expression of genes that contain complementary sequences in their mRNA.
RNA Primer
Sequence of RNA primers bound to a region of single-stranded DNA to initiate DNA replication.
Temperate phages
Phages capable of using both modes of reproducing within the bacterium.
Eukaryotic regulation: DNA packing
How tight it is packed (heterochromatin vs euchromatin) determines enzyme access
sense strand
strand that serves as the template in transcription
What was the code?
• Theoretical argument of a triplet• 3 letters represents the minimum to encode nformation to specify 20 amino acids• 43 =64 different possible combinations• 42= 16 not enough, 44=256 too much
What are the two long strands that form a double helix in a molecule of DNA?
Nucleotide chains.
How are the three genes of the lac operon transcribed?
null
one-gene-one-enzyme hypothesis
that the gene is defined as the segment of DNA that codes for a particular enzyme
Messenger RNA
a single strand of RNA that provides the template used for sequencing amino acids. A codon codes for one specific amino acids.
2 structural genes in alpha globin gene cluster
alpha and zeta
What enzyme is used in the synthesis of mRNA, tRNA, and rRNA?
RNA polymerase
transfer of a normal or modified gene into an individual to correvt a gentic deffect
gene therapy
Which of the following is a correct historical progression of these three events, from first to last?
III, I, II
Problems with Genetic Engineering
Transgenic crops like Bt corn may produce toxins that affect nontarget species like the monarch butterfly (via wind born toxic corn pollen settling on milkweed plants growing nearby.
anti codon
A nucleotide triplet at one end of a tRNA molecule that recognizes a particular complementary codon on an mRNA molecule.
What happens in post-translational modifications?
May attach sugars, phosphate groups. May remove amino acids, may be cleaved in two, two polypeptides may come together
What is an anticodon?
Opposite bases of codons to facilitate base pairing.
What if Overlapping tripletcode?
• Consider a sequence: GTACA• If the triplet code were overlapping, then GTA, TAC, and ACA are possible readingframe codons of this sequence• If overlapping, it restricted the amino acidsthat would be adjacent to the amino acid encoded by the central triplet• If true, then sequence of tripeptides would be limited, but that was not the case when peptide sequences were examined
Where is transfer RNA (tRNA) found in the cell?
In the cytoplasm.
complementary DNA
or cDNA, it is DNA obtained by using reverse transcriptase to make a DNA molecule directly from the mRNA and lacks the introns that suppress transcription
Function of RNA polymerase I
transcribes ribosomal RNA 28S, 18S, 5.8S
What are the two major types of nitrogenous bases that make up a nucleotide in a DNA chain?
Purines and pyrimidines.
Ribosomal RNA (rRNA)
A type of RNA molecule that makes up the major part of ribosomes
What is in a transcription initiation complex?
transcription factors, RNA polymerase II, promoter, RNA transcript
Discuss how segmentation genes and homeotic genes relate to one another.
Segmentation genes define the number of body segments that form on an organism after its axes have been formed. They then give rise to more specific details that are implemented into the body plan.
Homeotic genes regulate what specialized organs and structures form about these segments. Mutations in homeotic genes can result in appendages developing in wayward areas.
What is the function of deoxyribonucleic acid (DNA)?
To relay inherited information to messenger RNA (mRNA).
Step 3 of DNA replication
DNA polymerase attaches to the RNA primers and begins elongation, the adding of DNA nucleotides to the complement strand
Post-translational modification: What are meristylation and palmitoylation? What is it used for?
Addition of lipids to a protein by covalent bonding--important for protein signaling. Tethers to plasma membrane, used for membrane-bound proteins.
During transcription, how many strands of DNA serve as the template for RNA synthesis?
One strand. The other remains dormant.
The F1 offspring of Mendel's classic pea cross always looked like one of the two parental varieties because
one allele was completely dominant over another
Eukaryotic regulation: Regulation of mRNA degradation
Life span of mRNA determines how much protein synthesis it does. Poly-A tail and 5' cap. siRNA, proteasomes
What are the characteristics of genetic codes exhibits?
1. genetic code is written in linear form , using the ribonucleotide bases that compose mRNA molec. as 'letters'. the ribonucleotide sequence is derived from the complementary nucleotide bases in DNA2. Each "word" within the mRNA contains three ribonucleotides letters. each group of three ribonucleotides, called codon, specifies one amino acid 3.the code is unambiguous, meaning that each codon specifies only a single amino acid.4. the code is degenerate, meaning that given amino acid can be specified by more than one codon. this the case for 18 of the 20 amino acids5. the code contains "start and 'stop' signals, certain codons that are necessary to initiate and to terminate translation6. no internal puctuation'commas' is used in the code, thusthe code is said to be commaless. once translation of mRNA begins, the codons are read one after the other with no breaks between them.7. the code is nonoverlapping. after translation commences, any single ribonucleotides at a specific location within the mRNA is part of only one codon8. the code is nearly universal. with only minor exceptions a single coding dictionary is used by almost all viruses, prokaryotes, archea, and eukaryotes.
What are the two pyrimidine bases in DNA?
cytosine (C) and thymine (T)
Why are fetal hemoglobins made of different subunits than adult hemoglobins?
Fetus needs hempoglobin with higher affinity for oxygen
What are the three types of RNA?
ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA)
one gene one polypeptide hypothesis
The premise that a gene is a segment of DNA that codes for one polypeptide.
What are the Genetic Code characteristics?
• Code is in linear form• RNA sequence is derived from complementary bases of DNA• Each “word” of the code in mRNA contains three ribonucleotide “letters”• Each group of three ribonucleotides is calleda CODON, specifies one amino acid• Therefore, the code is a TRIPLET
How is the lagging strand synthesized during DNA replication?
In short segments in a 5'-3' direction (from the leading strand to the lagging strand).
What are sticky ends?
What is a vector? Give an example of a vector.
What is a pyrimidine made up of?
One ring of carbon and nitrogen atoms.
How to know which bacteria took up the recombinant plasmid (1)
We first eliminated bacteria that didn't take up any plasmids by growing them on media containing ampicillin, an antibiotic. Since the plasmid in the example shown contains an ampicillin resistance gene, bacteria with plasmids are unaffected
It is not transcribed because it inhibits the pathway upon binding.
If lactose is present in the media, some of it will be converted to what when it enters the cell?
How is the lagging strand synthesized during DNA replication?
In short segments in a 5'-3' direction (from the leading strand to the lagging strand).
Why is DNA replication referred to as "semiconservative replication"?
Because an old strand of DNA remains a part of the new DNA double helix.
If E. coli is grown with no lactose are the enzymes present?
no b/c the repressor gene will inhibit the pathway
transpoons
transposable genetic elements
the 3 end
polyadenine tail
Complimentary nitrogen bases
Adenine-thymine
Guanine- Cytosine
conservative
entire double helix copied together
introns
a non-coding, intervening sequence within a eukaryotic gene
Heterochromatin
Tightly wound chromatin, inaccessible to enzymes and thus no gene expression
mRNA
provides the instructions for assembling amino acids into a polypeptide chain, linear
What replaces gamma globin?
beta globin
RNA Polymerase
During transcription, RNA polymerase binds to DNA and separates the DNA strands. It then uses one strand of DNA as a template from which nucleotides are assembled into a strand of RNA
frameshift mutations
deletion/addition of DNA nucleotides that does not remove a multiple of three nucleotides
Induction
Cells cause nearby cells to change.
What do viruses do?
By themselves, nothing.
Erwin Chargaff
Wrote Chargaff's rules. Noticed equivalence in ratio of A to T and C to G in a given species.
polyA tail
added to the 3' end
What does DNA stand for?
deoxyribonucleic acid
What pyrimidine base does guanine complement?
cytosine
mutation causing agents in the enviroment
mutagens
Mutation
Any alteration or change in genes; Causes are mistakes in pairing during replication (spontaneous )(natural); also caused by X-Rays and U-V light (both causes increase mutation rate)
transformation
uptake of foreign DNA from surrounding environment
A sexually reproducing animal has two unlinked genes, one for head shape (H) and one for tail length (T). Its genotype is HhTt. Which of the following genotypes is possible in a gamete from this organism?
HT
Alternative Splicing
Allows different mRNA's to be generated from the same RNA transcript. By selectively rempving different parts of an RNA transcript, different mRNA's can be produced, each coding for a different protein product.
bacteriophages
A kind of virus which infects bacteria. One of the most complex kinds, with elongated icosahedral heads enclosing their DNA and a protein tail piece with fibers which the phages use to attach to bacterium.
Point mutation
Single base pair mistake. Ex. base-pair substitution, insertions, deletions
What step can gene expression be regulated at?
Transcription
allocis?
Does the repressor have negative or positive control on the lac operon?
Transfer RNA
short RNA molecule (80 nucleotides) that is used for transporting amino acids to their proper place on the mRNA template.
DNA Ligase
connects Ozaki Segments producing a single complement strand
sticky end
unpaired extension after a restriction enzyme makes a staggered cut across a DNA
Are the chemical bonds that hold together the two strands in a double helix of a DNA molecule weak or strong?
weak
determing the nucleotide sequecnce of DNA
Gene sequencing
Duplication
When a segment of a chromosome is repeated; the opposite of deletion
A site
where the next tRNA molecule is waiting
Elongation (Transcription)
This occurs as the RNA polymerase unzips the DNA and assembles RNA nucleotides using one strand of the DNA as a template. This occurs in the 5'--->3' direction.
Leading Strand.
Replicates continuously from 3' end of existing strand, with newest end of forming strand facing into replication fork.
topoisomerases
enzyme that cuts and rejoins helix to prevent tangling
lagging strand
The strand in replication that is copied 3' to 5' as Okazaki fragments and then joined up.
DNA polymerase I
Proofreader polymerase; only works at 20 bases/ sec but makes a lot less mistakes. Editing, repair, and primer removal
virus
very small nucleic acid that is either RNA or DNA but not both, either double or single stranded, capsid protein coat formed by capsomere encloses the nucleic acid. Sometimes further wrapped in membraneous envelope.
Cytoplasmic Determinants
the maternal substances in the egg that influence the course of early development by regulating the expression of genes that affect the developmental fate of cells
What is a nitrogenous base?
The nitrogen-containing molecules that make up DNA and RNA molecules. Two major types are purines and pyrimidines.
insertion
type of mutation when there is an additional nucleotide not present in the orignal DNA molecule
Codon
in mRNA, a triplet group of three adjacnt nucleotides that code for one specific amino acid. There are 64 possible codons but only 20 amino acids.
What types of bonds form between 2 amino acids in a growing protein?
covalent
What is mRNA?
Messenger RNA (ribonucleic acid): the RNA molecules that receive the genetic code in the DNA and carry the code in the DNA into the cytoplasm where protein synthesis takes place.
deoxyribonucleic acid
DNA- 1 deoxribose 1 phosphate 1 nitrogen base
thymine dimers
too much UV light, thymine adjacent to eachother on another strand bind with eachother
What is a genome?
the complete complement of an organism's genes
Control of mRNA degradation
Affects how much protein gets made.
Okazaki fragments
Small fragments of DNa produced on the lagging strand during DNa replication, joined later by DNA ligase to form a complete strand.
DNA polymerase III
1000 bases/ sec. Main DNA builder, makes mistakes.
polymerase chain reaction
Any specific target segment within one or two DNA molecules can be quickly amplified in a test tube. The mixture is heated to denature the DNA strands, cooled to allow annealing (h bonding) of short single stranded DNA primers, and the heat-stable DNA polymerase extend the primers.
Histone acetylation
acetyl groups are added to amino acids of histone proteins, making the chromatin in less tightly packed and encouraging transcription
Final codon table
• 61 triplet codons that specify aminoacids• 3 termination codons, stop amino acidincorporation
What enzyme is used in the synthesis of mRNA, tRNA, and rRNA?
RNA polymerase
Nucleotides
made up of polymers of either DNA or RNA
three steps in protein synthesis
transcription, RNA processing, and gtranslation
Post-translational modification: where does phosphorylation typically occur? What is it for?
Mostly threonine and serine, also tyrosine
Important for protein signaling
How is DNA replicated?
Specialized enzymes pull apart, or "unzip", the DNA double helix, exposing purine and pyrimidine bases. These bases then attract their complementary bases. DNA polymerase joins the nucleotides to form a new nucleotide chain under the direction of the old strand of DNA. These two strands then join together to form a new double helix.
What are the purine and pyrimidine bases attached to on the nucleotide chains?
Molecules of deoxyribose.
Sickle Cell Anemia
A human genetic disorder caused by a substitution mutation that causes the amino acid valine to replace glutamic acid in the hemoglobin protein; Effects are the hemoglobin molecule is less soluble so the red blood cells take on a sickle (half moon shape), the red blood cells carry less oxygen (anemia), and the Red Blood Cells are more rigid and block and damage capillaries in organs such as the brain, heart, and spleen
What is a karyotype?
a display of homologous chromosomes of a cell organized in relation to their number, size and type
Cloning in Animals
Nucleus of donor cell is inserted into an unfertilized egg cell which has had its nucleus removed
In the case of mammals, the "egg" is transplanted into a third animal for proper development to occur
Issues-something must happen to the nuclear material during aging, b/c cloned animals seem to have problems, such as premature aging
What is a 5' Cap?
Modified guanine nucleotides added to facilitate export from the nucleus, protect the mRNA from hydrolytic enzymes, help ribosomes attach in translation
Meselson and Stahl
Labeled parent DNA with 15N and new nucleotides with 14N. Determined semiconservative model of inheritance.
How is transcription initiation regulated?
DNA controls elements that bind transcription factors. DNA sequences called enhancer regions are bound to the promoter regions called activators and mediator proteins. This transcription initiation complex enhances transcription.
Define inducible enzyme.
It is an enzyme produced in response to inducer.
Nearly all recurrent point mutations are of what type?
Deamination of a methylated cytosine.
What is the 3'-5' strand called during DNA replication?
The lagging strand.
What are the sources of genetic variation in sexual life cycles of animals?
random fertilization, crossing over during meiosis, and independent assortment of chromosomes during meiosis
What happens in transcription?
mRNA is made from the DNA template strand
how such information stored as nucleic acids can be decoded into protien?
couple question address in chpter about gene expression,1. how is genetic information encoded?2. how does the transter from DNA to RNA occur, thus defing the process of transciption?-code are writen in units of three letter-ribonucleotides present in mRNA that reflects the stored information in gene-each triplet code word directs the incorporation of specific amino acid into a protien as it is synthesized.
The discovery of the structure of DNA allowed us to see how genes operate and how DNA can reproduce itself during mitosis. In addition to protein synthesis, what two fields of science did this discovery open?
Biotechnology and genetic engineering.
steps of RNA processing
before the mRNA leaves the nucleus, a 5' cap is addedand a poly-A tail, also some mRNA segments are removed
Post-translational modification: what is glycosylation?
addition of sugar groups to N- or O-
What is the S phase?
The phase within the cell division cycle in which DNA is replicated.
Two plants are crossed, resulting in offspring with a 3:1 ratio for a particular trait. This indicates
that the parents were both heterozygous
What are two types of point mutations?
Point mutations cause single base nucleotide replacement.
1. Base pairing substitution: missense and nonsense: replacement of 1 nucleotide and its complementary base pair in DNA with another pair of nucleotides.
2. Insertions and deletions: additions/losses of nucleotide pairs that cause a frame shift mutation.
what did the mixing of the copolymer Heteropolymers achieved?
Heteropolymer example• Produce RNA with 1A:5C ratio• Insertion of A or C at any particular position is determined by ratio of A:C• Eg., frequecy of AAA = 1/6 * 1/6 * 1/6 =(1/6)3 = 0.4%• Eg., frequency of AAC, ACA, CAA =(1/6)2 * (5/6)= 2.3% eachHeteropolymer example• Next: examine the percentages of incorporation of any given amino acidHeteropolymer example• Next: examine the percentages of incorporation of any given amino acid• Propose what triplet might encode that amino acid• Eg., proline seen 69% of the time: = CCC(57.9%) + 2C1A(11.6%), determines thecomposition of the triplet coding for an amino acid, not the specific sequence of the triplet yet• Next: examine the percentages of incorporation of any given amino acid• Propose what triplet might encode that amino acid• Eg., proline seen 69% of the time: = CCC(57.9%) + 2C1A(11.6%), determines the composition of the triplet coding for an amino acid, not the specific sequence of the triplet yet• Conduct many experiments of this type to work out the code!
What is the study of molecular genetics based on?
The activity of deoxyribonucleic acid (DNA) and how this activity brings about the production of proteins in the cell.
What proteins make up one hemoglobin unit?
2 alpha globins, 2 beta globins
What happens in RNA processing?
Enzymes add a 5' Cap and Poly-A tail. RNA Splicing to get rid of introns.
First evidence of triplet nature of code was discover by what experiment?
• Francis Crick involved in this as well• Insertion & Deletion mutations in T4 bacteriophage• Used intercalating agents, get into the stacked bases of DNA causing insertions or deletions upon replication
What two biochemists proposed a model for the structure of DNA in 1953 and later shared the Nobel Prize for their work in 1962?
James D. Watson and Francis H.C. Crick
What type of enzyme is used to cut up DNA? Where do they cut?
What is a palindrome?
What is the "Central Dogma" of molecular biology?
The flow of information from DNA to protein.
Where does the energy for bonding in replication come from?
Bases arrive as nucleosides with 3 phosphate groups. Release of these phosphate groups provides the energy
operon can be transcribed because it inactivates the repressor protein
So, allolactose is the _______ of the lac operon.
What is the function of ribosomal RNA (rRNA)?
This RNA is used to manufacture ribosomes.
If E. coli is grown with lactose are the enzymes present?
yes, because the the repressor gene will act on the lactose
What two other regions are found in the lac operon?
Is the repressor gene part of the lac operon?
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