Term
|
Definition
| Chromatin is the complex of DNA, RNA, histones, and nonhistone proteins that make up uncoiled chromosomes, charateristic of the eukaryotic interphase nucleus. |
|
|
Term
| Describe chromatin structures "nucleosomes" |
|
Definition
| In eukaryotes, a nuclear complex consisting of four pairs of histone molecules wrapped byt two turns of a DNA molecule. The major structure associated with the organization of chromatin on the nucleus. |
|
|
Term
| Define: Histone proteins plus associated DNA |
|
Definition
| Positively charged proteins complexed with DNA in the nucleus. They are rich in the basic amino acids arginine and lysine, and function in coiling DNA to form nucleosomes. They package the DNA into the nucleosome. |
|
|
Term
| Difference between euchromatin and heterochromatin in terms of its structure, composition (cytosine methylation of DNA, histone tail modification) and transcriptional activity. |
|
Definition
heterochromatin condenses DNA and transcription is repressed;
euchromatin uncondenses DNA and transcription is possible |
|
|
Term
| Difference between constitutive and facultative heterochomatin and be able to name two places on chromosomes where constitutive heterochromatin is found. |
|
Definition
Constitutive Heterochromatin - heterochromtin in all DNA cells
(ex. centromeres, telomeres)
Facultative Heterochromatin -
heterochromatic in some cells
(ex. X-inactivation)
|
|
|
Term
| Differences between simple sequence DNAs (satellite DNA sequences) and interspersed repeats and the percentage of the human genome that is composed each of these classes of repeated DNA sequences. |
|
Definition
Satellite DNAs or Simple Sequence DNA
short sequences (5-100 bases)
often in very large copy numbers (1000’s)
long tandem arrays of perfect repeats
localized sites on chromosomesnot transcribed
Percentage (About 5-10% of the Human Genome)
Interspersed Repeats
longer sequences (300 - 5000 bases)
copy number variable
not in tandem arrays
repeats are not perfectly identical
dispersed over the chromosomes
sometimes transcribed
Percentage (About 40% of the Human Genome)
|
|
|
Term
|
Definition
| process by which base sequence in DNA is converted into RNA. The enzyme responsible is RNA polymerase. |
|
|
Term
| How was the genetic code deciphered using synthetic mRNAs and in vitro translation. |
|
Definition
|
|
Term
|
Definition
mutations in which a purine is switched with another purine
(A with G)
Or
A pyrimidine is switched with another pyrimidine
(U with C)
Base transition mutations are 5-10 times
More common than base transversions |
|
|
Term
|
Definition
| Base transversions are mutations in which a purine is switched with a pyrimidine or vice versa |
|
|
Term
What is the organization of the genetic code and its important features (degenerate,
universal). |
|
Definition
The Code is degenerate and ordered - protects against point mutations.
Genetic code is Universal
All existing life arose from a common ancestor |
|
|
Term
How the genetic code is organized to protect against the effects
of base-substitution type point mutations at the 3rd and 2nd codon positions? |
|
Definition
Most mutations (base transitions)affecting the 3rd position do not change the amino acid.
Mutations affecting the second position often result in replacing one amino acid with a similar one. |
|
|
Term
| What the start codon is and what amino acid it codes for. |
|
Definition
|
|
Term
| Difference between missense and nonsense mutations. What are their potential effects on the protein that is encoded? |
|
Definition
Missense mutation is a mutation that alters amino acid and thus results in an altercation in the translation product. In a nonsense mutation a mutation creates a nonsense codon.
missense -- changes the meaning of
a codon
nonsense -- converts a codon from
an amino acid to stop |
|
|
Term
| Difference between insertions and deletions. What are their potential effects on the protein that is encoded? |
|
Definition
|
|
Term
What are the requirements of RNA polymerase as an enzyme (template, no primer,
substrate, direction of synthesis, nucleotides used). |
|
Definition
5’ to 3’ synthesis
DNA template
no primer needed |
|
|
Term
| What is a “promoter” is, what does it do? |
|
Definition
| The promoter is a base sequence at the front (5’ end) of a gene that RNA polymerase binds to in order to begin transcription. |
|
|
Term
What are the three steps in the processing of eukaryotic mRNAs and what are their
functions? |
|
Definition
|
|
Term
| Describe how splicing of mRNAs is done by the spliceosome? |
|
Definition
|
|
Term
| Which parts of the intron are important in RNA splicing? |
|
Definition
|
|
Term
| What are the major components of the translation apparatus? What are their roles are in translation? |
|
Definition
|
|
Term
| What is the tRNA charging reaction? What does it do? |
|
Definition
|
|
Term
What is the name of the enzymes
that carry out this reaction? What is their specificity? |
|
Definition
they recognize and join the
correct tRNA with the correct amino acid |
|
|
Term
| Name the three steps in protein synthesis in addition to tRNA charging. |
|
Definition
(chain
initiation, chain elongation, chain termination |
|
|
Term
Explain what happens in chain
initiation. |
|
Definition
| Small subunit binds to mRNA at position of start codon |
|
|
Term
| Explain what happens in chain elongation. |
|
Definition
1. Next charged tRNA
binds to A site
2. Peptide bond is formed
and tRNA shifts from
A site to P site
3. Ribosome slides 3
bases down the mRNA |
|
|
Term
| Explain what happens in chain termination. |
|
Definition
When stop codon is reached, Termination
factors bind, cleave polypeptide from
last tRNA and ribosome mRNA complex
falls apart |
|
|
Term
| Know the experiments done with the fungus Neurospora in which auxotrophic mutants were isolated and characterized and from which it was concluded that each gene contains the information for one polypeptide. |
|
Definition
Beadle & Tatum: Neurospora Mutants
show genes code for enzymes
“one gene --> one enzyme” |
|
|
Term
Explain the modern understanding of the limitations of Beadle
and Tatum’s one gene-one protein concept. |
|
Definition
1. Not all proteins are enzymes.
2. Many proteins have multiple subunits and each subunit is coded for by a separate gene.
3. Not all gene code for proteins, some code for RNAs that are never translated but that are biologically active
RNAs (for example the RNAs in ribosomes and spliceosomes and tRNAs). |
|
|
Term
| Meaning of genetic complementation. |
|
Definition
| it means that the parents each had mutations in different genes coding for enzymes in the pathway for melanin synthesis |
|
|
Term
How are genetic crosses are used to
identify alleles? |
|
Definition
|
|
Term
| Define the pathway for the metabolism of phenylalanine and tyrosine. |
|
Definition
|
|
Term
Identify where the pathway is blocked in the disorders phenylketonuria, albinism, and
alkaptonuria. |
|
Definition
| phenylketonuria-Resuilts from the absense (or a defect in) the enzyme phenylalanine hydroxlase (PAH) alkaptonuria- |
|
|
Term
explain why the genetic block results in the associated
phenotype. |
|
Definition
|
|
Term
Explain using specific examples, why some alleles are recessive, some exhibit
partial dominance, and some are dominant. |
|
Definition
|
|
Term
| Difference between spontaneous and induced mutations. |
|
Definition
Spontaneous Mutations -- due to natural
decomposition of DNA or to mistakes
in replication. frequency ~ 1 mutation per gene
per million cell divisions
Induced Mutations -- Caused by chemicals
or other agents from the environment |
|
|
Term
Difference between somatic and
gametic mutations. |
|
Definition
|
|
Term
| Difference between base substitutions and insertions and deletions. |
|
Definition
|
|
Term
| Name and describe the most common types of spontaneous damage to DNA. |
|
Definition
| cytosine deamination, depurination, and tautomeric shifts |
|
|
Term
Why types of spontaneous damage to DNA result in mutations
if unrepaired and what kinds of mutations each is most likely to lead to? |
|
Definition
Depurination: loss of the base, A or G
5000 per day per cell!
Deamination of Cytosine:
Cytosine to Uracil
converts a C-G pair to T-A
Tautomeric shifts during DNA Replication
can result in abnormal base pairing: T-G
A-C/ base transitions |
|
|
Term
| Identify “induced DNA damage” |
|
Definition
can be caused by alkylating or oxidizing agents, base
analogs, intercalating agents, UV light, and X-rays. Understand that the DNA damage results in mispairing of bases during
DNA replication, or an inability of base pairing, or a broken DNA strand (X-rays). |
|
|
Term
What type of damage each of these
agents causes? |
|
Definition
Alkylating Agents
add CH3 or C2H5 to keto groups
cause depurination and mispairing.
ntercalating Agents - insert into the double helix
and disrupt base pairing
– cause insertions and deletions
UV light -- thymine dimers
insertions, deletions, base substitutions |
|
|
Term
Explain how the organization of the genetic code protects against the effects of
base substitution type mutations. |
|
Definition
|
|
Term
Predict the consequence of base substitutions and insertions/deletions in the
coding regions of a gene, in its promoter, and in its introns. |
|
Definition
|
|
Term
What is expansion of trinucleotide repeats? How this leads to diseases such
as Fragile X syndrome? |
|
Definition
| normal gene contains a repeated trinucleotide mutant alleles have extra copies of the repeat disease is due to expansion of the repeat caused by DNA replication error |
|
|
Term
| 4 types of DNA repair that were discussed in class? |
|
Definition
Base excision
repair, nucleotide excision repair, mismatch repair, and recombination repair. |
|
|
Term
Name the enzymes involved in each repair mechanism and the types of DNA
damage that can be repaired by the mechanism. |
|
Definition
1. Base excision repair
base-specific deglycosylase - removes bad base
AP endonuclease - removes deoxyribose and PO3
DNA Pol I & DNA Ligase - fill in
2. Nucleotide excision repair
uvr genes - recognize and remove damaged site
DNA Pol & ligase - fill in
3. Mismatch repair
mut H,L,S - identify incorrect strand and remove
the mismatch -- depends on DNA methylation
4. Recombination repair
DNA Pol III skips damaged site, creates a gap
recA uses homologous strand to fill in the gap |
|
|
Term
| Inherited defects in DNA repair enzymes result in ________. |
|
Definition
An inherited predisposition to
cancer. |
|
|
Term
What is Xeroderma pigmentosum? What is the underlying genetic defect is in
this disorder? |
|
Definition
defect in nucleotide
excision repair. Seven genes XPA - XPG
susceptibility to skin cancer.
Defective DNA repair enzyme |
|
|
Term
| Why XP leads to extreme susceptibility to UV light-induced skin cancer? |
|
Definition
|
|
Term
| Define Transposable elements. |
|
Definition
| In eukaryotic genes that code for proteins. |
|
|
Term
What is the general structure of a mobile genetic element
(transposable element) as exemplified by bacterial insertion sequences - short inverted
repeats at ends of element and body of element encodes the enzyme "transposase". |
|
Definition
| Insertion Sequences: 1-2 kb long, end with inverted repeats |
|
|
Term
| What occurs when transposable elements move to a new site or leave in the genome? |
|
Definition
It can cause a mutation at that site if they interrupt the sequence of a gene. When they leave a
site the function of an interrupted gene at that site may be restored. |
|
|
Term
| The most important step in the choice of making a protein is? |
|
Definition
| The initiation of transcription by RNA polymerase. |
|
|
Term
| Define regulation of gene expression (in prokaryotes). |
|
Definition
Gene Expression in bacteria is controlled
by regulation of transcription
Regulation involves repressor and activator
proteins that block or help RNA polymerase
binding to the promoter
“Transcription Factors”
Small molecules regulate the activity of
the repressor and activator proteins |
|
|
Term
| Why is gene expression in bacteria(prokaryotes) is primarily regulated? |
|
Definition
to maximize growth
rate and so bacterial gene expression is mainly controlled by small molecules (nutrients)
from the environment. |
|
|
Term
| What is an operon? How they differ from typical monocistronic genes? |
|
Definition
|
|
Term
| Meaning of inducible gene expression. |
|
Definition
Transcription of the lac Operon is induced by lactose
And repressed by glucose |
|
|
Term
|
Definition
Makes B-galactosidase all the
time + or - lactose |
|
|
Term
|
Definition
Cannot make B-galactosidase
in presence of lactose |
|
|
Term
| Describe the regulation of the lac Operon by lactose and glucose. |
|
Definition
Lactose present: lactose (inducer) binds to the repressor protein, which now cannot bind to the operator --- transcription proceeds
Lactose induces (turns on) transcription.
Glucose inhibits transcription |
|
|
Term
Predict the effect of mutations in the lac Operon, the I gene, or the CAP gene on
expression of the lac Operon in the presence of lactose and/or glucose. |
|
Definition
lac Operon is also regulated by glucose
Lactose induces (turns on) transcription.
Glucose inhibits transcription
"Is" mutants are uninducible under all conditions |
|
|
Term
Why binding of the repressor to the operator blocks transcription of the lac
Operon? |
|
Definition
|
|
Term
| How does CAP activate transcription? |
|
Definition
Binding of CAP improves the binding of
RNA polymerase to the promoter
Lac operator sequence is recognized by the
repressor protein |
|
|
Term
State the active sites on the lac
Repressor and the CAP protein. |
|
Definition
|
|
Term
| Define the term “transcription factor”. |
|
Definition
Proteins that bind specific DNA sequences
and facilitate or inhibit the binding of RNA Polymerase |
|
|
Term
| Difference between positive and negative control of gene expression. |
|
Definition
|
|
Term
| Why is gene expression in bacteria(Prokaryotes) is primarily regulated? |
|
Definition
|
|
Term
| In eukaryotes how is the initiation of transcription is regulated? |
|
Definition
| Both through the activity of transcription factors and through the packing of chromatin. |
|
|
Term
| Difference between eukaryotic promoters and prokaryotic promoters. |
|
Definition
Eukaryotic promoters are much larger than prokaryotic promoters and contain
many more sequences that must be bound by specific transcription factors for RNA
polymerase to initiate transcription. This complexity allows for the increased regulation
of gene expression that is necessary in complex multicellular organisms. |
|
|
Term
| Difference between promoters and “enhancers”. |
|
Definition
Promoter: sequences adjacent to transcription start site
contains RNA polymerase binding site.
Enhancers: sequences needed for high level of
transcription can be far from the promoter. |
|
|
Term
|
Definition
| The heavily staining, late-replicating regions of chromosomes taht are prematurely condensed in interphase. Thought to be devoid of structural genes. |
|
|
Term
|
Definition
| True chromatin, or chromosomal regions that are relatively uncoiled during the interphase portion of the cell cycle. These regions contain most of the structural genes. |
|
|
Term
Histone deacetylation and
DNA methylation are involved in? |
|
Definition
| The inactivation of gene expression during differentiation. |
|
|
Term
Explain how steroid hormones activate the expression of specific genes in
specific cells. |
|
Definition
Only certain cells make the hormone receptor and this receptor is a
transcription factor, which when it has bound the hormone will activate the transcription
of specific genes that contain the right DNA sequences in their promoters. |
|
|
Term
| Define cell differentiation. |
|
Definition
Is ultimately the production of different cells that express different transcription factors and thus make a specific set of proteins. Each
differentiated cell type makes a characteristic set of proteins. |
|
|
Term
| In eukaryotes most gene expression is controlled where? |
|
Definition
| At the level of the initiation of transcription. |
|
|
Term
Describe examples in eukaryotes in which mRNA splicing (calcitonin gene
or the tropomyosin gene), mRNA stability (regulation of casein production by the
hormone prolactin), and protein stability (cyclin proteins) are regulated. |
|
Definition
|
|
Term
| What is RNA interference (RNAi)? |
|
Definition
| RNA-induced gene silencing. |
|
|
Term
How can dsRNA block expression of
specific genes? |
|
Definition
dsRNAs are cleaved by
DICER into siRNAs/miRNAs(small regulatory RNAs) |
|
|
Term
|
Definition
| Genes that codes for proteins |
|
|
Term
Describe monocistronic and
polycistronic mRNAs in bacteria. |
|
Definition
monocistronic - one mRNA codes for one protein
polycistronic - one mRNA encodes two or more proteins |
|
|
Term
|
Definition
1) 5' cap added
2) 3' cleavage
3) Addition of PolyA Tail
4) Removal of introns (splicing)/exons ligated
5) Mature mRNA is produced |
|
|
Term
| Where did introns come from??? |
|
Definition
| Self-splicing introns in protozoans |
|
|
Term
| Why did Introns Evolve ??? |
|
Definition
Alternative splicing combines different
exons to make different proteins from
the same gene
Exon shuffling |
|
|
Term
| What happens when splicing goes wrong? |
|
Definition
| Frame shift creates a nonfunctional beta chain (which is degraded) |
|
|
Term
What is the relationship between base
sequence and amino acid sequence? |
|
Definition
|
|
Term
How is the beginning and end of the gene
recognized during transcription? |
|
Definition
|
|
Term
| Steps in Protein Synthesis |
|
Definition
1. tRNA charging
2. Chain initiation
3. Chain elongation
4. Chain termination |
|
|
