Genetics questions

What are the general mechanisms that cells use to maintain stable patterns of gene expression as cells divide?

-A positive feedback loop, mediated by a transcriptional regulator that activates transcription of its own gene in addition to other cell-type specific genes -Faithful propagation of condensed chromatin structures as cells divide -Inheritance of DNA methylation patterns when cells divide

Phosphorylation of RNA Polymerase II

-Allows RNA-processing proteins to assemble on its tail -Capping factors, polyadenylation factors, splicing factors

DNA Methylaion in Eukaryotes

-Appropriate inheritance of DNA methylation patterns involves maintenance methyltransferase -DNA methylation involves a covalent modification of cytosine bases -Methylation of DNA attracts proteins that block gene expression -Form of epigenetic silencing

Terminating Translation

-Binding of release factor to an A-site bearing a stop codon terminates translation -Release factor binding alters activity of peptidyl transferase, causing it to catalyze the addition of H2O instead of an amino acid to peptidyl-tRNA -This releases the carboxyl end of the polypeptide chain from its attachment to the ribosome -The ribosome releases the mRNA and dissociates into its two separate subunits

DNA Duplications

-Can give rise to families of related genes within a cell/organism -A mechanism that can create new genes -May have no effect, or can have a selective advantage or disadvantage -Can occur by crossovers between short, repeated sequences on DNA ex: Single Globin gene gave rise to 4 chain hemoglobin in mammals

Point Mutations

-Cause by failures of the normal mechanisms for copying and repairing DNA -Happen within a gene -Most often have no effect because they don't change the amino acid encoded -Offer a way of fine-tuning a protein's function but can also eliminate a protein's function of drastically alter it

Housekeeping Genes

-Common among all cells -Required for the maintenance of basic cellular function -make ATP, RNA, protein, etc.

Initiation of protein synthesis

-Correct initiation is crucial because it sets the whole reading frame for the whole message -Only the charged initiator tRNA can bind tightly to the small ribosomal subunit -Loaded ribosomal subunit binds to the 5' end of an mRNA molecule signaled by the cap -Small ribosomal subunit moves forward searching for the first AUG

Restriction Enzymes

-Cut DNA at specific sites -Endogenous to bacteria as a defense mechanism -Immune response

Genetic Code Redundancy

-Each codon represents a single amino acid, though some amino acids have more than one codon -20 different amino acids, so some are encoded by more than one codon (redundancy) -No codon specifies more than one amino acid (no ambiguity)

Riboswitches

-Example of post-transcriptional controls -Short RNA sequences in mRNA that change conformation when bound to small molecules -Common in bacteria -Bypasses the need for regulatory proteins

Bacterial Transcription

-Has a promoter sequence that is recognized by a sigma factor in RNA Polymerase -Signal sequences are used to identify the start and end of transcription of bacteria

Ribosome binding sites

-Has one binding site for mRNA and three for tRNA -E-site, P-site, and A-site

Capping and Polyadenylation

-Increase stability of mRNA -Aid in nuclear export -Identify RNA as mRNA -Used as signals in protein synthesis

Introns and Exons

-Introns don't encode for proteins and must be removed -Specific sequences are required for intron removal (splicing) -Small nuclear RNAs are packaged with proteins to form snRNPs that carry out RNA splicing

Point Mutation in a Regulatory Region

-Knock out expression of a gene (if in TATA box) -Less affinity (lower # of RNA made, less protein) -Change temporal control (gene expressed at different times) ex: Lactose Intolerance

Lac operon

-Lac repressor binds when lactose is not present in the cell. -The CAP activator can only bind DNA when is it bound to cAMP. -The Lac operon only produces RNA when lactose is present and glucose is absent. -Even when the CAP activator is bound to DNA, if lactose is not present, the Lac operon will not be transcribed.

RNA Polymerase

-Makes RNA "message" using DNA as template -links ribonucleotides -Can start an RNA chain without a primer

Bacteria and Polycistronic mRNA

-Messenger RNA which encodes two or more proteins

Prokaryotic Translation

-No 5' cap to help in the recognition of the initiation site -Upstream of the AUG is specific ribosome-binding sequences ~6 nucleotides long

Ribosomes

-One of the largest and most complex structures in the cell -Found in the cytoplasm of eukaryotic cells - made of 2/3 RNA and 1/3 protein

Eukaryotic Transcription

-RNA Polymerase II cannot initiate transcription on its own, it needs general transcription factors

Peptidyl Transferase

-RNA in ribosome complex -Uncouples the carboxyl end of the polypeptide from the tRNA at the P-site and joins it by a peptide bound to the free amino group of the amino acid linked to the tRNA in the A-site

RNA splicing

-Spliceosome: complex of RNAs (snRNAs) and proteins (snRNPs) that removes introns

States of Chromatin Structure and Inheritance

-States of chromatin structure can be inherited directly during DNA Replication -Protein added by cooperative binding -Form of epigenetic silencing

Horizontal Gene Transfer

-Transmission of DNA between different genomes -Known to occur between different species -Rare in Eukaryotes -18% of Ecoli genome is due to HGT -Bacteria use a Sex Pilus to transfer genes

The Proteasome

-degrades unwanted proteins in the cytosol -Proteins destined for the proteasome are ubiquinated

Three RNA Polymerases in Eukaryotic Cells

1-Transcribes most rRNA genes 2-Transcribes protein-coding genes, miRNA genes, plus genes for some small RNAs 3-tRNA genes, 5S rRNA gene, genes for many other small RNAs

A-site

1st site of new added codon entry

What is false about gene families?

Because gene duplication can occur whenever crossover events occur, genes are always duplicated onto homologous chromosomes. (Regions of homology between nonhomologous chromosomes will cause gene duplication onto different chromosomes, as well as chromosome rearrangements)

The tryptophan operator ________________.

Binds to the tryptophan repressor when the repressor is bound to tryptophan.

miRNAs

Block mRNA translation, destabilize mRNAs

siRNAs

Block translation /Destabilize mRNAs, Recruit histone-modifying enzymes to DNA, resulting in heterochromatin formation

To be exported, mRNA must be:

Bound by proteins that signal that it has been correctly processed Ready when: -Cap-binding complex -Proteins that mark end of splicing (exon junction complex) -Poly-A-binding proteins

How are codons recognized?

By antiparallel base pairing with the tRNA

piRNAs

Degradation of transposable element mRNA, Facilitate histone modifications that inhibit transposable element transcription

mRNAs are eventually ________ by RNases

Degraded

A single regulatory protein can coordinate the expression of many _________ _____.

Different Genes

RNAi is triggered by the presence of foreign ______ ________ ___ molecules.

Double-stranded RNA

E-site

Ejection site for depleted tRNA

Stable patterns of gene expression can be transmitted to daughter cells

Examples: Hepatocytes (liver cells) produce hepatocytes, and fibroblasts produce fibroblasts -Other cells are terminally differentiated (muscle cells, neurons)

T/F: All mRNAs fold into particular three-dimensional structures that are required for their translation

False

T/F: A ribosome binds one tRNA at a time

False, Multiple tRNAs can be bound at the 3 different sites on the ribosomes.

T/F- Most genes in vertebrates are unique, and only a few genes are members of multigene families.

False. A large proportion of the genes in vertebrates (and many other species) are members of multigene families.

T/F- Horizontal transfer is very rare and thus has had little influence on the genomes of bacteria.

False. By some estimates, 20% of the genomic DNA in some bacterial species arose by horizontal gene transfer.

T/F- To meet challenge or develop a new function, evolution essentially builds from first principles, designing from scratch, to find the best possible solution.

False. Evolution can work only by tinkering with the tools and materials on hand, not by starting from scratch to make completely new genes or pathways. New functions arise from the ancestral functions by a process of gradual mutational change, and thus may not represent the best possible solution to a problem

T/F- Introns and transposons tend to slow the evolution of new genes.

False. Introns and transposons can act as sites where recombinational crossovers occur. Transposons can also catalyze genetic rearrangements. Rearrangements within these sequences are less likely to be detrimental than those occurring elsewhere in the genome.

T/F- Nearly every instance of DNA duplication leads to a new functional gene.

False. Many duplications are subsequently lost or become pseudogenes, and only a few evolve into new genes.

T/F- All highly conserved stretches of DNA in the genome are transcribed into RNA.

False. Many highly conserved stretches of DNA are not transcribed, but instead contain information critical for regulating where and when genes are expressed.

T/F: A mutation that arises in a mothers somatic cell often cause disease in her daughter

False. Only mutations in the germ-line in a mother are inherited by her daughter.

T/F: Because the two strands of DNA are complimentary, the mRNA of a given gene can be synthesized using either strand as template

False. The position of the promoter determines the direction in which transcription proceeds, and therefore which DNA strand is used as the template. Transcription in the opposite direction would produce an mRNA with a completely different/meaningless sequence.

rRNAs

Form the core of the ribosome and catalyze protein synthesis

Homologous Genes

Genes that are similar in their nucleotide sequence because they shared a common ancestor

P-site

Holds the growing polypeptide for addition of a new amino acid

Flavors of Transcription Regulators

Homeodomain -Helix-turn-helix Zinc-finger -alpha-helix & beta sheets Leucine zippers -Bind as dimers

The mediator

Is a complex of proteins that links distantly bound transcription regulators with the proteins bound closer to the transcriptional start site.

RNA in cells differ from DNA in that

It is single-stranded and can fold up into a variety of structures

DNA can be transcribed:

Many times at once

What does the number of protein molecules depend on?

Number depends on how many are made and how many are destroyed

Transcription is controlled by:

Proteins binding to regulatory DNA sequences -Work by controlling initiation of transcription -Can be activators or inhibitors of transcription

MicroRNAs are noncoding RNAs that are incorporated into a protein complex called _____.

RISC

What molecule is thought to have arisen first during evolution, proteins, DNA, or RNA?

RNA

How does RNA differ from DNA?

RNA has/is: -An extra hydroxyl group -Uracil base instead of Thymine -Single stranded

The sigma subunit of bacterial RNA Polymerase:

Recognizes promoter sites in the DNA

miRNAs

Regulate gene expression

RISC

Searches the mRNAs in the cytoplasm for sequence complementary to that of the miRNA. When such a molecule is found, it is then targeted for destruction.

RNA molecules can have extensive _________ __________

Secondary structure -Ability to form different structures is critical for RNA function -Conventional and Nonconventional base-pairing

If you are interested in a single-stranded DNA molecule, what sequence should the probe contain that you are using to hybridize to your sequence of interest?

The complementary sequence

What is true about the genetic code?

The genetic code is redundant

Where does transcription occur?

The nucleus of the cell

The distinct characteristics of different cell types in a multicellular organism are produced mainly by differential regulation of the

Transcription of genes transcribed by RNA Polymerase II

The distinct characteristics of different cell types in a multicellular organism are produced mainly by the differential regulation of the:

Transcription of genes transcribed by RNA Polymerase II

DNA can be introduced into bacteria by a mechanism called:

Transformation

During gel electrophoresis, DNA fragments ___________.

Travel through a matrix containing microscopic network of pores

Double-stranded RNA molecules

Trigger RNAi and are then digested by the dicer enzyme into shorter fragments approximately 23 nucleotide pairs in length.

T/F: A new RNA molecule can begin to be synthesized from a gene before the previous RNA molecules synthesis is completed.

True

T/F- Proteins required for growth, metabolism, and cell division are more highly conserved that those in development and in response to the environment.

True. All organisms need to perform a similar basic set of fundamental functions, such as those for metabolism, protein synthesis, and DNA replication. Proteins involved in these functions are shared by descent, and their evolution is constrained.

T/F-Most mutations and genome alterations have neutral consequences.

True. Most genomic changes do not alter the amino acid sequence of proteins or the regulatory properties of genes. Even some mutations that cause minor alterations have little effect on protein function.

T/F- A pseudogene is very similar to a functional gene but cannot be expressed because of mutations.

True. Pseudogenes look very similar to normal genes but cannot produce a full-length protein, as a result of one or more disabling mutations.

T/F- To find functionally important regions of the genome, it is more useful to compare species whose last common ancestor lived 100 million yrs ago rather than 5 million yrs ago.

True. Species that diverged recently have many identical stretches of DNA sequence by chance, whereas sequence similarity between species that diverged long ago is probably due to functional constraints. The sequences that are necessary to preserve the function of the gene will not be able to undergo changes and thus are more likely to be similar between species that diverged long ago.

What change is very unlikely to arise from a point mutation in a regulatory region of a gene?

A mutation that changes the sub cellular localization of a protein

MyoD

A regulator that controls muscle development -Expression of MyoD causes fibroblasts to become muscle cells -MyoD cannot convert "any" type of cell to muscle

What do differentiated cells contain?

All the genetic instructions to form a complete organism

Histone Acetylases

Alter chromatin by modifying lysine's in the tail of histone proteins to allow greater accessibility to the underlying DNA.

Key regulatory proteins can determine what?

An entire tissue type Ex: Ey (eyeless) in flies

mRNAs

Code for proteins

Aminoacyl-tRNA synthetases

Covalently couple each amnio acid to its appropriate tRNA

tRNAs

Serve as adaptors between mRNA and amino acids during protein synthesis

Double Strand and Transcription

Some genes are transcribed using one DNA strand as a template, and others are transcribed using the other DNA strand

mRNA nucleotide sequence is translated into protein via

The Genetic Code

What is the main reason that a typical eukaryotic gene is able to response to a far greater variety of regulatory signals than a typical prokaryotic gene or operon?

The transcription of a eukaryotic gene can be influenced by proteins that bind far from the promoter.

What region of the genome is least likely to be conserved over evolutionary time?

The upstream regulatory region of a gene that encodes the region conferring tissue specificity