ap bio - unit 6 gene expression
What is a promoter?
A sequence of nucleotides on the DNA that designates a start point
What are the three sites found on a ribosome and what is their function?
A site: accepts the incoming tRNA P site: holds the tRNA E site: binds a free tRNA A (aminoacyl) site, which accepts the incoming aminoacylated tRNA; P (peptidyl) site, which holds the tRNA with the nascent peptide chain; and E (exit) site, which holds the deacylated tRNA before it leaves the ribosome.
What are the nucleotide base pairing rules?
A with T and C with G
How do negative regulatory molecule inhibit gene expression?
Blocks RNA polymerase and minimizes gene expression
How is genetic information transmitted from one generation to the next?
DNA is organized in chromosomes which are separated and passed down from the parents through meiosis
How are histones modified to initiate transcription?
DNA loosens so RNA polymerase can get in more easily
Why are RNA primers required for DNA replication?
DNA polymerase can only extend a nucleotide chain, not start one
What is involved in the cell's DNA repair mechanisms
DNA repair, any of several mechanisms by which a cell maintains the integrity of its genetic code. DNA repair ensures the survival of a species by enabling parental DNA to be inherited as faithfully as possible by offspring.
How are histone modified to inhibit transcription?
DNA tightens around histones, RNA polymerase cannot get in
Why can different phenotypes result from different levels of gene expression?
Different tissues will express different genes based on which activators/transcription factors are present in those cell types.
Which direction is the template strand read?
3' to 5' direction
If there is 20% thymine in a DNA strand, how much cytosine is there?
30%
In what direction is DNA synthesized?
5' to 3'
What direction does the DNA polymerase READ the DNA template?
5' to 3'
Which direction does transcription take place (which direction is the RNA synthesized)?
5' to 3'
How does the leading and the lagging strand differ?
Leading: 5' to 3' and continuous Lagging: 3' to 5' and in fragments
How do transcription factors affect the binding at the promoter?
Makes it either easier or harder for RNA polymerase to bind to the promoter
How can a mutation have a positive effect of the product?
May help the organism in response to the environment
What amino acid sequence will be generated, based on the following mRNA codon sequence? 5' AUG-UCU-UCG-UUA-UCC-UUG 3'
Met-Ser-Ser-Leu-Ser-Leu
What is DNA?
Molecule that encodes the genetic instructions used in all known living organisms
What occurs during the process of DNA sequencing
One new sequencing technology involves watching DNA polymerase molecules as they copy DNA - the same molecules that make new copies of DNA in our cells - with a very fast movie camera and microscope, and incorporating different colors of bright dyes, one each for the letters A, T, C and G.
What happens when tryptophan is present for the trp operon?
RNA polymerase is blocked
How is DNA modified to inhibit transcription?
Repressors respond to external stimuli to prevent the binding of activating transcription factors.
How does the genetic code demonstrate common ancestry?
Similarities can be tracked back
What information can be drawn from DNA sequencing
Since the DNA sequence confers information that the cell uses to make RNA molecules and proteins, establishing the sequence of DNA is key for understanding how genomes work
What is siRNA?
Small interfering RNA. They block expression of a gene with the same sequence as the RNA
Why does a purine always pair with a pyrimidine?
So they can form hydrogen bonds and has consistent ratios
Describe the process of DNA replication using the enzymes described above (helicase, topoisomerase, DNA polymerase, primase, RNA primers, and DNA ligase)
The strands of DNA are separated using the helicase, the topoisomerase gets rid of the knots at the replication fork so that the strands can separate, then primers and primase act as a starting point so that the polymerase can add on nucleotides, then the ligase connects the okazaki fragments
Identify two examples of retroviruses
HIV, SIV
How is genetic engineering used to analyze DNA
In many cases genetic engineering through PCR, gel electrophoresis, and recombinant DNA technology, will be used to determine how the gene on the DNA is expressed to cause a specific phenotype in that organism and how we can manipulate that expression in other organisms.
What is the function of bacterial transformation
Incorporation of recombinant plasmids allows bacterial cells to express DNA from other organisms
what are transcription factors?
They are molecule complexes that control which genes are turned on and transcribed to mRNA
How do siRNA and miRNA affect gene expression?
They inhibit gene expression
What is the function of mRNA?
To bring the instructions to make a protein from the nucleus to the ribosome.
What is the function of gel electrophoresis
To separate the DNA bands (fragments) based on size
What is the function of RNA primers and primase?
To serve as a starting for DNA synthesis
True of False: All somatic cells have the same DNA
True
What is the function of PCR?
Used to make copies of DNA fragments, increasing the size of the sample
What is a repressor?
a protein that binds to the operator and prevents transcription
What is a plasmid?
a small, often circular DNA molecule found in bacteria and other cells—separate from chromosomal DNA
What is a codon?
a three-nucleotide sequence that codes for an amino acid
What is an operon?
a unit made up of linked genes that is thought to regulate other genes responsible for protein synthesis.
How can multiple proteins be synthesized from the same mRNA transcription?
alternative splicing - different combinations of exons = different amino acids = different protein
What is the promoter region?
area where RNA polymerase and transcription factors can attach to initiate expression
How does a retrovirus violate the central dogma?
by synthesizing DNA from their RNA genomes, and also by replicating their RNA genomes.
How does the location of translation affect gene expression in a prokaryote?
can be blocked, in cytosol means mRNA can easily be translated bc of their location in cytoplasm
Identify an error in mitosis that leads to a change in phenotype.
cancer due to unregulate division
What is the function of reverse transcriptase?
catalyzing the formation of DNA from a RNA template
How does insertion or deletion affect the protein product?
changes drastically
What are epigenetic changes?
changes in expression of a gene because of the tightness DNA is being wrapped around histones, does not change the sequence
What happens if an insertion or deletion occurs at a nucleotide base pair?
changes the codons for all the following amino acids
How can differential gene expression affect the cellular products?
changes which proteins are being translated and transcribed - different proteins are produced
How is prokaryotic DNA shaped?
circular chromosome without a nuclear membrane
True or false: One codon can code for more than one amino acid
false
True or False: Natural selection acts on genotype
false, phenotype
Where does translation start?
first start codon
What happens in the initiation step of translation?
first tRNA binds to the mRNA start codon methionine and starts the sequence of amino acids
How can differential gene expression affect the cellular functions?
functions change depending on which genes are expressed
How is genetic engineering used to manipulate DNA
genetic engineering is the process of using recombinant DNA technology to alter the genetic makeup of an organism; therefore, you are directly manipulating one or more genes to obtain a desired phenotype
What is horizontal transfer
genetic information transferred from one organism to another unrelated organism
What is the function of rRNA?
help hold ribosomal proteins in place and help locate the beginning and end of the mRNA message. They may also carry out the chemical reaction that joins amino acids together.
Identify two functions of plasmids.
help introduce DNA into cell, delivery vehicle/vectors
What chemical process releases the growing polypeptide?
hydrolysis - Release factors mess with the enzyme that normally forms peptide bonds: they make it add a water molecule to the last amino acid of the chain. This reaction separates the chain from the tRNA, and the newly made protein is released.
How does a genetic change enhance survival
increase variation and likelihood that phenotype changes to a more favorable phenotype for the environment
What is the function of the poly-A tail?
increases mRNA stability in eukaryotes
Is the lac operon repressible or inducible?
inducible
What are the three steps of translation?
initiation, elongation, termination
Identify two bio technical uses for plasmids.
insert DNA into bacteria (genetic engineering), replicate proteins such as human insulin
How does a virus form progeny viruses?
inserted DNA codes for viral progeny when translated
What is the central dogma?
it is a statement that summarizes how information flows in one direction from DNA to RNA to proteins
What information can be drawn from a gel electrophoresis
lengths of DNA segments
How is eukaryotic DNA shaped?
linear chromosomes, in a membrane-bound nucleus
What is the function of the promoter?
location where transcription factors and RNA polymerase bind
what is the function of transcription factors?
mediate the binding of RNA polymerase and the initiation of transcription
What is miRNA?
microRNA (miRNA) regulates gene expression by repressing translation or directing sequence-specific degradation of complementary mRNA
What causes errors in DNA replication
mispairings of a different nature
How can a mutation have a negative effect on the product produced
more detrimental phenotype for the environmental conditions
What happens in the elongation step of translation?
more tRNA bind and add to the polypeptide chain, leaving once their amino acids are attached to the growing chain
How do new phenotypes arise?
mutations
What is the cause of new genetic variation?
mutations
What are other names of the template strand?
noncoding strand
Identify an error in meiosis that leads to a change in phenotype
nondisjunction
How does each types of substitution point mutations affect the protein product?
nonsense prematurely end the protein sequence, missense change one amino acid, silent do not change the sequence at all bc multiple codons can code for one amino acid
How does each types of substitution point mutations affect the amount of the protein product?
nonsense reduce, missense and silent do not
What are regulatory sequences?
nucleic acid segment that can amplify or inhibit expression of a gene (regulate gene)
How does the genotype influence the phenotype?
phenotype expression is the physical reflection of the possible gene combination
How does natural selection affect phenotypes
phenotypes are a combination of genes and environmental influences, natural selection acts on the phenotype, which is the characteristics of the organisms which actually interact with the environment because a specific phenotype could provide a reproductive benefit and become more common in a population
Identify an example of when a bacterial transformation should be done
produce human insulin that is the same as typical human insulin
How does the mRNA, tRNA, and rRNA all interact?
rRNA forms ribosomes which physically move along an mRNA molecule to catalyze the assembly of amino acids into protein chains. They also bind tRNAs and various accessory molecules necessary for protein synthesis.
What is the function of transcription factors?
recognition of sequences within the enhancer and promoter and activation of transcription, and control expression
How is DNA stored?
relaxed form as chromatin in the nucleus
What is the function of topoisomerase?
relieving strain in the DNA ahead of the replication fork
Is the trp operon inducible or repressible?
repressible
Where does translation take place?
ribosomes in the cytoplasm
How can a mutation have a neutral effect on the product produced?
silent, doesn't change the sequence of amino acids
What are the three types of substitution point mutations?
silent, missense, and nonsense mutations
What is the structure of a pyrimidine?
single ring
How does horizontal transfer increase variation
spreads genetic information throughout the community, combining, and creating new variations
What happens in the termination step of translation?
stop codon is reached, no tRNA binds, and polypeptide chain is released
What is transcription?
synthesis of an RNA molecule from a DNA template
What is the function of tRNA?
transfers each amino acid to the ribosome as it is specified by the coded messages in the mRNA.
What is the structure of a purine?
two rings
What is the function of DNA sequencing
used to determine the exact sequence of bases (A, C, G, and T) in a DNA molecule.
How do triploids form
when a haploid cell is fertilized by a diploid cell
What occurs during a bacterial transformation
Addition of CaCl2 and heat shocking are used to induce bacterial cells to pick up recombinant plasmids and express foreign DNA
Which nitrogenous bases are purines?
Adenine and Guanine
How do mutations affect genes?
Alter the gene expression by changing the proteins that are coded for
Why is DNA a better hereditary material than RNA?
DNA is more stable
What occurs during a PCR?
DENATURING: DNA sample is heated so double stranded DNA separates ANNEALING- Sample is cooled allowing DNA primers bind to target sequences on DNA ELONGATION (EXTENSION): "Taq polymerase" enzyme synthesizes two new strands of DNA, using the original strands as templates. The cycle of heating and cooling repeated as many as 30 or 40 times, leading to more than one billion exact copies of the original DNA segment.
What is the primary source of heritable information?
DNA and sometimes RNA
What occurs during gel electrophoresis
DNA fragments are placed in gel, electric current is applied, DNA fragments move through the gel (smallest fragments move fastest); readable pattern of DNA fragments
Describe the process that takes place during transcription
DNA is loosened and split apart to create a template strand and coding strand. The RNA polymerase binds to the template strand and attaches complementary base pairs to the template strand, creating a transcripted mRNA that is a copy of the coding strand
How does the location of translation differ between a prokaryote and a eukaryote?
Eukaryotes: in the cytoplasm or rough er Prokaryotes: in the cytoplasm
What is the function of RNA polymerase?
Enzyme that makes mRNA from DNA during transcription.
What is the enhancer region?
Stretch of DNA that alters gene expression by binding transcription factors.
How does the DNA sequence determine the RNA sequence?
The DNA is the template
How are multiple codons able to code for the same amino acids?
The genetic code is degenerate, meaning that multiple codons can encode a single amino acid because of wobble pairing. Wobble pairing describes how tRNA molecules, each carrying an associated amino acid, can bind through their anticodon to multiple different mRNA codons during translation at the ribosome.
What is cell differentiation?
The process in which cells become specialized.
How is DNA modified to initiate transcription?
The promoter region of DNA opens up so that the RNA polymerase can begin
How does the repressor interact with the promoter?
The repressor protein works by binding to the gene's promoter region, preventing the production of mRNA
What is the TATA box?
a DNA sequence that indicates where a genetic sequence can be read and decoded. It is a type of promoter sequence, which specifies to other molecules where transcription begins.
What is the function of DNA ligase?
connects okazaki fragments
Identify an example of when a gel electrophoresis should be done
crime scene to determine whose DNA sample matches to the DNA at crime scene
How does insertion or deletion affect the amount of the protein product?
depends on if there was a stop codon prematurely or not
Identify an example of when DNA sequencing should be done
determine diagnosis and treatment for specific disease
How is the amount of DNA different between a prokaryote and a eukaryote?
eukaryotes have more because they have more functions to carry out
How does a virus incorporate its viral genome into a host genome?
the RNA of the retrovirus is reverse-transcribed into DNA by reverse transcriptase, then inserted into the host genome by an integrase
Identify three post-transcriptional modifications that alter the pre-mRNA prior to its release from the nucleus
the addition of a 5' cap, the addition of a 3' polyadenylated tail, and RNA splicing
What is the function of the GTP cap?
the cap plays a role in the ribosomal recognition of messenger RNA during translation into a protein
Identify an example of when a PCR should be done
the cloning of gene fragments to analyze genetic diseases, identification of contaminant foreign DNA in a sample, and the amplification of DNA for sequencing
What is differential gene expression?
the expression of different genes by cells with the same genome
How does natural selection affect genotypes
the genotype determines the phenotype, so if the phenotype is connected to the genotype due to a genetic basis, and a specific phenotype is better suited for the environment then that genotype will become more common in the population
What happens when lactose is absent for the lac operon?
the lac repressor binds tightly to the operator, preventing transcription by RNA polymerase
What happens when lactose is present for the lac operon?
the lac repressor loses its ability to bind DNA
What happens when tryptophan is absent?
the repressor protein does not bind to the operator and the genes are transcribed
Which strand is the template strand?
the strand of DNA from the previous DNA
What does it mean if an organism is a triploid
three copies of a chromosome
Which nitrogenous bases are pyrimidines?
thymine and cytosine
What is the function of DNA polymerase?
to add nucleotides to the end of a growing DNA strand
What is the function of RNA splicing?
to remove introns and connect the exons
What is the function of helicase?
to separate DNA strands
