DNA replication and transcription Flashcards
What is northern blotting used to detect for?
RNA
What is western blotting used to detect for?
proteins
What is ELISA used to detect?
proteins
What is southern blotting used to detect?
DNA
Name 2 main roles of transcription factors in eukaryotic organisms
recruiting RNA polymerase
regulating transcription rate
AUG is the start codon found on _____
RNA
Note AUG is not the start codon found on DNA (DNA does not contain uracil); AUG is the start codon on RNA sequences that signifies the start sequence for translation, not transcription
What is a ligand?
- a molecule that binds reversibly to a protein, delivering a signal in the process. In ligand and protein binding, there are no chemical bonds being broken or formed.
- ligands can be thought of as signaling molecules, and can travel through the bloodstream, watery fluids within the organism, or within a cell itself.
- Proteins receiving ligands can be receptors, channels, or the the start of a complex series of intertwined proteins. The protein will undergo a conformational change when bound to a ligand.
Describe the environments of the solvent surrounding DNA, the DNA backbone itself, and the nitrogenous base pairs in terms of hydrophilicity and hydrophobicity?
solvent surrounding DNA = hydrophilic
DNA backbone = hydrophiliic d/t the hydroxyl groups and the phosphate, which allow the DNA to interact with water
DNA nitrogenous base pairs = hydrophobic d/t the nitrogenous bases with many carbon atoms and few polar groups
What is chromosomal amiplification?
when a segment of a chromosome is duplicated
What is translocation?
when recombination occurs between nonhomologous chromosomes, creating gene fusion: where a new gene product is made from parts of two genes that were not previously connected.
What is balanced vs unbalanced translocation?
balanced: where no genetic information is lost
unbalanced: where genetic information is lost or gained
Distinguish between an oncogene and a tumor suppressor gene
oncogene: a gene that can cause cancer when it is mutated or expressed at high levels
tumor suppressors: opposite function in that their deletion or decreased levels of expression can cause cancer
Distinguish between excision repair and post replication repair
excision repair: DNA repair mechanism that occurs before DNA replication
Post-replication repair: DNA repair that occurs during or shortly after DNA replication
The 3’ end of the mRNA (after the stop codon) isn’t translated into protein, but often contains regulatory regions that influence _________ gene expression
post-transcriptional
function of small nuclear RNA (snRNA)
- associate with other proteins to form snRNPs (small nuclear ribonucleic particles) complexes in the spliceosome, and thus are used for splicing the introns out of hRNA (heterogenous nuclear RNA)
- regulation of transcription factors
- maintaining telomeres
the sequence of nucleotides on a chromosome that activates RNA polymerase to begin the process of transcription is called the __1__, and the point where RNA polymerization actually starts is called the ___2___
1) promoter
2) start site
The strand that is actually transcribed (in transcription) is called the _____ strand. Give 3 other names for this strand.
template strand
other names: non-coding, transcribed, or antisense strand
The strand that has the same sequence as the transcript RNA strand (except that it has T instead of U) is called the ____ or ____ strand
coding, or sense strand
In prokaryotes, the AUG start codon will only initiate translation when it is preceeded by a ______ sequence
Shine-Dalgarno
What nitrogenous base(s) makes up the 5’ cap on mRNA
guanine
What nitrogenous(s) bases makes up the ploy A tail on mRNA
adenine
what is a spliceosome?
a complex that performs hnRNA splicing
What is a somatic cell?
any cell in the body other than reproductive/germ cells
what is feedback inhibition?
refers to molecules regulating a process within the cell based on concentration of that molecule. A high concentration of that molecule can enhance one pathway while a low concentration of that molecule can inhibit that pathway, or vice versa i.e. presence of lactose and how it affects the lac operon
positive gene regulation
- a signaling molecule generates a complex that interacts with DNA to increase transcription rates
i. e. the activator increases the affinity that RNA polymerase has for the promoter, thus increase transcription rates
negative gene regulation
refers to signaling molecules that interact with repressor proteins that decrease/inhibit gene expression
True or False: in order to express a gene, the gene must be unwound from its histones
true
(histones must be deacetylated to unwind the DNA so that it can be transcribed)
how does methylation promote gene silencing?
a methyl group binds to cytosine via methyl transferase enzyme
methylation can affect transcription by either physically preventing the binding of transcriptional proteins to the gene, or by attracting additional proteins to that area of the DNA that will cause the DNA to become more condensely wrapped around histones, thus inactivating the transcription of those genes because those genes cannot be accessed by transcriptional proteins
what is gene expression?
refers to the ability of taking information on DNA to produce a product (proteins, rRNA, tRNA, etc.)
Distinguish between the function of a repressor protein and activator proteins
repressor proteins inhibit transcription
activator proteins enhance transcription
Where is snRNA found?
in the nucleus
-note that snRNA performs splicing of the hnRNA to make mRNA, and splicing occurs in the nucleus
Are gene products always proteins?
No. tRNA, rRNA, and snRNA genes are not polypeptides; they’re made of RNA
Function of DNA gyrase?
enzyme used to supercoil and condense the prokaryotic genome; uses ATP to cut the DNA and twist the 2 sides of the circle around each other
Eukaryotic DNA is wrapped around an octamer of ______ to make beads of nucleosomes
histones
the string between the histone beads in eukaryotic DNA is bound by a single _____ histone
linker
When stained, darker regions of DNA are called ______, whereas lighter regions of DNA are called _____
heterochromatin, euchromatin
centromeres are made of heterochromatin and ____ DNA sequences
repetitive
Where are the centromeres located in the following types of chromatin?
1) metacentric
2) submetacentric and acrocentric
3) telocentric
1) middle so that each chromatin arms are the same size
2) between middle and end so that each chromatin has both p (short) and q (long arms)
3) end so that each chromatin only has 1 long arm (hence no short arms)
Why aren’t telomeres found in prokaryotic DNA?
because prok. DNA is circular
What’s the common repeating unit of telomeres in many vertebrates, inc. humans and mice?
5’-TTAGGG-3’
What are intergenic regions of DNA?
noncoding DNA
-note that this DNA may direct the assembly of specific chromatin structures and contribute to the regulation of nearby genes, but they themselves have no known function
What is a gene?
a DNA sequence that codes a gene product
-aka coding DNA
What are single nucleotide polymorphisms (SNPs)?
refers to single nucleotide changes across members of the same species, which ultimately results in various mutations and gene differences
- most are found in noncoding regions
- SNPs found in coding regions can lead to specific traits and phenotypes i.e. something might taste bitter to one person but not to another