Chapter 15- Genes and How They Work Flashcards
Which British physician noted that certain diseases seemed to be more prevalent in particular families?
Archibald Garrod
In 1941, a series of experiments by these two scientists at Stanford provided evidence that the DNA of chromosomes acted to specify particular enzymes.
Beadle and Tatum.
In their experiments in Stanford, Beadle and Tatum deliberately set out to create what in chromosomes, which allowed them to verify that they behaved in a Mendelian fashion in crosses.
they deliberately set out to create mutations in chromosomes
What was Beadle and Tatum’s experiment where they deliberately set out to create mutations in chromosomes?
They mutated an organism, Neurospora with Xrays to produce mutants deficient in the synthesis of arginine. The specific defect in each mutant was identified by growing on medium supplemented with intermediates in the biosynthetic pathway for arginine. The enzymes in the pathway can then be correlated with genes on chromosomes.
What was the conclusion that Beadle and Tatum came up with after their experiment
The genes specify the structure of enzymes and that each gene encodes the structure of one enzyme: one gene/ one enzyme hypothesis.
Today, because we now know that many enzymes contain multiple polypeptide subunits, each encoded by a separate gene, the relationship is more commonly referred to as _____________________ hypothesis.
One gene / one polypeptide hypothesis
What is the central dogma of molecular biology.
DNA ==> RNA ==> protein
What is the term used when DNA is copied and an exact copy of the DNA is made into an RNA copy?
Transcription
What is the term used when RNA is used to make protein?
Translation
Since the original formulation of the central dogma, a class of viruses called ____________ was discovered that can convert their RNA genome into a DNA.
retroviruses.
So the central dogma is now modified as:
DNA RNA—-> protein
________________ is the DNA-directed synthesis of RNA by the enzyme RNA polymerase. This process uses the principle of complementarity to use DNA as a template to make RNA>
Transcription.
Because DNA is a double strand and RNA is a single strand, only _________________________ needs to be copied.
only one of the two DNA strands needs to be copied
During transcription of the DNA into a copy RNA, the strand that is copied is called: ____________ strand.
template
During transcription of the DNA into a copy RNA, the strand of DNA not used as a template is called the ________ strand.
coding strand
The ____________ strand has the same sequence as the RNA transcript, except that U (uracil) in the RNA is T (thymine) in the DNA-coding strand.
coding strand. The coding strand of the DNA is also known as the “sense” strand because it has the same “sense” as the RNA.
coding: 5’-TCAGCCGTCAGCT-3’
template: 3’-AGTCGGCAGTCGA-5’
mRNA - 5’UCAGCCGUCAGCU-3’
Translation takes place on _________, the cellular protein-synthesis machinery.
ribosome
___________________ is the intermediate form of the information in DNA that can be transported out of the eukaryotic nucleus to the cytoplasm for ribosomal processing.
messenger RNA (mRNA)
____________________ is the class of RNA found in ribosomes.
Ribosomal RNA (rRNA)
________________ is the intermediary adapter molecule between the mRNA and amino acids.
Transfer RNA (tRNA)
What type of RNA has amino acids covalently attached to one end and an anticodon that can base pair with an mRNA codon at the other end?
tRNA.
Two scientists, Crick & Brenner reasoned that the genetic code most likely consisted of a series of blocks of information called: _____________, corresponding to an amino acid in the encoded protein.
codons
How did Crick and Brenner come up with the hypothesis that there must be 64 different combinations of three codons vs 16?
Because there were 4 bases: G,C,T,A. If there were only 2 bases in each codon, then there could only be 16 different codons (4x4). Since there are 20 amino acids (each one having at least one codon representing it), there has to be 3 bases in each codon: 4x4x4 = 64.
Do the codons have space in between each other or no space?
no space. Codons are unspaced
True or False: in addition to at least one codon representing one amino acid (i.e. some amino acids might have more than one codon, but each codon only codes for one amino acid), there are also 3 codons that signal “stop” and one codon that signals “start.”
True.
3 codons signal stop: UAA, UGA, UAG
1 codon signals start: AUG (which also is the codon for methionine).
The genetic code is _____________________ in almost all organisms.
the same.
Because the code is universal, genes can be transferred from one organism to another and can be successfully expressed in their new host.
Although the genetic code is almost universal in almost all organisms, what two organelles differ in their genetic code?
mitochondria and chloroplast
What enzyme is needed to transcribe RNA from DNA?
RNA polymerase. Eukaryotes have 3 different RNA polymerases.
RNA polymerase II is the one that transcribes the mRNA from the DNA. RNA polymerase III transcribes the tRNA and RNA polymerase I transcribes the rRNA.
______ _________ interact with the RNA polymerase II during the transcription process of a mRNA from DNA and these form an inititiation complex at the promoter region of the DNA.
transcription factors.
After the mRNA is transcribed by the RNA polymerase and before the mRNA leaves the nucleus to go to the cytoplasm there are modifications made to the eukaryotic transcripts what are these modifications?
- Formation of a 5’ cap.
- a 3’ Poly A tail is added. The ekukaryotic transcript is cleaved downstream of a specific site prior to the termination site. A series of
A residues called the 3’ poly A tail is added. - pre-mRNA splicing by splicesome (introns are taken out and exons are spliced together)
The 5’cap protects that 5’ end of the mRNA from degradation and the 3’ tail plays a role in stability of the mRNA by protecting them from degradation.
Non-coding DNA that interrupts the sequence of the gene (intervening sequences) are called ________________ and the coding sequences are called _____________.
introns (noncoding); exons (coding).
What is the splicing organelle that is responsible for the splicing, or removal of introns is called: _____________.
Spliceosome
________________ is the larger complex that is composed of small nuclear ribonucleoprotein particles (snRNPs) and other associated proteins.
Spliceosome
The pre-mRNA splicing occurs where?
It occurs in the nucleus prior to the export of the mRNA to the cytoplasm.
The __________________ is the key organelle in translation, but it also requires the participation of ______________, _________________, and a host of other factors.
ribosome;
mRNA, tRNA
Each amino acid must be attached to a ____________ with the correct anticodon for protein synthesis to proceed.
This covalent attachment is accomplished by the action of activating enzymes called ______________________.
tRNA
aminoacyl-tRNA synthetases.One of these enzymes is present for each of the 20 amino acids. Very specific for each of the 20 amino acids
The tRNA structure is an L-shaped molecule that has two functional ends: the _______________ stem and the ___________ loop.
acceptor stem (ACC - see diagram); anticodon loop.
In tRNA, the acceptor stem is in the ___ end of the molecule. The ______ _________ is attached to this end of the molecule. The anticodon loop is the bottom loop of the cloverleaf structure and it can base pair with codons in ______.
3’ end;
amino acid
mRNA.
___________ is the energy used to attach a specific amino acid to the tRNA using the enzyme __________________.
ATP; aminoacyl tRNA synthetase
The ribosome has multiple tRNA-binding sites. Describe them: P-Site; A-Site; E-Site
P site is the site that binds to the tRNA attached to the growing peptide chain (peptidyl)
A site (aminoacyl) binds to the tRNA caryying the next amino acid to be added.
E site (exit) binds the tRNA that carried the previous amino acid added. This is the exit side.
The process of _______________ is one of the most complex and energy expensive tasks that cells perform.
Translation
In eukaryotes, the initiating amino acid is _________________ (“start” codon is AUG).
methionine
Describe the elongation process during translation.
- Matching tRNA anticodon with mRNA codon.
- Peptide bond formation. Peptidyl trnasferase, located in the large subunit of the ribosome, catalyzes the formation of a peptide bond between the amino group of the amino acid in the A site and the carboxyl group of the growing chain.
- Translocation of the ribosome. After the peptide bond has been formed, the ribosome moves relative to the mRNA and the tRNAs. The ribosome moves down the mRNA in a 5’to 3’ direction, reading successive codons. The tRNAs move through the ribosome in the opposite direction, from the A site to the P site and finally the E site, before they are ejected as empty tRNAs, which can be charged with another amino acid and used again
There is a ____________ __________ that is specifically recognized at the beginning of a polypeptide which is recognizeed by a receptor protein in the endoplasmic reticulum (ER). The binding of the ER receptor to the signal sequence holds the ribosome engaged in translation of the protein on the ER membrane. THis process is called: ___________.
signal sequence;
docking.
Summarize the key points of gene expression.
- The process of gene expression converts information in the genotype into the phenotype.
- A copy of the gene in the form of mRNA is produced by transcription, and the mRNA is used to direct the synthesis of a protein by translation
- Both transcription and translation have 3 components: initiation, elongation, and termination
The production and processing of eukaryotic mRNAs takes place in the _____________, whereas translation takes place in the _____________.
nucleus; cytoplasm
What does heat do to DNA strands?
Breaks the breaks up dna (denatures it) so that one strand fragments can be made
DNA _____ can be made by cutting the DNA with different enzymes, separating the fragments by ______________ and analyzing the resulting patterns.
maps; gel electrophoresis
Once a gene has been cloned, it may be used as a probe to identify the same or a similar gene in DNA isolated from a cell or tissue. This procedure is called: _____________.
Southern blot (named after Edwin Southern who developed the procedure in 1975)
One way to look at and analyze DNA fragment is by analyzing ________ ______ ______ _______ or ________.
restriction fragment length polymorphism or RFLP.
RFLP or ______ ______ _______ ______, can be used to diagnosis certain diseases where there has been a DNA mutation. Name 3 of these diseases.
restriction fragment length polymorphism;
cystic fibrosis, sickle cell anemia, Huntington’s disease.
RFLP is helpful in forensics because DNA is just like a ____________.
fingerprint
What is one process of being able to creating hundreds and thousands of DNA fragments quickly? How does it work?
Polylmerase Chain Reaction (PCR).
Two primers are used that are complementary to the opposite strands of a DNA sequence, oriented toward each other. When DNA polymerase acts on these primers and the sequence of interest, the primers produce complementary strands, each containing the other primer. If this procedure is done cyclically, the result is a large quantity of sequence corresponding to the DNA that lies between the two primers.
PCR has 3 steps.
In the 1st step, the DNA is denatured using what?
In the 2nd step, primers are laid down by ____ ___________. This is heat resistant so it doesn’t denature.
The 3rd step is done with intermediate temperature: ________.
1st step: High temperature
2nd step: Taq Polymerase (from hot springs bacteria; heatloving, so it doesn’t get taq polymerase is not denatured). Taq polymerase can lay down the primer after the heat is turned down.
- synthesis of the strand of DNA
Newer technniques of DNA sequences uses enzymes to sequence the DNA by adding a special terminator chain that can’t add any more amino acid to it. This method uses what?
dideoxynucleotide
(example: ddGTP, ddCTP, ddATP, ddTTP, etc.) By adding this to the end of a chain, you know that it can’t get longer so you can look for these markers in the DNA so you know exactly what fragment of DNA you are looking at.
Point mutations affect a single site in the DNA. There are 4 types. What are they?
- Base substitution - one base is substituted for another. If the new mutated codon encodes the same amino acid, the mutation is “silent.” When the substitution changes an amino acid in a protein, then it’s called a “missense mutation.”
- Nonsense Mutations - When a base is changed such that the transcribed codon is converted to a STOP codon
- Frameshift mutation - Addition or deletion of a single base, which shifts the reading frame in the mRNA downstream of the mutation. Means majority of the protein will be altered
- Triple repeat expansion mutations - A triplet codon is repeated either before or after the original codon. Example: Huntington’s disease
What is the point mutation on a single site in the DNA called when one base is substituted for another but that the same amino acid is coded?
Base substitution - “silent”
What is the point mutation on a single site in the DNA called when one base is substituted for another but that a different amino acid is coded?
Base substitution - “missense mutation”
