Bio check in quiz 9-12

link the different nitrogenous bases to their single letter code and base pairing partners in DNA and RNA

Adenosine (A) bonds with Thymine (T) in DNA and Uracil (U) in RNA. Guanine (G) always binds with cytosine (C) and vise versa

discuss the contributions of Watson

Crick, and Franklin to the discovery of DNA's chemical structure, these three scientists were the first ones to discover that DNA has a double helix structure and the strands are antiparallel to each other. They also discovered the base pairings of the molecule and did all of this through imaging techniques.

sketch the flow of information for the central dogma of molecular biology

DNA is transcribed into RNA, which is translated into proteins

sketch a growing peptide in a ribosome located at a given position of an ORF

and be able to provide its amino acid sequence if given the mRNA sequence and a codon table

sketch the general process of transcription from initiation to elongation to termination

and label the sequences and proteins involved, transcription begins with initiation, in which the ribosome parts bind to the start codon/promoter. This shifts to elongation as the sequence is being read and the amino acid chain is being extended. Lastly it hits termination, in which the terminator sequence signals to the RNA synthetase to stop. All of this can be helped by transcription factors

describe the relationship between: base-pair open reading frame gene chromosome and genome

base pairs are the complementary nucleotides on either strand of DNA. A number of those (multiple of 3) make up an open reading frame, which is the frame that actually codes for the amino acid sequence. The open reading frame plus the promoters, terminator, and any introns and exons that were taken out make up the gene. A number of genes (number can vary) make up the chromosome, all of which taken together make up the genome.

link the processes of codon recognition peptide bond formation and translocation with reference to the E P and A sites of the ribosome

codon recognition happens at the A site, peptide formation happens at the P site, and translocation occurs between each site and at the E section, the tRNA exits the ribosome

relate the genetic code to the theory of evolution

evolution occurs because of random mutations in the sequence of DNA. These random mutations change the codons and thus, amino acids, being created by the sequence. These changes will then be sorted out by survival of the fittest to see which ones are passed down to future generations

explain how a change in a gene's DNA sequence can affect the function of its encoded protein

if a DNAs sequence changes, this leads to the possibility that the encoded amino acid will not be the same due to the different codon that is being coded for. If the new amino acid being coded for has different properties than the original one, it can affect the shape and thus, function of the protein by affecting its primary, secondary, and tertiary structures.

differentiate between the sequences in a gene that are transcribed and translated

in a gene, both the introns and exons are transcribed into an mRNA sequence. However that mRNA sequence then has the introns taken out so that only the exons are actually turned into amino acids

explain how cells identify an open reading frame in an mRNA molecule

in an mRNA molecule, the start is signaled by the start codon, AUG. It is ended by one of the various termination codons, all of which don't code for an amino acid but rather tell the ribosome to break off.

draw out or describe the process and players of translation from initiation through elongation through termination

initiation begins when the initiator tRNA bound to the small ribosomal subunit is scanning along the mRNA strand and comes across the AUG (Start) codon. This then signals for the large ribosomal subunit, and thus elongation begins. Elongation carries on with the APE sections of the ribosome until the stop codon is encountered, in which there is no amino acid to be bound and the ribosome detaches.

explain the difference between introns and exons

introns are spots in the premRNA that are not part of the sequence for amino acids, and are therefore taken out of the premRNA sequence to make mRNA. The exons are the important parts of premRNA and are the sequences that actually code for the amino acids.

differentiate protein-coding vs. regulatory sequences in genetic information

regulatory sequences are throughout the gene and help it get turned on and off. For example, the promoter and termination sequences aren't actually turned into amino acids in the end. The promoter provides space for proteins to bind to and help initiate translation and termination sequences simply tell the cellular machinery to stop the transcription/translation

describe how tRNA is charged with its appropriate amino acid

tRNA is charged with the appropriate amino acid by tRNA synthase, which recognizes the anticodon on the tRNA and binds the correct amino acid. There is a different tRNA for each amino acid, and therefore it is able to make sure to be accurate with its bindings.

describe the roles of RNA polymerase promoter transcription factors in transcription

the RNA polymerase is the machine that is actually creating the new mRNA strand by splitting the DNA and reading the template strand. The promoter is the place that the RNA polymerase initially binds to, and the transcription factors are the ones who escort the RNA polymerase to that site

provide an example of how the genetic code is redundant but not ambiguous

the code is redundant because more than one codon can code for the same amino acid. There are 64 possible nucleotide combinations to make a codon but only 20 amino acids, so there is some overlap. However the code is not ambiguous because each codon can only code for one specific amino acid.

relate the direction of a DNA coding sequence to the direction of the encoded protein

the direction of the DNA coding sequence goes from 5' to 3'. Therefore, when reading a codon, it goes from the 5' end to the 3' end which will code for a certain protein

describe the difference between a purine and pyrimidine base

the essential difference between purine and pyrimidine is the number of rings that each molecule has. Purines A and G have 2 rings while the pyrimidines C T and U have 1 ring

use base-pairing rules to predict where hydrogen bonds will be found between two strands of DNA

the hydrogen bonds between two DNA molecules will be formed between the nitrogenous bases of the nucleotide. There will be 3 formed between G and C and 2 formed between A and T

describe how nucleic acid structure can be used to encode information

the nucleic acid structure can be used to encode information through the number of base pairs that can be attached. There are 4 base pairs, and when reading them in sets of 3, there are more than enough different sequences that can be made to encode for one of the 20 different amino acids to form proteins

calculate the length of a protein based on the length of an open reading frame and vice versa

the open reading frame will be 3 times longer than the protein, as such the protein will be 3 times shorter than the ORF

label phosphodiester linkages between nucleotides and identify the directionality (5' to 3' ends) of nucleic acids

the phosphodiester linkages are the links that make up the backbone of the nucleotide sequence. It occurs between the phosphate group of one nucleotide and the 3' carbon of another nucleotide. The way to tell the directionality is to look for the 5' carbon, which is detached from the main ring. Therefore, if it is on the top of the ring, the ring goes from 5' down to 3'.

relate the term "promoter" to each of the following concepts: 1) DNA structure 2) sequence as information and 3) gene structure

the promoter can be found at the beginning of the gene, it is a sequence of nucleotides that provide a place for the RNA polymerase to bind to

Describe the promoter sequence transcription unit open reading frame (ORF) untranslated regions (UTR) and termination sequence

the promoter sequence is the sequence that tells different proteins to bind there to begin transcription of the gene. The transcription unit is the entirety of the DNA that is being transcribed while the ORF is the specific sequences within the created RNA that code for amino acids. UTRs are the sequences in the transcription unit that aren't actually translated into amino acids. Lastly, the termination sequence is the sequence on the DNA that tells it to stop transcription.

explain how a stop codon is recognized during translation termination

the stop codon is recognized because there is no amino acid that corresponds to it and thus, causes the amino acid chain being formed to break off

relate results of historical experiments to the hypothesis stating that DNA is the hereditary material of life

the two scientists who determined that DNA is hereditary material is Hershey and Chase in their experiment where they used a phage labeled with a radioactive phosphorus for DNA and one labeled with a radioactive sulfur for RNA. They then had them both infect a cell and when they centrifuged out the remains, they found the radioactive phosphorus in the pellet (meaning it had actually went into the cell instead of staying on the outside like the radioactive phosphorus did)

explain what the phrase "the ribosome is a ribozyme" means relative to enzyme catalysis

this phrase is meant to signal that the ribosome is actually an enzyme that catalyzes the peptide bond formation between two amino acids.

relate the function of transcription factors to the regulation of gene expression

transcription factors are the initiators of gene expression. When they are bound to the protein, they signal for the RNA polymerase to begin transcription.