DNA, RNA, and Proteins - AP Biology

When nucleotides bond together and form DNA strands, the first and last nucleotides in the strand have slightly different structures than the rest of the nucleotides between them. On one end of the strand, the nucleotide has an exposed hydroxyl group bound to the third carbon in the carbon ring: this end of the strand is thus called 3'. On the opposite end of the strand, the nucleotide has a phosphate group attached to the 5' carbon in the carbon ring, and is thus called the 5' end. These two groups are exposed because they are used in the bonding of nucleotides to one another to form the strand, but each strand ends with one nucleotide that only is bound on one side: thus, leaving either the hydroxyl or phosphate group exposed (depending on which end you are observing).

These terms are useful because they allow us to discuss the directionality of DNA-related events- if we didn't have terms for directionality the concept would be much more confusing. Example: "DNA polymerase synthesizes the new DNA strand in the 5'-3' direction." Without 3'/5' how would we determine which way the reaction occurs?

DNA and RNA nucleotides are linked together through phosphodiester bonds. A strong covalent bond (ester bond) forms between the 3' carbon atom of the sugar pentose of one nucleotide and a phosphate group, and a second ester bond forms between the phosphate group and the 5' carbon atom of the sugar pentose of another nucleotide. This alternation of sugar and phosphate groups forms a strong backbone and is also the reason why DNA is antiparallel and forms in the 5' to 3' direction.

DNA nucleotides all contain one of four possible nitrogen bases: adenine (A), thymine (T), cytosine (C), or guanine (G). In forming base pairs, an A must always pair with a T and a C must always pair with a G: \[A-T\], \[C-G\]. This means that for any DNA composition, the percent of adenine (A) must be equal to the percent of thymine (T) and, likewise, the percent of cytosine (C) must be equal to the percent of guanine (G). Looking across the answer choices, there is only one choice that satisfies this condition while also correctly summing to 100%. The choice with uracil can be eliminated immediately, since uracil only replaces thymine in RNA and is not present in DNA.

In DNA, guanine pairs with cytosine and adenine pairs with thymine. In RNA, which does not have thymine, adenine pairs with uracil. Thus, if a sample contains guanine, it also contains cytosine. Together, the two make up of the total. The remaining is divided evenly between the paired adenine and thymine molecules, so the DNA sample contains percent each of adenine and thymine. is the correct answer.

DNA and RNA are both made of sugar-phosphate backbones. Ribose is the sugar found in RNA; deoxyribose is the sugar found in DNA. DNA also contains the nucleic acid bases adenine, guanine, cytosine, and thymine. Both DNA and RNA contain phosphate groups as part of the backbone.

This question ultimately hinges on knowing the difference between ribozymes and spliceosomes because transferase, hydrolase, and lyase should all be recognized as proteins that function as enzymes. Transferase catalyzes reactions that facilitate the transfer of functional groups. Hydrolase works to catalyze hydrolysis reactions. Lyase works to catalyze reactions that break down double bonds. Spliceosomes are a unit of proteins and RNA that work to catalyze reactions that splice out introns in RNA to form mature mRNA ready for translation. Ribozymes are important because they also splice RNA into mRNA, but they do not have a protein component to them. The discovery of Ribozymes was a breakthrough in that it was the first evidence that not all enzymes are proteins.

DNA helicase is an enzyme that is able to slip between the two strands of DNA and disrupt the hydrogen bonds that keep the DNA in the double helix structure. This disruption opens up the DNA helix, and exposes sections of DNA that can then be transcribed or replicated. As helicase moves down the double helix, the DNA reforms into a double helix since the enzyme is no longer blocking the hydrogen bonds.

These are all definitive traits of an enzyme. Enzymes are proteins which are extremely helpful in speeding up certain reactions without being depleted by the reactions themselves (as such, they are catalysts for these reactions). Enzymes reduce the amount of energy needed for a reaction to occur, generally because they facilitate reactions by recognizing reactants and bringing them into contact with each other. This occurs when the reactants bind to certain parts of the enzyme (active sites), which causes the enzyme to change shape and bring the reactants into contact with each other (and then the reactants can bind to form the product).

Peptidyl transferase is the enzyme that works in conjunction with tRNA molecules to extend a growing polypeptide chain at the ribosome during translation. Ligase is not used at all in translation, nor is topoisomerase or ATP synthase. tRNA synthetase is used to bind the correct amino acids to corresponding tRNA molecules, but it is not used to extend the polypeptide at the ribosome.

While all the answer choices are important in DNA replication, only DNA Polymerase I performs this particular function. Ligase helps bind the newly replaced DNA nucleotides to the rest of the DNA strand. DNA polymerase III is the main synthesizing enzyme of DNA replication, and creates the majority of the DNA strand. DNA polymerase II is less well known than I and III, but it is believed to perform as a repair enzyme which removes incorrectly paired segments of DNA (which can then be filled back in by DNA polymerase I).

Enzymes have an "optimal temperature," or best temperature that they work at. If that temperature is below or above its optimal temperature, the enzyme will decrease in activity; if the temperature change is great enough, the enzyme could even denature (no longer work).

An enzymes function is to speed up chemical reactions by lowering the activation energy. If our bodies did not have enzymes, the reactions would take place, but too slowly for our cells to adequately function.

The questions is asking how enzymes affect reactions. The function of an enzyme is to speed up chemical reactions, which will increase the overall rate of the reaction, thus "increasing the rate of the reaction" is the correct answer.

The primary structure of a protein is simply the linear amino acid sequence from which the protein is made. "Secondary structure" refers to the folding and coiling of this single strand as it interacts with itself, forming hydrogen bonds between amino acids of that strand. Alpha helices and beta-pleated sheets are two different types of secondary structures that can be formed by hydrogen-bonding between amino acids of a protein sequence that has folded over onto itself. "Tertiary structure" refers to the final three-dimensional structure of a single protein subunit. "Quaternary structure" refers to the non-covalent interactions between multiple protein subunits which come together to form a larger protein.

The three base grouping in RNA that determines the amino acid created in translation is known as a codon. Gene refers to the region on DNA that codes for a given trait. Operators and promoters are also located on DNA, and act as regulatory elements.

Histone acetylation is the process of adding acetyl groups to positively charged lysine groups of histones. This process loosens the histone which allows for an easier initiation of transcription, which will lead to greater gene expression. DNA methylation does the opposite by adding methyl groups to DNA and lowering the rate of transcription. Alternative RNA splicing deals with RNA having certain introns and exons spliced out in a manner that produces different strands of mRNA from the same template strand of RNA. Addition of 5’ Terminal Cap and the addition of 3’ Poly A Tail relate to gene expression in that they both have to do with creating mature mRNA that is ready for translation into protein.

mRNA will be found in both the nucleus and in the cytoplasm because it is transcribed from DNA in the nucleus and then exported to the cytoplasm to go through translation. tRNA will be found in the cytoplasm because it is an integral part of translation in that it delivers amino acids to the ribosome. rRNA will also be found in the cytoplasm because it couples with ribosomal proteins to make up the ribosomes found in the cytoplasm. scRNA is also known as small cytoplasmic RNA and has a function that is still not very well known, but they are mostly only found in the cytoplasm. snRNA, or small nuclear RNA, are only found in the nucleus and are an integral part of splicing introns of RNA so it can go onto becoming mRNA.

tRNA synthetase plays a vital role in translation, but not transcription. tRNA synthetase is the enzyme that binds specific amino acids to corresponding tRNA molecules, and then the tRNA molecules transport the amino acids to the ribosome to create a polypeptide. tRNA molecules are not consumed in this process, and tRNA reserves will not be depleted if tRNA synthetase were non-functional.

Post-transcriptional modification is very beneficial to eukaryotic cells, especially because spliceosomes allow for one primary mRNA transcript to code for multiple different proteins. During this modification, introns are removed from the mRNA transcript, and the exons (remaining segments of mRNA) are shuffled around into the order that creates the protein the cell needs at the moment. While the poly-A tail and methyl cap are also very useful, the poly-A tail is on the 3' end, and the methyl cap is on the 5' end.

A missense mutation is a type of point mutation (single base pair change) that alters the codon to the creation of a different protein.

A silent mutation is also a point mutation with a change in one base pair, but with the resulting strand still coding for the same protein (hence the term "silent").

A nonsense mutation changes a codon from coding for an amino acid to coding for termination of the protein. The protein may or may not still be functional depending on how much of it is terminated when the mutation occurs.

An insertion is a mutation in which one or more base pairs is added to the coding sequence. Unless the insertion is in a multiple of three (preserving the frame because a codon is made up of three base pairs), it results in a "frame shift" that alters the reading frame of the codons to the right, causing it to code for a different set of proteins.

A deletion is another type of frame shift mutation, in which a base pair (or more) is deleted from the coding sequence, altering the reading frame to code for different proteins in many cases. As with insertions, if the deletion is in a multiple of 3, the frame is preserved as each codon consists of 3 base pairs.