Term
| Other than hydrogen, the common elements found in biomolecules can be characterized based on polarity. Give an example of a non-polar element. |
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Definition
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Term
| Give two elements that tend to be polar. |
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Definition
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Term
| Molecules that due to their non-polar nature do not interact with water are called |
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Definition
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Term
| What are the ramifications of the division between hydrophobic and hydrophilic molecules? |
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Definition
| It means that molecules, or parts of molecules, will only interact with a subset of other molecules. Hydrophobic molecules will only interact with other hydrophobic molecules, and not hydrophilic ones, while hydrophilic molecules will only interact with other hydrophilic ones. |
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Term
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Definition
| Isomers are compounds with the same chemical formula (the same number of each element) but different structures. |
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Term
| What do you call a molecule made up of just carbon and hydrogen |
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Definition
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Term
| Describe how the addition of a phosphate group will change the characteristics of a molecule, and the effect this will have on its interactions with other molecules. |
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Definition
| By adding the relatively large, negatively charged moiety, the phosphate group will change both the shape and charge of a molecule. This can have any of several effects on molecular interactions. In changing the shape, it can modify either create a new interaction site or block one. It can create a new hydrophilic interacting surface, or block an existing hydrophilic one. It can also change the electron distribution throughout the molecule, perhaps even breaking bonds, and thereby altering the ability to form non-covalent bonds throughout the molecule. |
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Term
| When two side chains come off the same side of a double bond this is an example of a (cis/trans) isomer? |
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Definition
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Term
| Name two types of biological macromolecules. |
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Definition
| Proteins, carbohydrates, lipids nucleic acids |
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Term
| What is the name for a reaction that links molecules together by removing a water molecule? |
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Definition
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Term
| Describe the basic structure common to all amino acids. |
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Definition
| It consists of an amino group, a central ‘alpha-carbon’ onto which is linked the side chain, and a carboxyl group. |
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Term
| What is the name for a carbohydrate polymer with more than 2 linked sugars? |
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Definition
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Term
| The structure of proteins is characterized on four different levels. Give the name for one of these levels. |
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Definition
| Primary, secondary, tertiary, quaternary |
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Term
| What are the two types of protein secondary structure? |
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Definition
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Term
| What characteristics are shared by lipids? |
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Definition
| They are large and hydrophobic |
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Term
| Describe how a cell tries to fix misfolded proteins. |
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Definition
| Chaperonins locate misfolded proteins through the exposure of hydrophobic domains. It unfolds them, then releases them to allow the protein to attempt again to fold correctly. |
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Term
| Name one type of nucleic acid polymer. |
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Definition
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Term
| Which of the nucleic acid bases are purines? (A,C,G,T,U) |
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Definition
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Term
| What is the structure of a phospholipid? How does this play a role in the structures that they tend to form in a cell? |
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Definition
| A phospholipid will usually consist of a glycerol with two positions occupied by long-chain fatty acids, and one occupied by a phosphate-linked hydrophilic compound. This causes them to have a hydrophilic head attached to long hydrophobic tails. This allows them to form a micelle, sheet or vesicle with the hydrophobic tails facing in, excluding water, while the heads interact with the aqueous environment. |
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Term
| What are the components of a nucleotide? |
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Definition
| Pentose sugar, nitrogenous base, phosphate |
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Term
| Name one manner in which a eukaryotic cell structure differs from that of a prokaryote. |
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Definition
| Has organelles, internal membranes, nucleus, is bigger. |
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Term
| Name the two domains of life that fall within the prokaryotes. |
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Definition
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Term
| What is the technical name for spherical bacteria. |
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Definition
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Term
| You are looking at a sample of bacteria and wish to see the three-dimensional structure of their surface. What type of microscopy would you use? Explain why. |
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Definition
| You would use Scanning Electron Microscopy. Because bacteria are smaller than the wavelength of light, you need to use electron microscopy. Since you are looking at the shape of the surface, rather than looking though the sample, you would use SEM. |
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Term
| What is the general structure of a DNA molecule. |
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Definition
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Term
| Which of the three possible schemes for DNA replication was found to be used (conservative, semiconservative, dispersive)? |
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Definition
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Term
| When we say that DNA strands are antiparallel, what does this mean (be precise)? |
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Definition
| The two strands run in opposite orientations. If one is 5’-3’, the strand with which it is base pairing will run 3’-5’ |
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Term
| Describe how Hershey and Chase demonstrated that DNA was the genetic material? |
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Definition
| They made separate batches of virus with different radionuclides. They used radioactive sulfur to label proteins, and separately used radioactive phosphorus to mark DNA. They allowed the virus to infect cells, then broke the association, and separated the infected cells from the viral coats. They looked to see which radioactivity had been transferred from the coats to the cells. They found that the phosphorus and not the sulfur transferred, indicating that DNA was the transferred genetic material. |
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Term
| Name an enzyme that plays a role in DNA replication. |
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Definition
| Helicase, primase, topoisomerase DNA polymerase I, DAN polymerase III, ligase |
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Term
| Which strand of DNA is replicated discontinuously (leading/lagging)? |
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Definition
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Term
| Explain what primase does, and why its function is necessary for DNA to be replicated. |
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Definition
| Primase is an RNA polymerase that lays down the RNA primer. This is necessary because DNA polymerases can only add nucleotides to the 3’ end of an existing strand, they cannot begin from scratch. The action of primase provides an RNA with a 3’ hydroxyl on which DNA polymerase can begin building DNA. |
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Term
| In what orientation is DNA synthesized? |
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Definition
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Term
| What is the name for the process of making RNA from a DNA template? |
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Definition
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Term
| Which strand of DNA is used as the template by RNA polymerase (coding/template)? |
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Definition
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Term
| Describe the ‘central dogma’ and indicate the name of each step in the processes that it entails. |
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Definition
| The Central Dogma describes the flow of biological information, from DNA to RNA to proteins. This happens through sequential steps of transcription to made RNA from a DNA template, and translation to transfer the information from RNA to protein. |
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Term
| What are the raw materials used by DNA polymerase to build DNA. Be precise and explicit. |
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Definition
| Deoxynuleotide triphosphates, or dNTPs, consisting of dATP, dGTP, dCTP and dTTP. |
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Term
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Definition
| Uses an mRNA to make protein. |
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Term
| The sequences that remain in the mature eukaryotic mRNA after splicing are (exons/introns)? |
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Definition
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Term
| Which amino acid begins all proteins when they are translated? |
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Definition
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Term
| Describe the structure of the ribosome, including makeup, subunit(s) and binding sites. |
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Definition
| The ribosome is comprised of ribosomal RNA, plus associated proteins. It has a large and a small subunit, and has three tRNA binding sites, the amino-acyl (A) site, the peptidyl (P) site, and the exit (E) site. |
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Term
| What molecule provides the energy for translation? |
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Definition
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Term
| A mutation that results in the change of a single amino acid is a (frameshift/missense/nonsense/ silent) mutation. |
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Definition
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Term
| During translation initiation, what are the first components to interact? |
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Definition
| The small subunit of the ribosome binds to the mRNA (at the Shine-Dalgarno sequence in prokaryotes, at the 5’-cap in eukaryotes). |
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Term
| Describe in detail the three steps of translation elongation |
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Definition
| First, new aminoacyl-tRNA are sampled at the A site, and when one that matches the codon is found, a new peptide bond is formed, moving the growing peptide chain from the P-site tRNA to the amino acid linked to the A-site tRNA. Finally translocation shifts the ribosome one codon along the mRNA, relocating the deacylated P-site tRNA to the E site, where it can exit, and shifting the A-site peptidyl tRNA into the P-site, clearing the A-site to allow another round of addition. |
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Term
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Definition
| A set of genes with related function, located within a single transcription unit (producing a single polycistronic mRNA), along with the adjacent sequences that regulate its expression. |
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Term
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Definition
| A mutation that involves an insertion or deletion of at least one nucleotide. The reason the term is non-specific is that if you are comparing two sequences, there is no inherent way to tell which is the ‘original’ and which is the mutant sequence, so you cannot tell if the longer one gained an insertion, or if the shorter suffered a deletion. |
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Term
| A biochemical that interacts with a protein responsible for turning off a bacterial gene is called a (co-repressor/operator/repressor) |
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Definition
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Term
| Explain the advantage bacteria gain from arranging their genes into operons. |
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Definition
It places the expression of all of the proteins/enzymes necessary for a specific cellular pathway or process under the control of a single promoter. This enables coordinated expression, turning them all on or off at the same time with a single switch.
(As an aside, this is also a disadvantage – you automatically make exactly the same number of coding sequences for each protein because they are all on the same mRNA. If a cell gets lucky and finds a batch of material that is already part way along the pathway, it still has to express the entire operon even though it only needs the enzymes at the end of the pathway – it can waste energy.) If one of the enzymes is a homodimer (it has a quaternary structure consisting of two copies of the same polypeptide, then the cell has to figure out a way to make twice as much of that polypeptide fromt eh same number of mRNAs. |
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Term
| Eukaryotes frequently regulate gene expression at steps other than transcription. Name one of these other steps that is regulated. |
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Definition
| A lot of choices here: chromatin compaction, mRNA processing (splicing and poly-adenylation), transport of mRNA from the nucleus to the cytoplasm, mRNA stability/degradation, translation, protein processing, protein stability, protein transport. |
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