BMB 251 1st EditionExam # 2 Study Guide Lectures: 9 - 17Problem Set Three Review/Answers- Resolution is the minimum distinguishable distance needed between two objects to be seen as distinct from one another; depends on the wavelength of light usedo Light is around 400 nm whereas electrons are about 1 nm, electron microscopy has a higher resolution and more can be seen by using these microscopes- Contrast: has to do with how the light is passed through the microscope (bright vs.. dark-field microscopy) o This uses - Fluorescent molecules absorb light at one wavelength and emit it at a longer one, which then lights up and shows against a dark background- GFP is isolated from jellyfish and then used as tags in fluorescent microscopy  can be fused with proteins wile they remain functioning in a living cell- Deconvolution: mathematical method of reducing fluorescent noise; uses point-spread function. Functions out noise by putting wavelengths of light into computer and using math.- Confocal microscopy: method for reducing fluorescent noise optically; pinpointing light onto sample through use of fluorescence - Light microscopy: Electron microscopy:Lower resolution Higher resolutionSpecies must be fixed, dried and stainedSpecies must be fixed, dried and stainedCan use living organism samples Put into a vacuum; samples are deadUses slices of substance to be studied Must be cut into extremely small slices Thinly sliced so it transmits light Can see actual macromoleculesStained so it’s seen in bright-field Very detailed surface view of sampleBright vs. dark-field microscopy TEM vs. SEMGlass condenser lens Magnetic field condenser lensMust have a light source Heavy metals are added to sample- Noncovalent bonds lead to successful binding between proteins and ligands- Enzymes can be catalysts, which lower the activation energy and make it easier for a reaction to occur (less of an energy barrier to jump over). This successfully speeds up a chemical reaction.- Conenzymes are smaller molecules than enzymes, which attach to it and complete the parts of the cellular reaction that amino acids alone cannot; conezymes cannot be synthesized inside the body, so they are usually obtained through diet (ex. Biotin is a vitamin that humans can take)- Allostery is defined as using a small molecule to control the activity of a protein; this protein can therefore adopt two or more slightly different conformations and can shift from one the other due to a certain ligand binding onto it (resembling an on/off switch).- Positive allosteric regulation (aka cofactor): enzyme regulator that is needed to bind in the allosteric site in order for the reaction to occur- Negative allosteric regulation (aka inhibitor): an enzyme created later along in the reaction binds to an earlier allosteric site in the system and stops reaction from proceeding any further- Kinase: phosphorylates; catalyzes the protein phosphorylation (adding a PO4 group to a protein)- Phosphatase: dephosphorylates; catalyzes the reverse reaction where a PO4 group is removed from the protein molecule- A protein can be active with or without adding a PO4 group, and therefore the addition of a PO4 is not always necessary to activate the protein. Adding a phosphate means adding a charge group through covalent bonds, which can either activate or inhibit the activity of the protein.- Adding an acetyl (negative charge) changes the lysine (positive charge) to a neutral side chain, which can cause problems with DNA binding. On the other hand, if a methyl is added, the side chain will remain positively charged, but will have a different conformation, which affects the binding capabilities of the active site.- The binding site is where G proteins will dissociate from GDP and bind to form GTP. The G proteins are also known as GTPases, which hydrolyze GTP into GDP.------------- - DNA is considered antiparallel becausetheir 3’ and 5’ sides run opposite to each otherin order for complementary base pairingbetween two strands to occur- Guanine forms three H-bonds with cytosine andadenine forms two H-bonds with thymine; inRNA, thymine is replaced with uracil, and souracil will form two H-bonds with adenine. Aand G are purines, which means they contain a6-ring carbon base with a 5-ring structureattached to it. T, C, and U are pyrimidines, whichmeans they contain just a 6-ring carbon.- PO4 groups link 5’ and 3’ carbons on nucleotides together, and there is a hydroxyl group bound to the 2’ carbon in RNA and a hydrogen atom bound the 2’ carbon in DNA- 5’ and 3’ carbons are connected by phosphodiester bonds.- The backbone of each strand of DNA/RNA is linked together via phosphodiester bonds. The bondthat links the base onto a ribose is called the N-glycosidic bond.- Nuclear envelope: double membrane (containing two bilayers) surrounding the nucleus; consistsof an outer and inner membrane and contains nuclear pores. The outer membrane continues into the endoplasmic reticulum. This structure delimits and secludes nucleus/genetic info from the cytoplasm and the rest of the cell.Problem Set Four Review/Answers - Nucleolus: most visible part of nucleus; structure in which rRNA is transcribed into ribosomes and the ribosomal subunits are assembled- Nuclear pore: structures positioned at certain distances along the nuclear envelope; aqueous channel through the nuclear envelope that allows selected molecules to move between nucleus and cytoplasm- Three DNA structures in chromosomes required for inheritance of DNA:o Centromeres: holds the sister chromatids together following DNA replication in the S-phase of the cell cycle under they are ready to break apart during metaphase in mitosis. Site on the DNA where the kinetochores are formed which attach to the microtubules from the mitotic spindleo Telomeres: the end of a chromosome which protects it from being mistaken for damaged DNA in need of repair; has a characteristic G-rich repetitive DNA sequence which has its own special replication process. These keep the chromosome from shortening with every cell divisiono Origins of Replication: site in DNA where replication begins; one site in prokaryotes and multiple sites in eukaryotes to complete the process of replication rapidly and efficiently.- Histones are the most abundant protein in chromatin- A nucleosome consists of a octameric histone core molecule (containing 2H2A’s, 2H2B’s, 2H3’s and 2H4’s) which each have their