Study Guide for Lectures 8/24, 8/26, 8/31, and 9/2 Note: It is highly suggested that you reference the figures/figure legends shown in class to further help you understand class material. The Genome Project (~92% complete): • 20,000-28,000 genes in the human genome o The genome was found using a shotgun sequence. o 10% of the genome is Long Intersperse Nuclear Elements (=LINEs). This leaves the questions as to which part of the genome are LINEs? 80,000-120,000 proteins in a cell. 200,000-2,000,000 peptides in a cell. o Ex: Insulin A paper looked at 30% of the genome at 5 nucleotide resolutions and found: In terms of transcripts (mRNA) may not have a poly-A tail. 43.7% of transcripts never had a poly-A tail. 36.9% of transcripts had the poly-A tail removed. 19.4% of transcripts have a poly-A tail. Only 30% of mRNA associated with ribosome had a poly-A tail. Splicing: ~80% of human multi-exon genes have a splice variant. Moonlighting Proteins: term used to describe a protein that has more than one job. Ex: protein used in intermediate metabolism and mRNA destruction. Ornithine 1. 2. 3. 4. Decarboxylase (ODC) Short half-life ODC catalyzes the decarboxylation of Ornithine, which results in a polyamine. Ornithine Decarboxylase Antizyme is a Ornithine Decarboxylase inhibitor. Ornithine Decarboxylase Antizyme expression requires that ribosomes shift from the first open reading frame to a second opening reading frame. This shift is stimulated by polyamines.
Covalent Modifications or Post-Translational Modifications: • There are at least 200 known post-translational modifications. Ex: Phosphorylation
What does water do in a cell? (Panels 2-2; 2-3)
Water solvates proteins. Water forms hydration shells and exerts pressure on protein and lipids. It also helps determine protein structure, because otherwise the protein would unfold. Water and hydrogen bonds give more force. The force changes as it interacts with other molecules on a moment-by-moment basis. Thus, a protein is folding and unfolding, explains kinetics, “breathing” role of water. Water has a polar configuration, not symmetrical.
Even at 37°C, 15% of water molecules join to four others (transition), which gives proteins pressure. Force is caused by hydrogen bonds. Hydrogen bonds have 1/20th covalent bond strength.
Hydrophobic and Hydrophilic: Diabetes and high salt concentrations: each sodium and glucose needs to be solvated by 6 water molecules. If you have too many, you increase blood volume thus blood pressure increases. (Hypertension) Hydrophobic interactions: Proteins can take advantage of hydrophobic interactions; they may have a hydrophobic core, or hydrophilic shell. Electrostatic Attractions:
Weak in water because of the ability of water to enter and have multiple roles. By including or excluding water, the electrostatic interactions can be changed. Ions can also change the ability to interact. Salts can hinder basic processes such as protein synthesis because they change water composition, thus water interacts differently with proteins, thus ultimately can change protein function. o Example: potassium chloride and potassium acetate (salts). GRAPH FROM BOARD. Quantitatively, the same amount of anion, qualitatively, different anion, thus they interact with H2O differently. This is why you see different curves with potassium chloride and potassium acetate. [Rate of translation]
What makes up a cell?
and Precursors (~1%, 250 Types): Intermediate metabolism (energy) Signaling Glycosylated mucopolysaccarides. o Found outside of the heart, sole function is to bind calcium; in terms of cardiac function you have cycling (Calcium enters from t-tubules that surround the heart). Example: Trehalose is a sugar that humans do not produce. Tardigrades and artemia (sea monkeys) can lose up to 99% of bulk water, thus they dry out. They replace lost water with a sugar...