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Lecture 4: "Introductory Biochemistry"

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Biology 1002B
Tom Haffie

Biology Lecture No. 4: Introductory Biochemistry th Wednesday January 17 , 2012 Fundamentals Of Biochemistry: -Regarding the study of biological function, there are two main categories of understanding: protein function and gene function. -Protein function encompasses understanding biological function through isolated cellular components; focused greatly in biochemistry. -Gene function encompasses understanding biological function by using mutants and looking at the organism as a whole; focused greatly in genetics. -The tools of Molecular Biology have considerably narrowed the gap between the fields of genetics and biochemistry. Protein Abundance And The Points Of Control: -Understanding how proteins work helps identify how a cell works. Controlling protein abundance is important in bodily functions. -In order to control protein abundance, one can modulate the transcription of the DNA sequence that codes for that particular protein, modulate the translation of the necessary mRNA sequence, and/or modulate the decay rate of mRNA (post-transcriptional modulation). -An increase in transcription will increase the abundance of mRNA in the cell. Protein abundance is often associated with the activity of the protein however sometimes this is not the case. There are post- translational mechanisms that affect the protein’s abundance. -Protein abundance can be: constitutive expression (protein abundance is not changed; it remains constant), induced expression (protein abundance is changed, it increases over time), repressed expression (protein abundance is changed, it decreases over time). Northern (RNA) Blot Analysis: -A method of measuring abundance of transcription. The procedure begins with individual cell or tissue samples in which their respective RNA is run on an electrophoresis gel (and separated according to size). After transferring the results to a nylon membrane, it is probed with a radioactive “probe” (single- stranded DNA heated up to anneal to an RNA that is its compliment or homologue). The blot is then exposed to X-ray film and the abundance of gene transcription in the samples is observed. -Ribosomal RNA is the most abundant RNA molecule in the cell and it is definitively indicated in the Northern Blot Analysis. Measuring Transcription & Protein Abundance: -The Western Blot analysis is identical in its procedure to the Northern Blot analysis except that it measures protein abundance on an electrophoresis gel and uses anti-bodies as its radioactive probe. Peptides: -Polymers of amino acids. A single amino acid comprises of a carboxylic acid with the central carbon attached to an amino group and a variable R group. -Peptides form from a dehydration synthesis reaction and produce a peptide back-bone (the chain of amino acids that disregards their respective R groups). Amino Acids: -The charge of amino acids is dependent on the quality of their R group. Amino acids can be polar, positively-charged, negatively-charged, or non-polar. -Non-polar amino acids bring about the “Hydrophobic Effect” which is the tendency for amino acids to stay away from the polar aqueous environment and group with themselves instead. Primary Protein Conformation: -Recognizably the simplest structural form of a peptide. A conformation described as a linear sequence of amino acids. Secondary Protein Conformation: -Involves the bonding between atoms of the peptide backbone and hydrogen bonding. Alpha helices and Beta-pleated sheets are distinguishable sub-stru
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