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Biology 1002B - IS & Lecture Outcomes.docx
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Department
Biology
Course
Biology 1002B
Professor
Tom Haffie
Semester
Winter

Description
Biology 1002B - Independent Study Outcomes & Lecture Outcomes Lecture 1: Introducing Bio 1002B and Chlamydomonas Independent Study Outcomes 1. Identify criteria used to measure complexity. Criteria used to measure complexity include:  Genome size or the total number of genes in an organism  Gene (copy) number or the number of copies of a gene in a given gene family resulting from gene duplication  Increase in the size of organisms over the course of evolution  The number of genes that encode proteins  The number of parts or units in an organism (where parts might be segments, organs, tissues, and so forth)  The number of cell types possessed by an organism  Increased compartmentalization, specialization, or subdivision of function over the course of evolution  The number of gene, gene networks or cell-to-cell interactions required to form the parts or an organism  The number of interactions between the parts of an organism, reflecting increasing functional complexity and/or integration over the course of evolution 2. Identify the main structural components of Chlamydomonas cells. Chlamydomonas reinhardtii is a single-celled photosynthetic eukaryote that is commonly found in ponds and lakes. Each cell contains a single large chloroplast that harvests light energy and uses it to make energy-rich molecules through the process of photosynthesis. In addition, each cell contains a light sensor called an eyespot that allows individual cells to gather information about the location and intensity of a light source. Chlamydomonas reinharditii. Each cell contains a single chloroplast used for photosynthesis as well as an eyespot for sensing light in the environment. 3. Identify the relationship between Chlamydomonas and the evolutionary common ancestor of animals and plants. Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella. Chlamydomonas reinhardtii is a ~10-mm, unicellular, soil-dwelling green alga with multiple mitochondria, two anterior flagella for motility and mating, and a chloroplast that houses the photosynthetic apparatus and critical metabolic pathways. Chlamydomonas is used to study eukaryotic photosynthesis because, unlike angiosperms (flowering plants), it grows in the dark on an organic carbon source while maintaining a functional photosynthetic apparatus. It also is a model for explaining eukaryotic flagella and basal body functions and the extreme effects of their dysfunction. The Chlorophytes (green algae, including Chlamydomonas and Ostreococcus) diverged from the Streptophytes (land plants and their close relatives) over a billion years ago. These lineages are part of the green plant lineage (Viridiplantae), which previously diverged from opisthokonts (animals, fungi, and Choanozoa). Many Chlamydomonas genes can be traced to the green plant or plant-animal common ancestor by comparative genomic analyses. Specifically, many Chlamydomonas and angiosperm genes are derived from ancestral green plant genes, including those associated with photosynthesis and plastid function; these are also present in Ostreococcus spp. and the moss Physcomitrella patens. Genes shared by Chlamydomonas and animals are derived from the last plant-animal common ancestor and many of these have been lost in angiosperms, notably those encoding proteins of the eukaryotic flagellum (or cilium) and the associated basal body (or centriole). This analysis of the Chlamydomonas genome sheds light on the nature of the last common ancestor of plants and animals and identifies many cilia (flagellum) and plastid (chloroplast) related genes. Plastid - A double membrane bound organelle involved in the synthesis and storage of food, and is commonly found within the cells of photosynthetic organisms, like plants (chloroplast) Lecture Outcomes Lecture 2: Light Lecture Outcomes Lecture 3: Protein Structure & Function Independent Study Outcomes 1. Basic structure of an amino acid and what are the different classes of amino acids.  An amino acid contains a central carbon bonded to a carboxyl group, an amino group, an r-group, and a hydrogen. The r-group is what varies between the 20 amino acids and gives them unique characteristics. The covalent bonds between amino acids are called peptide bonds. It is a bond between the carboxyl group of one amino acid and the amino group of another amino acid. Amino acids are bonded through condensation reactions, which produces a water molecule. The basic structure of an amino acid is a carbon chain with an amino group (NH ) at one end, and a carboxyl 2 group (-COOH) at the other. The differences between amino acids lies in the carbon chain in the middle; it can be as simple as one carbon or as complex as many carbon atoms with branches and forks. Side groups can be added, such as sulphur.  Each amino acid contains a carboxyl group, an amino group and a variable side group (R). These all connect to a central carbon, termed the α-carbon  Amino acids have a two-carbon bond. On- of the carbons is part of a group called the carboxyl group (COO ). A carboxyl group is made up of one carbon (C) and two oxygen(O) atoms. That carboxyl group has a negative charge, since it is a carboxylic acid (-COOH) that has lost its hydrogen (H) atom. What is left — the carboxyl group — is called a conjugate base. The second carbon is connected to the amino group. Amino means there is an NH gr2up bonded to the carbon atom. In the image, you see a "+" and a "-". Those positive and negative signs are there because, in amino acids, one hydrogen atom moves to the other end of the molecule. An extra "H" gives you a positive charge.  There are basically four different classes of amino acids determined by different side chains: (1) non-polar and neutral, (2) polar and neutral, (3) acidic and polar, (4) basic and polar.  There are four different classes of amino acids: o Nonpolar amino acids o Uncharged polar amino acids o Negatively charged (acidic) polar amino acids o Positively charged (basic) polar amino acids 2. Chemistry of the peptide bond and how it is formed.  Peptide bonds - Chemical bonds that link amino acids in a polypeptide chain.  A peptide bond (amide bond) is a covalent chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, causing the release of a molecule of water (H2O), hence the process is a dehydration synthesis reaction (also known as a condensation reaction), and usually occurs between amino acids. The resulting C(O)NH bond is called a peptide bond, and the resulting molecule is an amide.  A peptide bond is a linkage between the building blocks of proteins called amino acids (shorter strings of linked amino acids are known as peptides). A peptide bond forms when the carboxylic acid group (R-C[O]OH) of one amino acid reacts with the amine group (R-NH ) 2f another. The resulting molecule is an amide with a C–N bond (R-C(O)-NH-R).  Amino acids are linked together in proteins by a special kind of bond, the peptide bond. A peptide bond is a special case of a functional group called the amide group. o 1. First, two amino acids are brought together. The acid group of the first is close to the amine group of the second. o 2. Next, a water molecule is eliminated, leaving a bond between the acid carbon of the first amino acid and the amine nitrogen of the second. o 3. The peptide bond is left between the two amino acids. 3. The four levels of protein structure.  The four levels of proteins are: 1) Primary Structure 2) Secondary Structure 3) Tertiary Structure 4) Quaternary Structure The primary structure is just the amino acids bonded to each other in a linear fashion. Secondary structure is where the alpha-helices, beta-sheets, and b-turns come into play. The tertiary structure is when a single amino acid chain forms a 3D structure. And lastly, the quaternary structure is when 2 or more tertiary structures complex.  Structural features of proteins are usually described at four levels of complexity:  Primary structure: the linear arrangement of amino acids in a protein and the location of covalent linkages such as disulfide bonds between amino acids.  Secondary structure: areas of folding or coiling within a protein; examples include alpha helices and pleated sheets, which are stabilized by hydrogen bonding.  Tertiary structure: the final three-dimensional structure of a protein, which results from a large number of non-covalent interactions between amino acids.  Quaternary structure: non-covalent interactions that bind multiple polypeptides into a single, larger protein. Hemoglobin has quaternary structure due to association of two alpha globin and two beta globin polyproteins. 4. What bonding arrangements give rise to primary, secondary and tertiary structure. 5. How are alpha helices and beta sheets formed. 1) Alpha Helices
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