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Lecture 3

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Biology 1002B
Tom Haffie

Lecture 3: Protein Structure and Function Independent Study Outcomes: Basic structure of an amino acid and what are the different classes of amino acids. • Proteins are polymers of amino acids 20 amino acids • General structure: central carbon atom attached to amino group (--NH )2 carboxyl group (--COOH), and Hydrogen atom • Remaining R group is 1 of 20 side chains • Referred to as residues • Proteins synthesized from 20 different amino acids • Grouped according to properties of side chains 1. Nonpolar 2. Uncharged polar 3. Negatively Charged (Acidic) polar 4. Positively charged (basic) polar Chemistry of the peptide bond and how it is formed. • Covalent bonds link amino acids into chains called polypeptides • Link is peptide bond formed by dehydration synthesis between –NH 2 group of one amino acid and the –COOH group of a second • N-terminal end has –NH 2 • C-terminal end –COOH • Amino acids added only to the –COOH end of the growing peptide strand • Polypeptide is string of amino acids; protein is specific 3D shape that is required for most functional proteins The four levels of protein structure. • Primary Structure: sequence of amino acids forming polypeptide • Secondary structure: regions of alpha helix, beta strand, or random coil in a polypeptide chain • Tertiary structure: folding of amino acid chain with its secondary structure, into overall 3D shape of a protein • Quaternary structure: polypeptide chains in a protein that is formed from more than one chain What bonding arrangements give rise to primary, secondary and tertiary structure./ How are alpha helices and beta sheets formed. • Primary Structure: complete amino acid sequence, determined by nucleotide sequence of coding region of protein’s corresponding gene. • Secondary Structure: folded structure based on hydrogen bonds between atoms of backbone. o Hydrogen bonds between H atom attached to nitrogen of the backbone and the O attached to one of the carbon atoms of the backbone o Alpha helix:  Formed when hydrogen bonds form between every N—H group of backbone and the C=O group of the amino acid four residues earlier.  Depicted as a cylinder or barrel (F-32) o Beta Sheet:  Formed by side-by-side alignment of beta  Sheet is formed by hydrogen bonds between atoms is each strands o Random coil/loop formation • Tertiary structure: o Four major interactions between R groups that contribute to tertiary structure 1. Ionic bonds 2. Hydrogen bonds 3. Hydrophobic interactions 4. Disulfide bridges Lecture Outcomes: reasons why photosystems have antenna proteins while the eye doesn’t. • Why is there an antenna in photosystem and not photoreceptor? o We don’t want to harvest light in the eye because every photon hits a separate photoreceptor to form an image. In a photosystem must absorb as much energy as possible because that energy is used for growth. points of control for regulation of protein abundance. • Transcription: copying of DNA into messenger RNA mRNA o can regulate transcription of specific genes and alter abundance of mRNA o can measure transcript abundance- how much of the corresponding mRNA do we have? Ex, opsin in chlamy, how much of it is floating in the chlamy cell? How much transcript you have? o Higher transcription = more mRNA, more protein being made! But we are not measuring translation. • Translation: mRNA to protein o can regulate translation to influence protein abundance (using polypeptide sequence of amino acids) • mRNA Decay o Dependent also on how long mRNA stick around- they do not have an infinite life span (some decay within minutes or hours) break down. factors affecting mRNA transcript abundance. • Balance between rates of transcription and rates of decay steps in making a Northern Blot for measuring mRNA transcript abundance. Northern Blot-Single Stranded DNA 1. Isolate total RNA and run on a gel (it is easy) o 97% RNA is ribosomal RNA- giant bands are rRNA o Humans have 20,000 expressed genes (transcripts), but we don’t see mRNA, the only thing that you can detect is the whole RNA in the ribosome. o Prokaryotic ribosomes are different than eukaryotic o We have similar amounts of RNA 2. Transfer gel to nylon membrane (which is much more stable and make it much easier to use!) 3. Radioactive gene-specific “probe” -- to detect the presence of a specific RNA o Label single stranded DNA radioactively and it will hybridize to mRNA corresponding to gene o Radioactive probe (that have a complementary sequence) will stick to membrane exactly where the other complementary sequence is through hydrogen bonds. I need prior information at leat the sequence to put in the probe, otherwise, this cant work.
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