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Posts Tagged ‘biochemistry’

This course is part of a series taught by Kevin Ahern at Oregon State University on General Biochemistry. For more information about online courses go to ecampus.oregonstate.edu 1. An interesting transporter is the Na+/Ca++ exchange pump (not shown in a figure in class, but described). It uses movement of Na+ in to cells to be a driving force for pumping Ca++ out. Remember than Ca++ stimulates muscular contraction. If Ca+ is not pumped OUT, its concentration in muscle cells remains high, stimulating contraction. Digitoxigenin is a compound from foxglove that binds the Na+/K+ ATPase, preventing development of a Na+ gradient. As a consequence, digitoxigenin increases Ca++ concentration, since Ca++ pumping requires a Na+ gradient. Digitoxigenin is used as a heart stimulant. 2. Nerve cells use the gradient of Na+ and K+ built up by the Na+/K+ pump to transmit signals. In nerve transmission, special “gates” open and close to allow Na to diffuse into nerve cells and K to diffuse out of nerve cells. 3. The first step in nerve transmission involves opening of Na+ gates. These allow Na+ to diffuse into the cell, since Na+ concentration is higher outside of cells than inside. Movement of the positively charged sodium ion causes a change in the electrical potential of the cell near the Na+ gate. To compensate for the voltage change, the K+ gates open and Na+ gates close, allowing K+ to flow out of the cell. This results in an overcompensation of the voltage. The K+ gates close and …

“Helicases separate nucleic acid duplexes into their component strands using energy from ATP hydrolysis. The crystal structure of this DNA helicase from bacteriophage T7, reveals an hexagonal arrangement of six identical subunits. Surprisingly, the ring is not sixfold symmetric, but is slightly squished. A model for the mechanism of how the enzyme might work explains this structural asymmetry. Of the six potential ATP binding sites, two opposing ones bind ATP tightly, two are more likely to bind ADP and phosphate, and two are empty. These three states may interconvert in a coordinate fashion as ATP is hydrolyzed, creating a ripple effect that continuously runs around the ring. Because of these conformational changes, the loops that extend into the center hole of the ring—that are proposed to bind DNA—oscillate up and down, as seen in this cross section. The oscillating loops might pull a DNA strand through the central hole, thus unwinding the double helix in the process. A frontal view shows the full dynamics of this fascinating protein machine.”

We have seen how proteins are broken down in order to sequence them. How do we proceed in the reverse direction, from amino acid monomers to polypeptides?

Organic chemistry: Biochemistry. How to draw amino acids. Acid/base properties of amino acids. Finding net charge of amino acids and peptides (proteins) at a specified pH. Zwitterions; finding the pI of amino acids and peptides. Peptide (amide) bonds. Amino acid sequencing with partial digestion by proteolytic enzymes such as trypsin. Total acid hydrolysis (TAH) This is a recording of a tutoring session, posted with the student’s permission. These videos are offered on a “pay-what-you-like” basis. You can pay for the use of the videos at my website: www.freelance-teacher.com For printable documents containing the amino acid table and a problem discussed in this video series, go to my website. For a list of all the available video series, arranged in suggested viewing order, go to my website. For a playlist containing all the videos in this series, click here: www.youtube.com (1) Nucleophilic attack of an amine on a carboxylic acid to form an amide (peptide) bond. How to draw amino acids—alanine, isoleucine (2) Valine, arginine, lysine, glycine, histidine (3) Proline, tyrosine (4) Acid/base properties of amino acids; how to determine net charge of an amino acid at varying pHs (5) Continued (6) Determining the net charge on an amino acid at a specified pH (arginine) (7) Continued. pI of an amino acid (8) Continued (9) Continued (10) Peptides; peptide (amide) bonds (11) Continued. pI of a peptide (12) Continued (13) Continued (histidine) (14) Continued (15) Amino acid …

Organic chemistry: Biochemistry. How to draw amino acids. Acid/base properties of amino acids. Finding net charge of amino acids and peptides (proteins) at a specified pH. Zwitterions; finding the pI of amino acids and peptides. Peptide (amide) bonds. Amino acid sequencing with partial digestion by proteolytic enzymes such as trypsin. Total acid hydrolysis (TAH) This is a recording of a tutoring session, posted with the student’s permission. These videos are offered on a “pay-what-you-like” basis. You can pay for the use of the videos at my website: www.freelance-teacher.com For a printable document containing the amino acid table discussed in this video series, go to my website. For a list of all the available video series, arranged in suggested viewing order, go to my website. For a playlist containing all the videos in this series, click here: www.youtube.com (1) Nucleophilic attack of an amine on a carboxylic acid to form an amide (peptide) bond. How to draw amino acids—alanine, isoleucine (2) Valine, arginine, lysine, glycine, histidine (3) Proline, tyrosine (4) Acid/base properties of amino acids; how to determine net charge of an amino acid at varying pHs (5) Continued (6) Determining the net charge on an amino acid at a specified pH (arginine) (7) Continued. pI of an amino acid (8) Continued (9) Continued (10) Peptides; peptide (amide) bonds (11) Continued. pI of a peptide (12) Continued (13) Continued (histidine) (14) Continued (15) Amino acid sequencing with …

Organic chemistry: Biochemistry. How to draw amino acids. Acid/base properties of amino acids. Finding net charge of amino acids and peptides (proteins) at a specified pH. Zwitterions; finding the pI of amino acids and peptides. Peptide (amide) bonds. Amino acid sequencing with partial digestion by proteolytic enzymes such as trypsin. Total acid hydrolysis (TAH) This is a recording of a tutoring session, posted with the student’s permission. These videos are offered on a “pay-what-you-like” basis. You can pay for the use of the videos at my website: www.freelance-teacher.com For a printable document containing the amino acid table discussed in this video series, go to my website. For a list of all the available video series, arranged in suggested viewing order, go to my website. For a playlist containing all the videos in this series, click here: www.youtube.com (1) Nucleophilic attack of an amine on a carboxylic acid to form an amide (peptide) bond. How to draw amino acids—alanine, isoleucine (2) Valine, arginine, lysine, glycine, histidine (3) Proline, tyrosine (4) Acid/base properties of amino acids; how to determine net charge of an amino acid at varying pHs (5) Continued (6) Determining the net charge on an amino acid at a specified pH (arginine) (7) Continued. pI of an amino acid (8) Continued (9) Continued (10) Peptides; peptide (amide) bonds (11) Continued. pI of a peptide (12) Continued (13) Continued (histidine) (14) Continued (15) Amino acid sequencing with …

Organic chemistry: Biochemistry. How to draw amino acids. Acid/base properties of amino acids. Finding net charge of amino acids and peptides (proteins) at a specified pH. Zwitterions; finding the pI of amino acids and peptides. Peptide (amide) bonds. Amino acid sequencing with partial digestion by proteolytic enzymes such as trypsin. Total acid hydrolysis (TAH) This is a recording of a tutoring session, posted with the student’s permission. These videos are offered on a “pay-what-you-like” basis. You can pay for the use of the videos at my website: www.freelance-teacher.com For a printable document containing the amino acid table discussed in this video series, go to my website. For a list of all the available video series, arranged in suggested viewing order, go to my website. For a playlist containing all the videos in this series, click here: www.youtube.com (1) Nucleophilic attack of an amine on a carboxylic acid to form an amide (peptide) bond. How to draw amino acids—alanine, isoleucine (2) Valine, arginine, lysine, glycine, histidine (3) Proline, tyrosine (4) Acid/base properties of amino acids; how to determine net charge of an amino acid at varying pHs (5) Continued (6) Determining the net charge on an amino acid at a specified pH (arginine) (7) Continued. pI of an amino acid (8) Continued (9) Continued (10) Peptides; peptide (amide) bonds (11) Continued. pI of a peptide (12) Continued (13) Continued (histidine) (14) Continued (15) Amino acid sequencing with …

Organic chemistry: Biochemistry. How to draw amino acids. Acid/base properties of amino acids. Finding net charge of amino acids and peptides (proteins) at a specified pH. Zwitterions; finding the pI of amino acids and peptides. Peptide (amide) bonds. Amino acid sequencing with partial digestion by proteolytic enzymes such as trypsin. Total acid hydrolysis (TAH) This is a recording of a tutoring session, posted with the student’s permission. These videos are offered on a “pay-what-you-like” basis. You can pay for the use of the videos at my website: www.freelance-teacher.com For a printable document containing the amino acid table discussed in this video series, go to my website. For a list of all the available video series, arranged in suggested viewing order, go to my website. For a playlist containing all the videos in this series, click here: www.youtube.com (1) Nucleophilic attack of an amine on a carboxylic acid to form an amide (peptide) bond. How to draw amino acids—alanine, isoleucine (2) Valine, arginine, lysine, glycine, histidine (3) Proline, tyrosine (4) Acid/base properties of amino acids; how to determine net charge of an amino acid at varying pHs (5) Continued (6) Determining the net charge on an amino acid at a specified pH (arginine) (7) Continued. pI of an amino acid (8) Continued (9) Continued (10) Peptides; peptide (amide) bonds (11) Continued. pI of a peptide (12) Continued (13) Continued (histidine) (14) Continued (15) Amino acid sequencing with …

Organic chemistry: Biochemistry. How to draw amino acids. Acid/base properties of amino acids. Finding net charge of amino acids and peptides (proteins) at a specified pH. Zwitterions; finding the pI of amino acids and peptides. Peptide (amide) bonds. Amino acid sequencing with partial digestion by proteolytic enzymes such as trypsin. Total acid hydrolysis (TAH) This is a recording of a tutoring session, posted with the student’s permission. These videos are offered on a “pay-what-you-like” basis. You can pay for the use of the videos at my website: www.freelance-teacher.com For printable documents containing the amino acid table and a problem discussed in this video series, go to my website. For a list of all the available video series, arranged in suggested viewing order, go to my website. For a playlist containing all the videos in this series, click here: www.youtube.com (1) Nucleophilic attack of an amine on a carboxylic acid to form an amide (peptide) bond. How to draw amino acids—alanine, isoleucine (2) Valine, arginine, lysine, glycine, histidine (3) Proline, tyrosine (4) Acid/base properties of amino acids; how to determine net charge of an amino acid at varying pHs (5) Continued (6) Determining the net charge on an amino acid at a specified pH (arginine) (7) Continued. pI of an amino acid (8) Continued (9) Continued (10) Peptides; peptide (amide) bonds (11) Continued. pI of a peptide (12) Continued (13) Continued (histidine) (14) Continued (15) Amino acid …