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#4 BB 350 Amino Acids - Kevin Ahern's Biochemistry Online
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#4 BB 350 Amino Acids - Kevin Ahern's Biochemistry Online

Introduction and Overview How's the Week Going?

Class Updates

  • The speaker opens with a light-hearted comment about potentially losing their voice but reassures students not to worry.
  • Students are encouraged to download the textbook, which will eventually be available in an iPad format, although it may take time to finalize.

Transition to Amino Acids

  • The focus of today's lecture is on amino acids, which are essential for understanding proteins—the workhorses of the cell.
  • Discussion will cover amino acid properties, particularly ionization and how protonation affects charge.

Understanding Amino Acids Properties and Structure

Basic Concepts

  • Introduction to peptide bonds formed when two amino acids join together.
  • Biochemists simplify stereoisomeric considerations; only basic knowledge of D and L forms is expected from students.

Structural Details

  • Explanation of d-glyceraldehyde and l-glyceraldehyde as examples of stereoisomers in three-dimensional space.
  • A schematic representation illustrates all amino acids, highlighting the alpha carbon that connects four different groups: hydrogen, amine group, R group (variable), and carboxyl group.

Diversity Among Amino Acids

Key Characteristics

  • All 20 standard amino acids can be represented by the alpha carbon structure; differences arise primarily from variations in the R group.
  • Glycine is noted as unique because its R group is simply a hydrogen atom, making it non-asymmetric.

Conclusion on Amino Acids

  • There are 20 primary amino acids that form proteins in biology; a mention of a potential twenty-first amino acid indicates further discussion later in the term.

Understanding Amino Acids and Their Configurations

Commonality of Amino Acids Across Life Forms

  • All living organisms utilize the same 20 amino acids to construct proteins, including bacteria, yeast, dogs, and cats.
  • These amino acids are exclusively in the L configuration; biological processes favor this form over the D form typically produced in chemical synthesis.
  • The specificity for L amino acids is due to enzymes that create them with distinct three-dimensional configurations, establishing a universal language for protein synthesis.

Biological Interactions and Exceptions

  • The ability of different life forms to consume each other is facilitated by the shared use of L amino acids, promoting interspecies interactions.
  • There are rare exceptions where D amino acids exist in biology, often as a defense mechanism employed by certain organisms.

Categorization of Amino Acids

  • It’s essential to know the names of all 20 amino acids and their categories rather than memorizing their structures.
  • Amino acids can be categorized into four groups: hydrophobic (nonpolar), polar, charged (acidic or basic), and special cases. Different texts may use varying categorizations.

Hydrophobic Amino Acids

  • Nonpolar amino acids do not ionize or form hydrogen bonds; they are hydrophobic and dislike water.
  • Leucine is an example of a hydrophobic amino acid characterized by its R group that lacks functional groups capable of forming hydrogen bonds.

Unique Characteristics of Proline

  • Proline has a unique structure where its R group connects back to the alpha amine group, making it distinct from other amino acids.
  • This ring structure limits flexibility compared to other amino acids; proline is considered the least flexible due to this characteristic.
  • Understanding proline's inflexibility is crucial as it influences protein folding and structural integrity within proteins.

Amino Acids and Their Properties

Hydrophobic Amino Acids

  • Valine is similar to leucine, both having hydrophobic side chains. Glycine is categorized with hydrophobics but doesn't fit well due to its unique hydrogen atom.
  • Methionine contains sulfur in its side chain, making it an unusual hydrophobic amino acid. It’s one of two amino acids that contain sulfur.
  • The sulfur in methionine is bound to two carbons, rendering it relatively unreactive compared to other sulfur-containing compounds.

Polar Amino Acids

  • Isoleucine is related to leucine through a rearrangement of carbon atoms off the alpha carbon.
  • Polar amino acids like serine form hydrogen bonds with water due to their hydroxyl groups, enhancing their hydrophilicity.
  • Asparagine features an amide group that readily forms hydrogen bonds with water, contributing to its polar nature.
  • Glutamine shares similarities with asparagine and also has a carboxy amide that facilitates hydrogen bonding with water.

Unique Characteristics of Cysteine

  • Cysteine is another sulfur-containing amino acid characterized by a thiol (SH) group, which has reactive properties important for protein stability.
  • The SH group can ionize and act as a weak acid, leading to the formation of S⁻ ions in solution.
  • Cysteine can combine with another cysteine's SH group to form disulfide bonds, crucial for stabilizing protein structures.

Ionizable Amino Acids

  • Aspartic acid contains an additional carboxyl group in its R group, allowing it to act as a weak acid and ionize similarly to the alpha carboxyl group.
  • When aspartic acid loses protons from either carboxyl group, it becomes negatively charged (co⁻), indicating its polar nature while also being classified as an ion.
  • Glutamic acid mirrors aspartic acid's structure and behavior regarding ionization due to its extra carboxyl functional group.

This structured overview captures key insights into the properties and classifications of various amino acids discussed in the transcript.

Understanding Amino Acids and Their Ionization

Ionization of Amino Acids

  • The amine groups in amino acids can ionize, specifically the alpha amines, which behave differently than carboxyl groups. They ionize by gaining an extra proton.
  • When an amine group gains a proton, it changes from NH₂ to NH₃⁺. Conversely, when it loses this proton, it transitions from a +1 charge (NH₃⁺) to a neutral state (NH₂).
  • There are two possible states for an amine: with one proton (+1 charge) or without any protons (neutral). In contrast, carboxyl groups can exist in states of 0 or -1 charge.

Basic vs Acidic Groups

  • The term "basic" is used here to categorize amino acids with amine-containing R groups. This terminology is reluctantly adopted as the speaker prefers not to use "base" unless referring to strong bases.
  • An R group with an extra proton carries a +1 charge; upon losing that proton, it becomes neutral. Histidine is highlighted as one of three amino acids categorized as basic.

Categories of Amino Acids

  • Four categories of amino acids are discussed: hydrophobic (water-repelling), hydrophilic/polar (water-attracting), acidic (can lose protons from carboxyl groups), and basic (contain amines).
  • Cysteine is noted for its ability to lose a proton but falls under the polar category rather than acidic. Understanding these categories is crucial for calculating protein charges.

Importance of Ionizable Groups

  • Six key amino acids possess R groups that can ionize: three basic ones—histidine, lysine, arginine—and two acidic ones—aspartic acid and glutamic acid. Cysteine also has polar characteristics.
  • Recognizing which amino acids have ionizable R groups is essential for determining protein charges later on in biochemical studies.

Lighthearted Interlude

  • A humorous anecdote about "Artie the hitman" serves as comic relief during the lecture. It illustrates how humor can be integrated into educational settings despite serious topics being discussed.

This structured summary provides insights into the complex topic of amino acid ionization while maintaining clarity and engagement through organized headings and bullet points linked directly to timestamps for easy reference.

Understanding Amino Acids and Their Ionization

Class Policies on Abbreviations

  • The instructor emphasizes that students are not required to memorize abbreviations for amino acids but must use exact forms if they choose to abbreviate.
  • There are 20 naturally occurring amino acids in proteins, with some modified post-insertion into proteins.

Modifications and Derivatives of Amino Acids

  • Hydroxyproline and hydroxylysine are examples of amino acids modified by enzymes after being incorporated into proteins.
  • Serotonin, derived from tryptophan, is mentioned as a hormone involved in sleep; the myth about turkey causing drowsiness due to its tryptophan content is discussed.
  • Dopamine, made from tyrosine, serves as a neurotransmitter associated with happiness and is a precursor to epinephrine (adrenaline), which can enhance physical performance in emergencies.

Ionization of Amino Acids

  • The discussion shifts towards the ionization properties of amino acids, starting with their basic structure including alpha carboxyl and amine groups.
  • At low pH, an amino acid carries a net charge of +1 due to both functional groups being protonated.

Titration Curves and pKa Values

  • A titration curve illustrates how the charge changes as protons are removed; flattening points correspond to pKa values where protons dissociate.
  • Carboxyl groups typically have a pKa around 2.2 while amine groups have a pKa around 9.5; understanding these values helps predict which group loses protons first during titration.

Zwitterions and Charge States

  • As pH increases, the carboxyl group loses its proton first leading to zwitterion formation—a molecule with both positive and negative charges that sum to zero.
  • Further increasing pH results in the loss of another proton, resulting in an overall negative charge for the amino acid at high pH levels.

Plotting Ionization Changes

  • The plot representing ionization shows initial conditions at low pH where all protons are present; it highlights confusion regarding half-off states during titration.

Understanding Zwitterions and pH in Amino Acids

The Concept of Zwitterions

  • The discussion begins with the formation of zwitterions from a solution containing half salt and half acid, highlighting that only certain species exist as zwitterions.
  • As pH increases, the speaker notes the transition into another buffering region where both salt and acid are present, prompting questions about their differentiation.
  • The distinction between acids and salts is clarified: acids have more protons while salts have fewer, depending on the system being analyzed.

Proton Release and Acid Strength

  • The process of proton release is described as occurring one at a time; this leads to a charge of -1 when fully deprotonated.
  • A question arises regarding why carboxylic acids lose protons before amines; it’s explained that this is due to differing pKa values which indicate acid strength.
  • The speaker expresses discomfort with labeling amine groups as basic since they can also act as weak acids by donating protons.

Defining Isoelectric Point (pI)

  • The definition of pI is introduced: it is the pH at which a molecule has an exact charge of zero. This concept will be elaborated upon later.
  • Isoelectric refers to having no charge; understanding this term helps clarify discussions around amino acids in proteins.

Charge Estimation Techniques

  • It’s noted that most protein charges come from R groups rather than alpha carboxyl or amine groups, emphasizing practical shortcuts for estimating protonation states.
  • A rule about buffering related to pKa is established: if within ±1 unit of pKa, buffering occurs. This aids in determining whether protons are on or off based on pH levels.

Practical Applications in Charge Calculation

  • Simplified rules for estimating molecular charge based on pH relative to pKa are discussed. If below the range, protons remain attached; if above, they detach.
  • An example illustrates how to determine approximate charges at specific pH levels using known pKa values for alpha carboxyl and amine groups.
  • Further examples demonstrate how varying pH affects molecular charge, reinforcing that precise calculations yield exact points like the isoelectric point (pI).

This structured overview captures key concepts discussed in relation to zwitterions, proton behavior in amino acids, and methods for calculating charges based on environmental conditions such as pH.

Understanding the Isoelectric Point and Its Calculation

The Concept of Isoelectric Point (pI)

  • The isoelectric point (pI) is introduced as a critical concept, emphasizing that it represents the average of two specific values related to amino acids.
  • A caution against averaging multiple values indiscriminately is highlighted; students are advised not to simply average three different points when calculating pI.
  • The instructor expresses a desire for the class to collectively avoid incorrect averaging methods during exams, hinting at potential rewards for compliance.

Engaging Students in Learning

  • The instructor humorously engages with students by suggesting they could come up with creative ideas for incentives or challenges related to their learning process.
  • A personal anecdote about hair dyeing serves as a light-hearted way to connect with students and encourage participation in discussions about learning strategies.

Calculating the Isoelectric Point

  • To calculate pI accurately when dealing with three regions, it's essential to focus on the two surrounding points around the zwitterion rather than averaging all three indiscriminately.
  • An interactive approach is suggested where if one student makes an error, it could lead to consequences for everyone, reinforcing collective responsibility in learning.

Song of the Day: Amino Acids Overview

  • A fun segment introduces a song that lists various amino acids and their properties, aiming to make memorization easier through music.
  • Key characteristics of amino acids are mentioned, including basic ones like lysine and arginine, alongside structural features such as side chains and functional groups.
Video description

1. Contact Kevin at tubs_quota0s@icloud.com 2. Kevin's lectures with The Great Courses - https://www.thegreatcoursesplus.com/biochemistry-and-molecular-biology-how-life-works?tn=Expert_tray_Course_1_0_12943 3. Kevin's Lecturio videos for medical students - https://www.lecturio.com/medical-courses/biochemistry.course 4. Course materials at https://kevingahern.com/biochemistry-resources/ 5. Course video channel at https://www.youtube.com/watch?v=83eElQinqCI&list=PL74ED4174166F94A8 6. Metabolic Melodies at https://teeheetime.com/category/lyrics-science/ 7. Kevin's Free Biochemistry books - https://kevingahern.com/biochemistry-resources/ 8. Kevin's Pre-med Audio course on Listenable - https://listenable.io/web/courses/143/kevin-aherns-guide-to-getting-into-medical-school/ Lecture Highlights Amino Acid Highlights 1. Amino acids are the building blocks of proteins. They all contain an alpha carboxyl group and an alpha amino group. The carbon attached to the alpha carboxyl and the alpha amino group is known as the alpha carbon. 2. All amino acids except glycine have four different groups attached to the alpha carbon. As a result, all amino acids have at least one asymmetric center (the alpha carbon). We call a compound with such an arrangement 'chiral.' The two chiral forms of amino acids are called 'D' and 'L'. If one uses ordinary chemistry to make amino acids, mixtures of D and L are always produced. However, cells use enzymes to make amino acids and those enzymes always give the same configuration - L. 3. Glycine is the only amino acid with no asymmetric (chiral) carbon because it has two hydrogens attached to alpha carbon. 4. Only L amino acids are found in proteins formed biologically. We can think of D and L forms similar to left and right hands. Indeed, sometimes the two possible forms are referred to as 'handedness'. D and L alanine are mirror images of each other. Simple amino acids with only one asymmetric center will always have D and L forms as mirror images of each other. 5. Twenty amino acids are commonly found in proteins. The properties of the amino acids are determined by the composition of the R groups on each of them. 6. Amino acids with non-polar side chains can be amphipathic (amphiphilic) because part of them is hydrophobic (water hating) and part is hydrophilic (water liking). 7. Amino acids are grouped according to the properties of their R groups. You are responsible for knowing the names of the 20 amino acids, the groups they belong to as shown in class and the composition of any groups with ionizing side chains. For example, so-called acidic amino acids have carboxyl groups (COOH/COO-) in their side chain. These include glutamic acid and aspartic acid. 8. Amino acids with amine-containing side chains (arginine, lysine, histidine) have groups that vary in charge from +1 (proton on) to 0 (proton off). Loss of a proton from the side chain causes the side chain to have no charge. Gain of the proton causes the side chain to have a positive charge. 9. Hydroxyl amino acids include serine, tyrosine and threonine, which contain hydroxyl groups in their side chains. 10. Proline is an amino acid with a ring structure as past of its side chain AND its. It is the only amino acid with an alpha amino group that is not a primary amine (it is a secondary amine). 11. Cysteine is the only amino acid with a sulfhydryl group. 12. Glycine is the simplest amino acid with only a hydrogen as its side chain. 13. The other amino acids (tryptophan, phenylalanine, methionine, alanine, leucine, isoleucine, valine, asparagine, glutamine) have varying properties. 14. Amino acids with acid side chains have R groups that 1) can lose/gain a proton and 2) are negatively charged upon losing the proton (and neutral when they have the proton). 15. Some amino acids are modified after they are incorporated into proteins. The best examples are hydroxylysine and hydroxyproline. Both of these are found in the protein called collagen. 16. Because amino groups and carboxyl groups can gain or lose protons, amino acids can have a variety of charges. 17. I noted on a titration plot how to approximate the charge on a molecule at a given pH, if you know the pKa. The rules I gave are that if the pH is more than one unit below the pKa, you may assume for approximating that the proton is ON the relevant group (carboxyl or amine). If the pH is more than one unit above the pKa, you may assume for approximating that the proton is OFF the relevant group. 18. The pI of a molecule is the pH at which its charge is exactly equal. The pI of a molecule must be calculated and is equal to the average of the pKa values immediately adjacent to zwitterion point.