Lecture 1 Flashcards

Question

What is the amino acid structure and classification? For each classification,state three examples of amino acids under them

Answer 1

Non polar amino acids -examples:glycine,alanine,valine,leucine,isoleucine,tyrosine,phenylalanine,tryptophan,methionine,proline Non-polar side chains:Grandma Always Visits London In May For Winston's Party. G: Glycine (Gly). A: Alanine (Ala). V: Valine (Val). L: Leucine (Leu). I: Isoleucine (Ile). M: Methionine (Met). F: Phenylalanine (Phe). W: Tryptophan (Trp). P: Proline Polar but not charged amino acids-cysteine,serine,threonine,asparagine,glutamine Clever Sweethearts Test All Genotypes” Breakdown: • Cysteine • Serine • Threonine • Asparagine • Glutamine Tyrosine is polar and aromatic Polar Charged basic amino acids(are positive) - arginine,lysine,histidine Love And Happiness are positives Polar Charged acidic amino acids(are negative) -aspartic acid(Asp D) and glutamic acid(Glu E) Anger and Greed are negative feelings Acid and basic amino acids are charged amino acids 2. All aliphatic amino acids, as well as methionine - a sulfur-containing amino acid - and phenylalanine and tryptophan, which are aromatic amino acids, are nonpolar amino acids 3. All alcohols and amides, as well as cysteine, which is a sulfur-containing amino acid, and tyrosine, which is an aromatic amino acid, are polar amino acids The alcohols are serine and threonine Amides are glutamine and asparagine

Answer 2

Non polar amino acids -examples:glycine,alanine,valine,leucine,isoleucine,tyrosine,phenylalanine,tryptophan,methionine,proline Polar but not charged amino acids-cysteine,serine,threonine,asparagine,glutamine Charged basic amino acids(these are positively charged)-arginine,lysine,histidine Charged acidic amino acids(these are negatively charged)-aspartic acid(Asp D) and glutamic acid(Glu E)

Answer 3

Most amino acids are non polar. Nonpolar amino acids are those that have hydrophobic (water-repelling) side chains. These amino acids tend to be found in the interior of proteins, where they contribute to the protein's structural stability by forming hydrophobic interactions with other nonpolar amino acids. Here are the nonpolar amino acids: 1. **Glycine (Gly)**: Although glycine itself is polar due to its hydrogen atom side chain, it is often considered nonpolar because of its small size and high flexibility, allowing it to fit into tight spaces within protein structures. 2. **Alanine (Ala)** 3. **Valine (Val)** 4. **Leucine (Leu)** 5. **Isoleucine (Ile)** 6. **Methionine (Met)** 7. **Proline (Pro)**: Proline is unique in that its side chain forms a covalent bond with the amino group, resulting in a rigid, cyclic structure. While it is classified as nonpolar, its structure and properties differ from other nonpolar amino acids. 8. **Phenylalanine (Phe)** 9. **Tryptophan (Trp)** These nonpolar amino acids tend to cluster together in the interior of proteins, away from the surrounding aqueous environment, helping to stabilize the protein's structure. These non polar proteins hide in the interior part of the protein structure while the charged and polar proteins are exposed to the exterior part Glutamic acid is for red blood cell normality. If it’s swapped with valine, you’ll get sickle cell. So, glutamate is the anionic form of glutamic acid that predominates at physiological pH. Glutamic Acid: This term typically refers to the non-ionized or protonated form of the amino acid at a low pH. In this form, glutamic acid has a carboxyl group that is protonated, making it more acidic. 2. Glutamate: This is the deprotonated or ionized form of glutamic acid, which occurs at physiological pH (around 7.4). In this form, one of the carboxyl groups has lost a proton, giving glutamate a negative charge at physiological pH.

Answer 4

Aromatic: Phenylalanine Tryptophan Tyrosine Please Take The rings. Sulphuric: Cysteine Methionine Sulfur Creates More

Answer 5

The lower the pka, the easier the amino acids can easily give away their hydrogen ions when placed in solution Actually, **pKa** is not the pH at which an acid dissolves completely; rather, it’s the pH at which the acid is half dissociated. Here’s a clearer explanation: 1. **pKa and Dissociation:** The pKa of an acid is the pH at which half of the acid molecules are dissociated (i.e., they have donated a proton) and half remain undissociated. At this pH, the concentrations of the acid (HA) and its conjugate base (A⁻) are equal. 2. **pKa and pH Relationship:** When the pH of a solution is equal to the pKa of the acid, there's an equilibrium between the protonated (HA) and deprotonated (A⁻) forms. If the pH is lower than the pKa, the acid will mostly remain in its protonated form (HA). If the pH is higher than the pKa, the acid will mostly be in its deprotonated form (A⁻). 3. **Complete Dissociation:** Strong acids (with very low pKa values) are often completely dissociated at a pH much higher than their pKa, meaning almost all of the acid molecules have donated their protons. However, for weak acids, the dissociation is partial and depends on the pH relative to the pKa. In summary, **pKa** is the pH at which half of the acid is dissociated, not the pH at which the acid dissolves or dissociates completely. . It is defined as the negative logarithm (base 10) of the acid dissociation constant (Ka) of the substance. The pKa value indicates the degree to which a molecule or ion will donate or accept a proton (H+ ion) in a substance(could be water or something else). At a pH higher than the pKa, the amino acid tends to accept protons and exist predominantly in its deprotonated (negative) form, while at a pH lower than the pKa, it tends to donate protons and exist predominantly in its protonated (positive) form. Ka is the degree to which an acid dissociates in a water or another substance. A high ka means that the acid easily dissociates in water hence it is a strong acid. A high ka means a low pka because they are inversely proportional. The acid is strong if it easily dissociates in water because it is highly reactive in acid base reactions due to the fact that it easily dissociates in water. Strong acids means lower ph because The more H⁺ ions an acid releases into a solution, the lower the pH of that solution, making it more acidic. Strong acids significantly lower the pH because they donate many H⁺ ions. It looks like there may be some confusion regarding acids and their behavior in different environments, particularly with respect to proton donation and acceptance. Let's clarify how acids behave in acidic environments and how this relates to amino acids: ### Acids and Proton Behavior 1. **Definition of an Acid**: An acid is defined as a substance that can donate protons (H⁺) in solution. When an acid donates a proton, it becomes a conjugate base (which often has a negative charge). 2. **Acidic Environment**: An acidic environment is characterized by a high concentration of H⁺ ions (low pH). In this situation: - **Acids in an Acidic Environment**: Strong acids will dissociate completely, donating protons and existing mostly in their deprotonated (conjugate base) form. Weak acids, however, may not dissociate completely. - **Protonation of Bases**: In an acidic environment, weak bases (which can accept protons) will tend to become protonated. ### Amino Acids in Acidic Environments - **Amino Acid Behavior**: Amino acids contain both an amine group (–NH₂) and a carboxylic acid group (–COOH). The behavior of these groups is influenced by pH: - **At Low pH (Acidic Environment)**: - The carboxylic acid group (–COOH) is protonated (stays as –COOH) and does not release its proton, meaning it retains a neutral charge. - The amine group (–NH₂) becomes protonated (–NH₃⁺), resulting in a positive charge overall. - If the side chain of the amino acid is also acidic (like in glutamic acid or aspartic acid), it can still lose a proton, but overall, the amino acid can have a net positive charge. - **At High pH (Basic Environment)**: - The carboxylic acid group deprotonates (–COO⁻), leading to a negative charge. - The amine group may remain protonated (–NH₃⁺) depending on how high the pH is, potentially leading to a zwitterionic state (where the amino acid has both positive and negative charges but is overall neutral). ### Summary - In an **acidic environment**, weak acids can remain protonated (not donating protons) and bases become protonated, leading to positive charges. - In a **basic environment**, acids tend to lose protons (deprotonate) and become negatively charged. So, while it is true that acidic substances tend to release protons, it’s essential to consider the specific context of the chemical groups involved (like those in amino acids) and how they interact with protons in different pH environments.

Answer 6

Electrophoresis: solution in a rectangular shape basin with a cathode and an anode Mixture of amino acids to separate them. Apply electric current to the basin. Manipulate the ph to the point where the amino acids will either release the hydrogen ions or hold on to it. Those who retain their positive charge will migrate to the negatively charged electrode (cathode) and those who are negatively charged will migrate to the positively charged electrode (anode)

Answer 7

Solution: calculate overall net charge of each amino acid. Serene net charge is zero or uncharged, aspartic acid is -1, lysine is +1 The net charge for all combined is 0 and so at a ph of 6, it wil have a net negative charge and hence migrate to the anode or either anode or cathode (I don’t understand this part well) To predict the migration behavior of a peptide containing the amino acids aspartic acid (Asp), serine (Ser), and lysine (Lys) in a solution with a pH of 6, we need to consider the pKa values of the ionizable groups in each amino acid. 1. **Aspartic Acid (Asp)**: - Aspartic acid has two ionizable groups: the carboxyl group (pKa ~ 2.1) and the side chain carboxyl group (pKa ~ 3.9). - At pH 6, both carboxyl groups will be predominantly deprotonated (-COO⁻), as the pH is higher than their pKa values. 2. **Serine (Ser)**: - Serine is uncharged (pKa ~ 13.0). - At pH 6, the hydroxyl group will be mostly protonated (-OH), as the pH is significantly lower than its pKa value. 3. **Lysine (Lys)**: - Lysine has one ionizable group: the amino group on its side chain (pKa ~ 10.5). - At pH 6, the amino group will be mostly protonated (-NH3⁺), as the pH is lower than its pKa value. Considering the net charge of the peptide at pH 6: - Aspartic acid contributes a negative charge (-1). - Serine is uncharged so zero and lysine contribute positive charge - The overall charge of the peptide is 0. Since the overall charge of the peptide is neutral at pH 6, it will migrate towards the region in the gel where molecules with no net charge typically migrate, which is near the center of the gel during gel electrophoresis. To address the question and solution provided, let’s break down the process: ### **Understanding Net Charge and Migration in Electrophoresis** **1. Determine the Net Charge of Each Amino Acid:** - **Aspartic Acid**: Has a side chain carboxyl group with a pKa of around 4.0, which is deprotonated and carries a -1 charge at pH 6. - **Serine**: Has a side chain hydroxyl group with a pKa far above 6 (typically around 13), so it remains uncharged (0 charge) at pH 6. - **Lysine**: Has a side chain amino group with a pKa around 10.5, which is protonated and carries a +1 charge at pH 6. **2. Calculate the Overall Net Charge:** - **Aspartic Acid**: -1 - **Serine**: 0 - **Lysine**: +1 **Net Charge** = -1 (Aspartic Acid) + 0 (Serine) + +1 (Lysine) = 0 At pH 6, the peptide overall has a net charge of 0, meaning it is at its isoelectric point and does not migrate towards either the anode or cathode in an electric field. ### **Examples of Peptide Migration Based on Net Charge** 1. **Peptide: Glycine, Glutamic Acid, and Arginine** **Net Charge Calculation:** - **Glycine**: Neutral (0 charge) - **Glutamic Acid**: -1 (pKa of side chain ~4.0) - **Arginine**: +1 (pKa of side chain ~12.5) **Net Charge** = 0 (Glycine) - 1 (Glutamic Acid) + 1 (Arginine) = 0 **Migration**: At pH 6, the peptide has a net charge of 0 and will not migrate. 2. **Peptide: Alanine, Aspartic Acid, and Lysine** **Net Charge Calculation:** - **Alanine**: Neutral (0 charge) - **Aspartic Acid**: -1 - **Lysine**: +1 **Net Charge** = 0 (Alanine) - 1 (Aspartic Acid) + 1 (Lysine) = 0 **Migration**: At pH 6, the peptide has a net charge of 0 and will not migrate. 3. **Peptide: Glutamine, Aspartic Acid, and Histidine** **Net Charge Calculation:** - **Glutamine**: Neutral (0 charge) - **Aspartic Acid**: -1 - **Histidine**: +1 (pKa of side chain ~6.0) **Net Charge** = 0 (Glutamine) - 1 (Aspartic Acid) + 1 (Histidine) = 0 **Migration**: At pH 6, the peptide has a net charge of 0 and will not migrate. ### **Additional Points to Consider** - **Isoelectric Point (pI)**: If the pH is at the isoelectric point, the peptide will have no net charge and won’t migrate in an electric field. - **Migration Direction**: If the peptide has a net positive charge, it will migrate towards the cathode (negative electrode). If it has a net negative charge, it will migrate towards the anode (positive electrode). In summary, the key is to calculate the net charge of the peptide at the given pH and predict its migration based on its overall charge.

Answer 8

Peptide = < 50 amino acid long Polypeptide = > 50 amino acid long Protein More than 1 polypeptide

Answer 9

Each trna has its own amino acid. Trna brings anticodon and mRNA has codons Long chain peptides are primary structure of protein. Example is keratin. Bonds here is covalent or peptide Keratin is mostly helical. Protein in aqueous solution for coil or helix. Lots of glycine here in the helix structure cuz of the turning plenty. Bond between each amino acid is colvalent and is a peptide bond.covalent bonds are strong. Or it forms beta sheets Bonds holding secondary structure: Hydrogen bonds across R polar groups. Polar amino acids form more hydrogen bonds. When you heat it a little, the hydrogen bonds break. Tertiary structure: It’s built upon the secondary structure. Has combinations of alpha and beta structures For tertiary structure to hold, the bonds holding it are sulphide or disulphide bonds (cysteine cysteine disulphide bonds ) that are formed across across. It’s relationship with cystein. Hydrophobic interactions (example is van der waals) between R groups Hydrogen bonds too are here Protein in aqueous solution for coil or helix. Lots of glycine here in the helix structure cuz of the turning plenty. Bond between each amino acid is colvalent and is a peptide bond.covalent bonds are strong. Or it forms beta sheets Quartenary : Prosthetic group(for hemoglobin, it’s iron heme). Hold something soncerning quartenary structure 4 different peptides in hemoglobin (2alpha globin peptides and 2 beta globin peptides) plus a prosthetic group (iron) Insulin is tertiary cuz it has disulphide bonds in only one peptide Ionic bonds in quartenary structure. Ionic bonds are not strong Primary structure: Linear arrangement of the amino acid sequences Peptide bonds are the most important bonds Example is a line in the polypeptide insulin hormone Insulin is classified as a **quaternary protein**. Here’s why: - **Primary Structure**: This refers to the sequence of amino acids in a protein. - **Secondary Structure**: This involves local folding into alpha-helices and beta-sheets. - **Tertiary Structure**: This is the overall three-dimensional shape of a single polypeptide chain. - **Quaternary Structure**: This refers to the arrangement of multiple polypeptide chains (subunits) into a functional protein complex. Insulin is composed of two polypeptide chains (A and B chains) linked by disulfide bonds. This combination of multiple polypeptide chains into a single functional unit gives insulin its quaternary structure. An example of a primary protein structure is the **sequence of amino acids in a polypeptide chain**. For instance, the primary structure of **insulin** includes a specific sequence of amino acids in its polypeptide chains. The sequence of amino acids in one of insulin's chains might look something like this (simplified for illustration): **Chain A**: Glycine - Valine - Glutamic Acid - Cysteine - Phenylalanine - … This sequence determines the protein's higher-level structures and functions. Secondary structure: The secondary structure of a protein refers to localized folding patterns or arrangements of amino acid residues within a protein chain. •Within each peptide small regions may adopt specific folding patterns. •These are called secondary structure. Tertiary structure: 3-D arrangement of polypeptides Built upon the secondary structure Disulphide (-S-S-) bonds, hydrophobic interactions and H-bonds Quartenary structure: Multiple polypeptides (subunits) combine to form a functional protein Held together by weak interactions Example is hemoglobin Protein structures refer to the three-dimensional arrangements of atoms within proteins, which are essential for their function and activity. Proteins are polymers made up of amino acids linked together by peptide bonds, and the specific sequence of amino acids determines the protein's primary structure. However, proteins are not linear; they fold into complex three-dimensional structures dictated by the interactions between amino acid residues. There are four levels of protein structure: 1. **Primary Structure**: The linear sequence of amino acids in a protein chain, which is determined by the genetic code. This sequence is crucial, as it determines how the protein will fold and ultimately its function. 2. **Secondary Structure**: Localized folding patterns within a protein chain, primarily driven by hydrogen bonding between the backbone atoms (amino and carboxyl groups) of amino acid residues. The two most common types of secondary structure are alpha helices and beta sheets. 3. **Tertiary Structure**: The overall three-dimensional arrangement of a protein chain, resulting from interactions between amino acid side chains (R-groups), such as hydrogen bonding, hydrophobic interactions, van der Waals forces, and disulfide bonds. Tertiary structure determines the overall shape and stability of the protein molecule. 4. **Quaternary Structure**: The arrangement of multiple protein subunits (polypeptide chains) to form a functional protein complex. Quaternary structure is only applicable to proteins composed of multiple subunits, such as hemoglobin or DNA polymerase.

Answer 10

Alpha helix and beta-pleated sheet If alpha helix dominates, the protein will be more soluble in water Collagen isn’t soluble in water cuz the beta plated sheets dominates. It is made of glycine,lysine and propene • Within these structures, intramolecular interactions, hydrogen bonding between the backbone amine and carbonyl functional groups are critical to maintain 3-dimensional shape Alpha helices and beta sheets are two common types of secondary structures in proteins. Here’s a detailed overview of each: ### **Alpha Helices:** - **Structure:** - **Shape:** Right-handed spiral or coil. - **Formation:** Each turn of the helix involves approximately 3.6 amino acids. The backbone of the polypeptide chain coils around an imaginary axis. - **Stabilization:** Stabilized by hydrogen bonds that form between the carbonyl oxygen of one amino acid and the amide hydrogen of another amino acid located four residues earlier in the sequence. - **Properties:** - **R Group Position:** The side chains (R groups) of the amino acids extend outward from the helix, avoiding steric clashes with the backbone. - **Occurrence:** Common in many proteins, including structural proteins like keratin. - **Function:** - Provides stability and elasticity to proteins. The helical structure contributes to the protein's overall stability and flexibility. ### **Beta Sheets:** - **Structure:** - **Shape:** Composed of beta strands that are aligned side by side, forming a sheet-like structure. - **Formation:** Each beta strand is a linear segment of the polypeptide chain. The strands are held together by hydrogen bonds between the carbonyl oxygens and amide hydrogens of adjacent strands. - **Types:** Can be parallel (strands run in the same direction) or antiparallel (strands run in opposite directions). - **Properties:** - **R Group Position:** The side chains of the amino acids alternate above and below the plane of the beta sheet. - **Occurrence:** Common in proteins with a high content of beta sheets, such as fibroin in silk. - **Function:** - Provides strength and structural support. The beta-sheet structure is often found in proteins that require strength and rigidity, such as in silk fibers and certain enzymes. ### **Key Differences:** - **Shape and Stability:** - **Alpha Helices:** Coiled, forming a helical shape with hydrogen bonds stabilizing the coil. - **Beta Sheets:** Extended, forming a pleated sheet with hydrogen bonds between adjacent strands. - **Bonding:** - **Alpha Helices:** Hydrogen bonds are intra-chain (within the same helix). - **Beta Sheets:** Hydrogen bonds are inter-chain (between different strands). - **Side Chain Orientation:** - **Alpha Helices:** Side chains project outward from the helical axis. - **Beta Sheets:** Side chains alternate above and below the plane of the sheet. These secondary structures contribute significantly to the overall folding and functionality of proteins. Here is a list of bonds associated with each level of protein structure: ### **Primary Structure:** - Peptide bonds ### **Secondary Structure:** - Hydrogen bonds: beta sheets and alpha helices. Alpha helices and beta sheets are stabilized primarily by hydrogen bonds ### **Tertiary Structure:** - Hydrogen bonds - Ionic bonds - Disulfide bonds - Hydrophobic interactions - Van der Waals forces ### **Quaternary Structure:** - Hydrogen bonds - Ionic bonds - Disulfide bonds - Hydrophobic interactions - Van der Waals forces Tertiary and secondary: hydrogen bonds Tertiary : hydrogen bonds and di sulphide bonds Tertiary protein also has di sulphide bonds. Secondary: hydrogen bonds and peptide bonds Primary: peptide bonds or amine bonds Quartenary structures are held by weak van der waals bonds and electrostatic forces

Answer 11

The cell cycle in meiosis is similar to the mitotic cell cycle but includes two rounds of division (meiosis I and meiosis II) and results in four non-identical daughter cells with half the chromosome number of the original cell. Here's how it works: ### **Phases of the Cell Cycle in Meiosis** #### **Interphase (Prior to Meiosis)** - **G1 Phase (First Gap):** The cell grows and carries out normal functions. - **S Phase (Synthesis):** DNA is replicated, resulting in chromosomes that consist of two sister chromatids. - **G2 Phase (Second Gap):** The cell continues to grow, produce proteins, and prepare for division. #### **Meiosis I (Reductional Division)** - **Prophase I:** Chromosomes condense, homologous chromosomes pair up forming tetrads(synapsis), and crossing over (exchange of genetic material between each tetrad) occurs between non-sister chromatids (idk how to explain this so watch this video for more understanding of crossing over and you’ll understand non sister chromatids. https://youtu.be/kQu6Yfrr6j0?si=IHvh2NWUNCtAkG1w ) of homologous chromosomes. The nuclear envelope breaks down, and spindle fibers form. Tetrads are 4 sister chromatids of paired homologous chromosomes. - **Metaphase I:** Homologous chromosome pairs align at the metaphase plate. Each chromosome attaches to spindle fibers from opposite poles. - **Anaphase I:** Homologous chromosomes are pulled apart to opposite poles of the cell, reducing the chromosome number by half. Sister chromatids remain attached.(so the tetrad divides but retain each sister chromatid retains it centromere until each sister chromatid is finally pulled apart and the centromere is split into two in the anaphase II) - **Telophase I:** The chromosomes arrive at the poles, the nuclear envelope may reform, and the cell may begin to divide. - **Cytokinesis:** The cytoplasm divides, resulting in two haploid daughter cells. These cells have half the number of chromosomes (but each chromosome still consists of two sister chromatids). #### **Interkinesis (Between Meiosis I and Meiosis II)** - This is a brief interphase-like stage. There is no DNA replication during this period. The cell prepares for the second round of division. #### **Meiosis II (Equational Division)** - **Prophase II:** Chromosomes condense again, and the nuclear envelope (if reformed) breaks down. Spindle fibers reform. - **Metaphase II:** Chromosomes align individually along the metaphase plate, similar to mitosis. - **Anaphase II:** Sister chromatids are finally separated and pulled toward opposite poles. - **Telophase II:** Chromatids (now individual chromosomes) arrive at the poles, and the nuclear envelope reforms. - **Cytokinesis:** The cytoplasm divides, resulting in four haploid daughter cells, each with a single set of chromosomes. These cells are genetically distinct due to the recombination and independent assortment of chromosomes during meiosis I. ### **Key Points:** - **Meiosis I** is where the chromosome number is reduced by half (from diploid to haploid). - **Meiosis II** is similar to mitosis but occurs in haploid cells and separates sister chromatids. - The result of meiosis is four genetically distinct haploid cells, which are the basis of gametes (sperm and egg cells) in sexually reproducing organisms. These haploid cells can fuse during fertilization to form a diploid zygote, restoring the diploid chromosome number in the offspring. You're correct that the processes of mitosis and meiosis share similarities, but they differ significantly in their outcomes and specific mechanisms. Here’s a breakdown of the key differences: ### **Key Differences Between Mitosis and Meiosis** 1. **Number of Divisions:** - **Mitosis:** Involves one division, resulting in two daughter cells. - **Meiosis:** Involves two divisions (meiosis I and meiosis II), resulting in four daughter cells. 2. **Number of Daughter Cells:** - **Mitosis:** Produces two genetically identical diploid daughter cells (same number of chromosomes as the parent cell). - **Meiosis:** Produces four genetically distinct haploid daughter cells (half the number of chromosomes as the parent cell). 3. **Chromosome Number:** - **Mitosis:** Maintains the chromosome number. If the parent cell is diploid (2n), the daughter cells will also be diploid. - **Meiosis:** Reduces the chromosome number by half. If the parent cell is diploid (2n), the daughter cells will be haploid (n). 4. **Genetic Variation:** - **Mitosis:** Produces genetically identical cells, with no variation unless a mutation occurs. - **Meiosis:** Introduces genetic variation through crossing over (exchange of genetic material between homologous chromosomes) during prophase I and independent assortment (random separation of homologous chromosomes) during metaphase I. 5. **Pairing of Homologous Chromosomes:** - **Mitosis:** Homologous chromosomes do not pair up. - **Meiosis:** Homologous chromosomes pair up and undergo synapsis during prophase I, leading to crossing over. Point 5: Pairing of Homologous Chromosomes • Mitosis: • Homologous chromosomes (the two chromosomes of a pair, one from each parent) do not pair up during mitosis. Each chromosome behaves independently. • This means that during cell division in mitosis, each daughter cell receives an identical set of chromosomes, ensuring the same genetic material as the parent cell. • Meiosis: • In prophase I of meiosis, homologous chromosomes pair up in a process called synapsis. This pairing is crucial because it allows for the exchange of genetic material between the paired chromosomes through a process called crossing over. • This exchange of genetic material is a key feature of meiosis that contributes to genetic diversity in the resulting gametes 6. **Function:** - **Mitosis:** Primarily for growth, repair, and asexual reproduction. It produces cells for tissue growth and regeneration. - **Meiosis:** Produces gametes (sperm and eggs) for sexual reproduction, ensuring genetic diversity in offspring. 7. **Stages:** - **Mitosis:** Consists of prophase, metaphase, anaphase, telophase, and cytokinesis (one cycle of these stages). - **Meiosis:** Consists of two cycles of these stages: meiosis I (which includes crossing over and reduction of chromosome number) and meiosis II (which resembles mitosis but starts with haploid cells). 8. **Crossing Over:** - **Mitosis:** Does not involve crossing over. - **Meiosis:** Crossing over occurs in prophase I, leading to genetic recombination and variation. Mitosis: • Crossing over does not occur in mitosis. The chromosomes replicate and divide, but there is no exchange of genetic material between them. • As a result, the two daughter cells are genetically identical to the parent cell and to each other. • Meiosis: • During prophase I of meiosis, homologous chromosomes undergo crossing over. This is where segments of DNA are exchanged between the paired chromosomes. • Crossing over creates new combinations of genes, which increases genetic variability in the gametes (sperm and egg cells). This genetic diversity is important for evolution and adaptation in sexually reproducing organisms. Summary: • Point 5 (Pairing): Homologous chromosomes pair up in meiosis (not in mitosis), which is necessary for crossing over and genetic diversity. • Point 8 (Crossing Over): Crossing over occurs in meiosis, allowing for the exchange of genetic material and contributing to genetic diversity; it does not happen in mitosis. ### **Summary:** - **Mitosis** creates two identical daughter cells with the same chromosome number as the parent, used for growth and repair. - **Meiosis** creates four genetically distinct daughter cells with half the chromosome number, used for sexual reproduction and contributing to genetic diversity. While the processes of division (prophase, metaphase, anaphase, telophase) are similar in both, the critical differences lie in the pairing of homologous chromosomes, the reduction of chromosome number, and the introduction of genetic variation in meiosis.

Answer 12

Explanation: • Chromatin: This refers to the complex of DNA and proteins (primarily histones) that make up the contents of the nucleus during the interphase of the cell cycle. During this phase, chromatin is loosely packed, allowing for processes like transcription and replication to occur. • Chromosome Condensation: As a cell enters mitosis or meiosis, the chromatin fibers undergo condensation, becoming highly organized and compacted into distinct structures called chromosomes. This process is referred to as chromosome condensation. Summary: • Chromatin condensation refers to the initial packing of DNA and proteins into chromatin. • Chromosome condensation refers to the further compaction of chromatin into visible chromosomes during cell division. In the context of cell division, chromosome condensation is the more accurate and commonly used term. Yes, chromosomes are **compacted chromatin**. ### **Explanation:** - **Chromatin** is a complex of DNA and proteins (mainly histones) that is loosely packed within the nucleus during interphase. - During cell division (mitosis or meiosis), chromatin fibers condense and coil tightly to form **chromosomes**, which are the distinct, visible structures that ensure accurate distribution of genetic material to daughter cells.

Answer 13

Transcription Translation Of course! Here’s the explanation with key terms and enzymes included: --- Imagine your body is like a big, busy factory that makes lots of different things. One of the most important things the factory makes is **proteins**, which are like tiny machines that do lots of different jobs in your body, like helping you grow or fixing things when you get hurt. Here’s how the factory makes these proteins: 1. **Making the Blueprint (Transcription):** - First, the factory needs a blueprint (which is like a special set of instructions) to make the protein. This blueprint is written in a special language called **DNA**, which is inside the **nucleus** of the cell. - The factory workers (called **RNA polymerase**) read the DNA blueprint and make a copy of it called **mRNA** (messenger RNA). This mRNA is like a message that tells the rest of the factory how to build the protein. **RNA polymerase** is the enzyme that helps to create this mRNA copy from the DNA. (Transcription) 1. DNA Blueprint: • Inside the nucleus, the DNA holds the instructions for making proteins. • The enzyme RNA polymerase reads the DNA and makes a copy called mRNA (messenger RNA). 2. **Building the Protein (Translation):** - Next, the mRNA message travels out of the nucleus to the part of the cell where proteins are made (called **ribosomes**). - The ribosomes read the mRNA message in small steps and put together the protein by joining tiny building blocks called **amino acids**. These amino acids are like the parts of a LEGO set that snap together to build something new. - **tRNA** (transfer RNA) brings the amino acids to the ribosome, matching them to the mRNA code. The ribosome uses these amino acids to build the protein. - **Peptidyl transferase** is the enzyme inside the ribosome that helps link the amino acids together to form a chain. Translation) 2. Role of rRNA: • rRNA (ribosomal RNA) is a key component of the ribosome, which is the part of the cell that assembles proteins. • The ribosome is made up of rRNA and proteins and functions like a machine that reads the mRNA message and helps link amino acids together to form the protein. 3. Role of tRNA: • tRNA (transfer RNA) brings the building blocks, or amino acids, to the ribosome. • Each tRNA has an anticodon that matches a specific codon on the mRNA. The codons are like codes that tell the ribosome which amino acid to add next. • For example, if the mRNA code says “AUG,” the corresponding tRNA with the anticodon “UAC” will bring the amino acid methionine to the ribosome. • The tRNA molecules make sure that the amino acids are added in the correct order as specified by the mRNA code. 4. Protein Assembly: • The ribosome reads the mRNA message, and tRNA molecules bring the appropriate amino acids to the ribosome. • Inside the ribosome, the enzyme peptidyl transferase helps link the amino acids together to form a chain. This chain then folds into a functional protein. When all the amino acids are joined in the right order, the new protein is finished! So, in short, the factory first writes down the instructions (transcription) with the help of **RNA polymerase**, then follows those instructions to build something (translation) with the help of **ribosomes**, **tRNA**, and **peptidyl transferase**. That’s how your body makes the proteins it needs to keep everything running smoothly! ---Translation: • Location: Cytoplasm (specifically at the ribosomes) • Process: 1. Initiation: The mRNA binds to a ribosome. The ribosome reads the mRNA sequence in sets of three nucleotides (codons). The start codon (usually AUG) signals the beginning of translation. 2. Elongation: Transfer RNA (tRNA) molecules, each carrying a specific amino acid, bind to the complementary mRNA codons through their anticodons. The ribosome facilitates the formation of peptide bonds between adjacent amino acids, elongating the polypeptide chain. 3. Termination: When the ribosome encounters a stop codon on the mRNA, translation ends. The newly synthesized polypeptide chain is released and folds into its functional three-dimensional structure. 4. Folding and Post-Translational Modifications: The polypeptide chain folds into its functional shape, often with the assistance of chaperone proteins. It may also undergo post-translational modifications, such as phosphorylation or glycosylation, to become fully functional. Summary: • Transcription: DNA → mRNA • Translation: mRNA → Protein Here is an MCQ based on stop codons: **Which of the following codons does NOT serve as a stop signal during protein synthesis?** A) UAA B) UGA C) AUG D) UAG **Answer: C) AUG** **Explanation:** UAA, UGA, and UAG are stop codons that signal the end of protein synthesis, while AUG is a start codon that also codes for methionine, marking the beginning of protein synthesis.

Answer 14

Here are five multiple-choice questions (MCQs) on the common enzymes used in replication, transcription, and translation: ### Question 1: **Which enzyme is responsible for unwinding the DNA double helix during replication?** A) DNA polymerase B) RNA polymerase C) Helicase D) Ligase **Answer:** C) Helicase ### Question 2: **What is the main function of DNA polymerase during DNA replication?** A) Synthesizes RNA from a DNA template B) Adds nucleotides to a growing DNA strand C) Joins Okazaki fragments on the lagging strand D) Unwinds the DNA double helix **Answer:** B) Adds nucleotides to a growing DNA strand ### Question 3: **Which enzyme catalyzes the synthesis of RNA during transcription?** A) DNA ligase B) RNA polymerase C) Topoisomerase D) Reverse transcriptase **Answer:** B) RNA polymerase ### Question 4: **During translation, which enzyme is responsible for forming peptide bonds between amino acids?** A) Peptidyl transferase B) Aminoacyl-tRNA synthetase C) Helicase D) DNA polymerase **Answer:** A) Peptidyl transferase ### Question 5: **Which enzyme is involved in removing RNA primers and filling in the gaps with DNA nucleotides during DNA replication?** A) DNA polymerase I B) DNA ligase C) RNA polymerase D) Primase **Answer:** A) DNA polymerase I These questions cover key enzymes involved in DNA replication, RNA transcription, and protein translation processes. Here are ten more multiple-choice questions (MCQs) on the common enzymes used in replication, transcription, and translation: ### Question 6: **Which enzyme is responsible for sealing nicks and joining Okazaki fragments on the lagging strand during DNA replication?** A) DNA polymerase III B) Topoisomerase C) DNA ligase D) Primase **Answer:** C) DNA ligase ### Question 7: **What is the role of topoisomerase during DNA replication?** A) Synthesizes RNA primers B) Unwinds the DNA double helix C) Relieves supercoiling ahead of the replication fork D) Adds nucleotides to the growing DNA strand **Answer:** C) Relieves supercoiling ahead of the replication fork ### Question 8: **Which enzyme synthesizes short RNA primers that are necessary for DNA replication to begin?** A) DNA polymerase I B) Primase C) Ligase D) RNA polymerase **Answer:** B) Primase ### Question 9: **Which of the following enzymes is involved in the process of RNA splicing in eukaryotic cells?** A) Ribonuclease B) Spliceosome C) RNA polymerase D) DNA ligase **Answer:** B) Spliceosome ### Question 10: **Which enzyme is used to charge tRNA molecules with their respective amino acids during translation?** A) Aminoacyl-tRNA synthetase B) Peptidyl transferase C) Helicase D) RNA polymerase **Answer:** A) Aminoacyl-tRNA synthetase ### Question 11: **Which enzyme catalyzes the removal of supercoils generated ahead of the replication fork during DNA replication?** A) DNA polymerase II B) Helicase C) DNA gyrase D) RNA primase **Answer:** C) DNA gyrase ### Question 12: **During transcription, what is the function of RNA polymerase II in eukaryotic cells?** A) Synthesizes ribosomal RNA (rRNA) B) Synthesizes transfer RNA (tRNA) C) Synthesizes messenger RNA (mRNA) D) Synthesizes DNA **Answer:** C) Synthesizes messenger RNA (mRNA) ### Question 13: **Which enzyme degrades RNA primers during DNA replication in eukaryotes?** A) RNA polymerase B) DNA polymerase α C) DNA polymerase I D) RNase H **Answer:** D) RNase H ### Question 14: **What enzyme synthesizes the leading strand continuously during DNA replication?** A) DNA polymerase III B) DNA polymerase I C) RNA polymerase D) DNA ligase **Answer:** A) DNA polymerase III ### Question 15: **Which enzyme is responsible for the synthesis of the RNA component of telomerase that elongates telomeres in eukaryotic cells?** A) RNA polymerase I B) RNA polymerase II C) RNA polymerase III D) Telomerase **Answer:** D) Telomerase These questions provide a broader understanding of the various enzymes involved in the key biological processes of replication, transcription, and translation. ### Explanation for Question 11: **Question 11: Which enzyme catalyzes the removal of supercoils generated ahead of the replication fork during DNA replication?** **Answer: C) DNA gyrase** **Explanation:** During DNA replication, the unwinding of the DNA double helix by helicase creates tension and supercoiling ahead of the replication fork. **DNA gyrase**, a type of **topoisomerase (specifically, Topoisomerase II in prokaryotes)**, is responsible for relieving this supercoiling by cutting both strands of the DNA, allowing it to untwist and then resealing the strands. This action prevents the DNA from becoming too tightly coiled, which would otherwise impede the replication process. ### Explanation for Question 7: **Question 7: What is the role of topoisomerase during DNA replication?** **Answer: C) Relieves supercoiling ahead of the replication fork** **Explanation:** **Topoisomerase** is a crucial enzyme during DNA replication that helps manage the topology of DNA. As helicase unwinds the DNA strands, it introduces positive supercoiling ahead of the replication fork. Topoisomerases work by creating temporary nicks in one or both strands of the DNA, allowing the DNA to unwind and relieve the supercoils. There are two main types of topoisomerases: - **Topoisomerase I** cuts one strand of the DNA to relieve supercoiling. - **Topoisomerase II** (such as DNA gyrase in prokaryotes) cuts both strands of DNA to manage supercoils, which is particularly important during replication and transcription. Both enzymes play a critical role in maintaining the structural integrity and stability of DNA during cellular processes

Answer 15

To **relieve supercoils** means to reduce the overwinding or underwinding of DNA that occurs when the double helix is unwound during processes like replication or transcription. Supercoiling is a natural consequence of the helical structure of DNA; when the DNA double helix is unwound by enzymes like helicase to allow replication or transcription to occur, it causes stress on the DNA strand, leading to supercoils forming ahead of the unwound region. ### Types of Supercoiling 1. **Positive Supercoiling**: This occurs when the DNA helix is overwound. It happens ahead of the replication fork where helicase unwinds the DNA strands. Overwinding increases tension and compacts the DNA even more tightly, making it harder to separate the strands. 2. **Negative Supercoiling**: This occurs when the DNA helix is underwound. Underwinding can occur naturally and makes it easier to open the DNA strands, which is helpful for processes like transcription and replication. ### Role of Topoisomerases in Relieving Supercoils **Topoisomerases** are enzymes that manage the level of supercoiling in DNA to maintain stability and allow replication and transcription to proceed smoothly. Here's how they work: - **Topoisomerase I**: Cuts one strand of the DNA helix, allowing it to rotate and relieve tension. This reduces supercoiling without causing extensive breaks. After relieving the tension, the enzyme reseals the cut strand. - **Topoisomerase II (e.g., DNA gyrase in prokaryotes)**: Cuts both strands of the DNA helix, passes another segment of the double helix through the break, and then reseals the cut. This process is particularly useful for untangling DNA molecules that become knotted or supercoiled. ### Why Relieving Supercoils is Important Relieving supercoils is crucial because: - **Prevents DNA Breakage**: Excessive supercoiling can cause the DNA strand to break or become damaged. - **Facilitates Replication and Transcription**: Removing supercoiling helps replication and transcription machinery (such as DNA polymerase and RNA polymerase) move along the DNA strand without obstruction. - **Maintains DNA Integrity**: Proper management of DNA supercoiling ensures that the DNA remains stable and compacted properly within the cell. Overall, relieving supercoils is essential for the proper functioning of cells and for maintaining the integrity of genetic information during cellular processes.

Answer 16

Types of isomers Structural isomers and stereoisomers. Structural isomers: have same molecular formula but different structural formula(as in different bonding) Stereisomers have same structural formula but different spatial arrangements or geometries. Geometric and optical isomerism as types of stereoisomers. Here’s a summary of the amino acids you mentioned, categorized by their properties: ### Branched Amino Acids - **Valine**: Non-polar, branched chain. - **Isoleucine**: Non-polar, branched chain. ### Aromatic Amino Acids - **Phenylalanine**: Non-polar, aromatic ring. - **Tyrosine**: Polar, aromatic ring (contains a hydroxyl group). - **Tryptophan**: Non-polar, aromatic ring. ### Polar (but not charged) Amino Acids - **Serine**: Polar, has a hydroxyl group (–OH). - **Threonine**: Polar, has a hydroxyl group (–OH). - **Cysteine**: Polar, contains a sulfhydryl group (–SH), which can form disulfide bonds. ### Charged Basic Amino Acids - **Arginine**: Basic, positively charged at physiological pH (7.4). - **Lysine**: Basic, positively charged at physiological pH (7.4). - **Histidine**: Basic, can be positively charged depending on the pH. ### Charged Acidic Amino Acids - **Aspartate (Aspartic Acid)**: Acidic, negatively charged at physiological pH (7.4). - **Glutamate (Glutamic Acid)**: Acidic, negatively charged at physiological pH (7.4). - **Asparagine**: Neutral, contains an amide group, not charged. ### Other Amino Acids - **Methionine**: Non-polar, contains sulfur. - **Proline**: Non-polar, rigid structure due to its unique cyclic form. - **Glycine**: Non-polar, the smallest amino acid, and flexible; it can fit into tight spaces in protein structures. ### Sickle Cell Disease - In sickle cell disease, the mutation changes glutamate (an acidic amino acid) to **valine** (a non-polar amino acid), which affects the protein's structure and function. ### Memorization Tips - **Aromatic**: Remember the "Phe, Tyr, Trp" trio for phenylalanine, tyrosine, and tryptophan. - **Polar**: Think of serine and threonine as the "hydroxyl heroes" for their –OH groups. - **Charged**: Use the phrase "Positive Arg, Lys, His" for basic and "Negative Asp, Glu" for acidic. - **Branched**: Valine and isoleucine are both "V" for branched. Feel free to ask if you need more specific details or help with memorization!

Answer 17

### 4. A mutation changes tyrosine to phenylalanine in a protein. What effect might this have? A. Increase in protein flexibility B. Loss of phosphorylation site C. Gain of new hydrogen bonds D. Introduction of disulfide bridges **Answer:** B. Loss of phosphorylation site **Explanation:** Tyrosine can be phosphorylated due to the hydroxyl group in its side chain. Phenylalanine lacks this hydroxyl group, so the mutation would eliminate potential phosphorylation, which could affect signaling pathways. --- ### 5. A mutation in the hydrophilic region of a protein changes glutamate to glutamine. What is the likely effect? A. Significant disruption due to charge change B. Minimal effect due to similarity C. Increased structural rigidity D. Increased interaction with hydrophobic regions **Answer:** B. Minimal effect due to similarity **Explanation:** Glutamate and glutamine are both polar, but glutamate is negatively charged, while glutamine is neutral. Since they are similar in size and polarity, this substitution would likely have a minimal effect compared to changes involving non-polar or charged residues. --- ### 6. Substitution of cysteine with serine in a protein might affect the protein in what way? A. Loss of disulfide bond formation B. Enhanced hydrophobic interactions C. Increased protein flexibility D. Formation of more hydrogen bonds **Answer:** A. Loss of disulfide bond formation **Explanation:** Cysteine can form disulfide bonds, which are crucial for protein stability. Serine lacks the thiol (-SH) group required for disulfide bonding, so this substitution would prevent the formation of these stabilizing interactions. --- ### 7. What might be the consequence of replacing lysine with alanine in a protein’s active site? A. Loss of hydrogen bonding potential B. Increase in enzyme specificity C. Introduction of a positive charge D. Disruption of hydrophobic interactions **Answer:** A. Loss of hydrogen bonding potential **Explanation:** Lysine, with its long positively charged side chain, can form hydrogen bonds and electrostatic interactions with substrates. Replacing it with alanine, which is small and non-polar, would likely result in a loss of these interactions, reducing enzyme activity. --- ### 8. Which substitution would be the least likely to affect the function of a transmembrane helix? A. Leucine to alanine B. Valine to lysine C. Isoleucine to threonine D. Serine to tyrosine **Answer:** A. Leucine to alanine **Explanation:** Both leucine and alanine are non-polar and hydrophobic. Since transmembrane helices are usually composed of hydrophobic residues, this change would have minimal impact compared to introducing polar or charged residues like lysine or threonine. --- ### 9. Replacing proline with glycine in a loop region of a protein would likely: A. Increase loop rigidity B. Decrease loop flexibility C. Increase loop flexibility D. Form new disulfide bonds **Answer:** C. Increase loop flexibility **Explanation:** Proline is rigid and limits flexibility, whereas glycine is small and highly flexible. Replacing proline with glycine would increase flexibility in the loop region. --- ### 10. A mutation changes a hydrophobic residue in the core of a protein from leucine to arginine. How might this affect the protein? A. No significant effect B. Improved stability in non-polar environments C. Disruption of protein folding and stability D. Enhanced hydrophobic interactions **Answer:** C. Disruption of protein folding and stability **Explanation:** Arginine is charged and hydrophilic, whereas leucine is non-polar and hydrophobic. Introducing a hydrophilic residue into a hydrophobic core would destabilize the protein and disrupt proper folding. --- These questions are designed to help you understand how changes in amino acids can affect the structure and function of proteins, particularly focusing on their hydrophobic or hydrophilic nature and their roles in protein stability. Which of these changes would cause the least damage to the protein structure? A. Alanine to valine B. Valine to lysine C. Leucine to arginine D. Methionine to serine Answer: A. Alanine to valine Explanation: Alanine and valine are both small, non-polar amino acids, so this change Which of the following substitutions would most likely disrupt the center of a protein? A. Phenylalanine to tryptophan B. Valine to leucine C. Methionine to arginine D. Isoleucine to alanine Answer: C. Methionine to arginine Explanation: Methionine is non-polar and likes to be in the center of proteins (away from water), while arginine is charged and prefers water. This change would mess up the protein’s core structure. Replacing lysine (positively charged) with alanine (neutral) in an enzyme’s active site would likely result in: A. Loss of enzyme’s ability to bind its substrate B. More specific enzyme action C. Introduction of a positive charge D. Disruption of hydrophobic interactions Answer: A. Loss of enzyme’s ability to bind its substrate Explanation: Lysine helps in binding the substrate by forming electrostatic interactions. Replacing it with alanine, which is neutral, would likely weaken substrate binding. 8. Which substitution would have the least effect on a part of the protein that crosses a cell membrane? A. Leucine to alanine B. Valine to lysine C. Isoleucine to threonine D. Serine to tyrosine Answer: A. Leucine to alanine Explanation: Both leucine and alanine are non-polar and hydrophobic, so swapping one for the other in the membrane region would not cause much disruption

Answer 18

Question 2: Disruption in hydrogen bonding between two (2) different polypeptide subunits of a protein will MOST LIKELY affect: 1. A. Primary structure. • Explanation: The primary structure of a protein refers to its linear sequence of amino acids. This structure is determined by peptide bonds (covalent bonds) between amino acids, not hydrogen bonds. Therefore, disruption in hydrogen bonding would not affect the primary structure. 2. B. Secondary structure. • Explanation: The secondary structure refers to local folded structures (like alpha-helices and beta-pleated sheets) formed by hydrogen bonding between backbone atoms in the polypeptide chain. While hydrogen bonds are crucial for stabilizing secondary structures, this question refers to bonds between different subunits, which is more relevant to quaternary structure. 3. C. Tertiary structure. • Explanation: The tertiary structure is the overall three-dimensional shape of a single polypeptide chain, determined by various interactions, including hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges. However, this question specifically concerns bonds between different subunits, not just a single chain. 4. D. Quaternary structure. • Explanation: The quaternary structure refers to the arrangement and interaction of multiple polypeptide subunits within a protein. Hydrogen bonding plays a significant role in stabilizing these interactions. If hydrogen bonds between different subunits are disrupted, it will directly affect the quaternary structure, potentially leading to loss of function or stability