Amino Acids, Proteins and DNA Flashcards

Amino Acids, Proteins and DNA

A-Level AQA Chemistry

This pack of flashcards encompasses foundational concepts related to amino acids, proteins, and DNA, including their structures, properties, and roles in biological systems. It also covers enzyme function, drug interactions with enzymes, and the molecular details of DNA bases and nucleotides, as well as cisplatin's mechanism as an anticancer drug.

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Define nucleotides.	Nucleotides are composed of a phosphate ion bonded to 2-deoxyribose, which is in turn bonded to one of the four bases: adenine, cytosine, guanine, or thymine.
What are ionic interactions in the context of protein tertiary structure?	Ionic interactions can form between acidic amino acids (e.g., aspartic acid) and basic amino acids (e.g., lysine) in the folded protein chain.
Describe the formation of sulfur bridges in protein tertiary structure.	If two cysteine side chains end up near each other due to folding, they can react to form a covalent sulfur bridge.
What is the role of hydrogen bonds in protein tertiary structure?	Hydrogen bonds contribute to the stability and folding of the protein by forming interactions between different amino acid side chains.
Define ionic interactions in the context of protein tertiary structure.	Ionic interactions refer to the attraction between positively charged and negatively charged amino acid side chains in the folded protein chain.
How do sulfur bridges contribute to the stability of protein tertiary structure?	Sulfur bridges, formed by the reaction of cysteine side chains, provide covalent bonds that help stabilize the folded protein structure.
Describe enzymes.	Enzymes are proteins that act as catalysts in biological reactions.
What is the active site of an enzyme?	The active site of an enzyme is a hollow substrate in the globular protein structure where a substrate molecule can bind.
How do substrate molecules bind to the active site of an enzyme?	Substrate molecules bind to the active site of an enzyme through a variety of interactions, including hydrogen bonding, van der Waals forces, and ionic interactions.
Define the lock and key hypothesis.	The lock and key hypothesis states that only substrate molecules with the right shape and correct positions of functional groups will fit and bind to the active site of an enzyme.
Describe the role of drugs as enzyme inhibitors.	Many drugs act as enzyme inhibitors by blocking the active site of an enzyme, preventing the substrate from attaching and inhibiting the enzyme's function.
How can computers be used to help design drugs that act as enzyme inhibitors?	Computers can be used to simulate and model the interactions between drugs and enzymes, aiding in the design of drugs that specifically target and inhibit enzyme activity.
What are some of the interactions involved in substrate binding to the active site of an enzyme?	Some of the interactions involved in substrate binding to the active site of an enzyme include hydrogen bonding, van der Waals forces, and ionic interactions.
Describe the role of the active site in enzyme catalysis.	The active site of an enzyme is where the substrate binds and undergoes a catalyzed reaction. It provides a specific environment for the reaction to occur, increasing the rate of the reaction.
Describe the key molecules in DNA.	The key molecules in DNA are phosphate ions, 2-deoxyribose (a pentose sugar), and the four bases: adenine, cytosine,anine, and thymine.
How do hydrogen bonds contribute to the tertiary structure?	Hydrogen bonds can form between different amino acid side chains in the folded protein chain.
How are the bases in DNA attached to the sugar?	The bases in DNA are attached to the sugar (2-deoxyribose) through specific atoms on the base that join onto the sugar molecule.
What are the four bases in DNA?	The four bases in DNA are adenine (A), cytosine (C), guanine (G), and thymine (T).
Describe the structure of a nucleotide.	A nucleotide consists of a phosphate ion bonded to 2-deoxyribose, which is further bonded to one of the four bases: adenine, cytosine, guanine, or thymine.
Describe the structure of a single strand of DNA.	A single strand of DNA is a sugar-phosphate polymer chain with bases attached to the sugars in the chain.
What is the role of hydrogen bonding in DNA?	Hydrogen bonding between base pairs leads to the formation of the two complementary strands of DNA.
Define complementary strands in DNA.	Complementary strands in DNA refer to two strands that have base sequences that match, with adenine (A) pairing with thymine (T) and cytosine (C) pairing with guanine (G).
How do guanine and cytosine pair in DNA?	Guanine pairs with cytosine in DNA through three hydrogen bonds.
Describe the structure of DNA.	DNA exists as two complementary strands of the sugar-phosphate polymer chain arranged in the form of a double helix.
Describe the structure of cisplatin.	Cisplatin is a Pt(II) complex with two chloride ions and two ammonia ligands bound to a central platinum atom.
What is the function of cisplatin as an anticancer drug?	Cisplatin prevents DNA replication in cancer cells by forming a dative covalent bond with a nitrogen atom on guanine.
How does cisplatin prevent the replication of cancerous cells?	Cisplatin displaces two chloride ions and binds to the DNA, inhibiting replication.
Define ligand replacement reaction.	A ligand replacement reaction is a chemical reaction in which one ligand is replaced by another ligand in a coordination complex.
What are the potential side effects of cisplatin?	Potential side effects of cisplatin include hair loss and replication inhibition in healthy cells.
What is the purpose of wearing plastic gloves during the chromatography of amino acids?	Wearing plastic gloves is necessary to prevent contamination.
What is the significance of the alpha in 'a' amino acid?	The alpha in 'a' amino acid means that both the NH2 and COOH groups are joined to the same carbon.
Define optical activity in relation to amino acids.	Optical activity refers to the ability of amino acids to rotate plane polarized light.
What are zwitterions?	Zwitterions are dipolar forms of amino acids that have both a positive and negative charge.
Describe the acidity and basicity of amino acids.	The amine group in amino acids is basic, while the carboxylic acid group is acidic.
What is the role of amino acids as buffers?	Amino acids act as weak buffers and can gradually change pH when small amounts of acid or alkali are added.
Explain the difference between the no charge form and the dipolar zwitterion form of an amino acid.	The no charge form of an amino acid never occurs, while the dipolar zwitterion form is the most stable and exists in solution.
What is the effect of pH on the form of amino acids with extra carboxylic acid or amine groups?	In alkaline conditions, the extra carboxylic acid group will react and change form, while in acidic conditions, the extra amine group will react and change form.
What are dipeptides?	Dipeptides are simple combination molecules of two amino acids with one amide (peptide) link.
How many possible combinations of amino acids are there in a dipeptide?	For any two different amino acids, there are two possible combinations in a dipeptide.
Describe the reactions that can occur with the carboxylic acid and amine groups in amino acids.	The carboxylic acid group and amine group in amino acids can undergo the usual reactions of these functional groups, such as esterification.
What happens when proteins are heated with concentrated hydrochloric acid or strong alkalis?	They can be hydrolysed and split back into their constituent amino acids.
How can the composition of a protein molecule be deduced?	The composition of the protein molecule can be deduced by using TLC chromatography.
Describe the process of splitting a protein into amino acids.	A protein can be split into amino acids by reacting with concentrated hydrochloric acid.
How can you ensure that the spots for each sample are equally spaced along the pencil line on the TLC plate?	By drawing a pencil line 1 cm above the bottom of the TLC plate and marking spots for each sample equally spaced along the line.
Define the Rf value in chromatography.	The Rf value is calculated by dividing the distance moved by the amino acid by the distance moved by the solvent.
What is the purpose of spraying ninhydrin on the amino acids and heating them?	Spraying ninhydrin on the amino acids and heating them causes red to blue spots to appear, making the transparent amino acids visible.
Describe the primary structure of proteins.	The primary structure of proteins is the sequence of combinations of amino acids.
What are proteins made from?	Proteins are polymers made from combinations of amino acids.
Define peptide links.	Peptide links are the amide functional group that join amino acids together in proteins.
How are amino acids linked together in proteins?	Amino acids are linked together by condensation reactions with peptide links.
Describe the secondary structure of proteins.	The secondary structure of proteins can take the form of an alpha-helix or a pleated sheet structure.
What holds the alpha-helix structure of proteins in place?	The alpha-helix structure of proteins is held in place by hydrogen bonds between the H of -N-H group and the -O of C=O of the fourth amino acid along the chain.
How is the pleated sheet structure of proteins formed?	The pleated sheet structure of proteins is formed when the protein chain folds into parallel strands held together by hydrogen bonds between the H of -N-H group and the -O of C=O of amino acids further along the chain in the parallel region.
What is the role of R-groups in the secondary structure of proteins?	The R-groups on the amino acids are all pointed to the outside of the alpha-helix structure of proteins.
What is the tertiary structure of proteins?	The tertiary structure is the folding of the secondary structure into more complex shapes.
Describe the interactions that hold the tertiary structure in place.	The tertiary structure is held in place by interactions between the R-side groups in more distant amino acids, including hydrogen bonding, sulfur-sulfur bonds, and ionic interactions.

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