Proteins, DNA Replication, and Metabolic Pathways: Key Concepts for Biochemistry

What are proteins composed of?

Proteins are composed of one or more polypeptide chains.

What is the difference between monomeric and multimeric proteins?

Monomeric proteins consist of a single polypeptide chain, while multimeric proteins contain multiple chains.

What is a hetero-tetramer?

A hetero-tetramer is a multimeric protein consisting of two different types of polypeptide chains.

What role do proteins play in biological systems?

Proteins perform functions such as catalysis, transport, structural support, and regulation.

What is the primary structure of a protein?

The primary structure is the linear sequence of amino acids linked by peptide bonds.

What stabilizes the secondary structure of proteins?

Hydrogen bonds between backbone atoms stabilize the secondary structure.

What are the common motifs found in secondary protein structures?

Common motifs include α-helices and β-sheets.

What determines the tertiary structure of a protein?

The tertiary structure is determined by interactions among side chains.

What are salt bridges in protein structures?

Salt bridges are ionic bonds formed between ionized R groups of basic and acidic amino acids.

What is the role of hydrogen bonds in protein folding?

Hydrogen bonds help stabilize protein structures by forming between polar R groups.

What are disulfide bonds and their significance?

Disulfide bonds are covalent bonds that provide stability to protein structures, especially in extracellular proteins.

What is myoglobin and its function?

Myoglobin is a globular protein that serves as an oxygen-binding protein in muscle tissues.

What is the quaternary structure of a protein?

The quaternary structure refers to the arrangement of multiple polypeptide chains in a protein.

How many subunits does hemoglobin have?

Hemoglobin is a tetramer composed of two alpha and two beta subunits.

What is the importance of protein folding?

Protein folding determines the three-dimensional structure of a protein, which dictates its function.

What is the directionality of protein synthesis?

Proteins are synthesized from the amino (N) terminal to the carboxyl (C) terminal.

What is the role of angiotensin in the body?

Angiotensin is an 8 amino acid peptide that regulates blood pressure.

What type of protein is collagen?

Collagen provides structural integrity to tissues.

What is the function of insulin?

Insulin regulates metabolic processes in the body.

What is the significance of the β-turn in protein structure?

The β-turn allows the polypeptide chain to reverse direction, facilitating compact protein folding.

What is the composition of the heavy chain of antibodies?

The heavy chain of antibodies consists of immunoglobulin folds, including both beta sheets and alpha helices.

What stabilizes the tertiary structure of proteins?

Interactions such as hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bonds stabilize the tertiary structure.

What can misfolded proteins lead to?

Diseases such as Alzheimer's and cystic fibrosis.

What is the relationship between a protein's structure and its function?

The structure-function relationship is exemplified by hemoglobin and myoglobin, which have distinct roles in oxygen transport despite structural similarities.

What allows hemoglobin to bind oxygen cooperatively?

Hemoglobin's quaternary structure allows for cooperative binding.

What is the role of the heme group in hemoglobin?

The heme group contains iron (Fe2+) which binds oxygen (O2) reversibly.

What structural change occurs upon oxygen binding to hemoglobin?

The Fe2+ ion moves into the plane of the heme, accompanied by a shift in the position of the histidine (His) residue.

What is cooperativity in hemoglobin?

Cooperativity refers to the phenomenon where the binding of one O2 molecule increases the likelihood of additional O2 binding.

What is the Bohr effect?

The Bohr effect describes how increased levels of CO2 and H+ (lower pH) decrease hemoglobin's affinity for O2, promoting oxygen release.

What is the effect of 2,3-Bisphosphoglycerate (2,3-BPG) on hemoglobin?

2,3-BPG stabilizes the T state of hemoglobin, promoting oxygen release.

What causes sickle cell hemoglobin (HbS)?

A mutation from Glu to Val that causes deformed red blood cells.

What are the clinical manifestations of sickle cell anemia?

Pain crises, anemia, and increased susceptibility to infections.

What are antibodies and their role in the immune system?

Antibodies are produced by B cells and play a crucial role in identifying and neutralizing foreign invaders.

What is the structure of antibodies?

Antibodies are Y-shaped proteins composed of heavy and light chains, with variable regions that bind specific antigens.

How do T cell receptors (TCRs) function?

TCRs recognize peptide antigens presented by MHC molecules, crucial for T cell activation.

What are carboxylic acids important for?

They are found in amino acids and fatty acids, crucial for protein structure and function.

What role do esters and thioesters play in metabolism?

They are key intermediates in metabolic pathways, including DNA and RNA synthesis.

What is the role of T cells in the immune response?

T cells recognize antigens presented by MHC molecules and are essential for adaptive immunity.

What is the relationship between protein folding and disease?

Misfolded proteins can lead to diseases, highlighting the importance of proper folding in health.

What are amines and where are they found?

Amines are found in hormones and neurotransmitters, influencing various physiological functions.

What role do aromatics play in biomolecules?

Aromatics are present in amino acids, hormones, and nucleic acids, playing roles in structure and function.

What is the significance of alkenes in biochemistry?

Alkenes, such as unsaturated fats, are important for energy storage.

What is the role of esters in biology?

Esters are found in DNA and RNA, which are crucial for genetic information.

What types of weak forces are important in biomolecules?

Weak forces include van der Waals interactions, hydrogen bonds, ionic interactions, and hydrophobic interactions.

What is the hydrophobic effect?

The hydrophobic effect describes how nonpolar molecules aggregate in aqueous solutions, minimizing their exposure to water.

What are amphiphilic molecules?

Amphiphilic molecules have both polar and nonpolar regions, allowing them to interact favorably with diverse environments.

What is chirality in biochemistry?

Chirality refers to molecules that cannot be superimposed on their mirror images.

What are enantiomers?

Enantiomers are chiral molecules that are mirror images of each other.

What is optical activity?

Optical activity is the ability of chiral substances to rotate the plane of polarized light.

What are racemic mixtures?

Racemic mixtures contain equal amounts of both enantiomers and are optically inactive due to cancellation of optical activity.

What is the role of hydrogen bonds in biological systems?

Hydrogen bonds stabilize the three-dimensional structures of proteins and nucleic acids.

How do hydrogen bonds contribute to DNA structure?

Hydrogen bonds between complementary bases stabilize the double helix structure of DNA.

What is the significance of polarity in biomolecules?

Polarity affects the behavior of biomolecules, influencing solubility and interactions in biological systems.

What is the general structure of amino acids?

Amino acids have a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable R group.

What is a peptide bond?

A peptide bond is a covalent bond formed between the carboxyl group of one amino acid and the amino group of another.

What is the primary structure of proteins?

The primary structure is the specific sequence of amino acids in a protein.

What are secondary structures in proteins?

Secondary structures are local folded structures formed within a protein due to hydrogen bonding, such as α-helix and β-sheet.

What is the isoelectric point (pI) of an amino acid?

The isoelectric point is the pH at which an amino acid has no net charge.

How does the pH of a solution affect amino acids?

The pH affects the ionization state of amino acids, influencing their behavior in biological systems.

What is the significance of weak forces in protein folding?

Weak forces are crucial for maintaining the integrity of cellular structures and processes, influencing protein folding.

What are the unique properties of water that support life?

Water has high boiling and melting points, heat of vaporization, and surface tension, making it essential for life.

How does water's polar nature affect its solvent properties?

Water's polar nature allows it to effectively dissolve ionic and polar substances, facilitating biochemical reactions.

What is the secondary structure of a protein?

Local folded structures formed by hydrogen bonding, such as α-helices and β-sheets.

What is the primary function of enzymes?

To catalyze biochemical reactions.

How do structural proteins function?

They provide support and shape to cells and tissues, e.g., collagen and keratin.

What role do transport proteins play?

They carry substances, such as hemoglobin transporting oxygen.

What is the function of antibodies?

To help defend against pathogens in the immune response.

Which protein carries oxygen in red blood cells.

Hemoglobin.

What is myoglobin?

A monomeric protein that binds oxygen in muscle cells.

What disease is caused by a mutation in hemoglobin?

Sickle Cell Anemia.

What is cystic fibrosis related to?

Mutations in the CFTR protein affecting ion transport.

What is a zwitterion?

A dipolar ion of amino acids at physiological pH.

What are lipids?

Biomolecules that are soluble in organic solvents but not in water.

What are fatty acids?

Carboxylic acids with long hydrocarbon chains, classified as saturated or unsaturated.

What are triacylglycerols?

Storage lipids formed from glycerol and three fatty acids.

What is the role of glycerophospholipids?

They are major components of cell membranes.

What are steroids?

Lipids characterized by a core structure of fused rings, including cholesterol.

What is the function of essential fatty acids?

Crucial for human health and must be obtained from the diet.

What is the difference between saturated and unsaturated fatty acids?

Saturated fatty acids have only single C-C bonds, while unsaturated have one or more cis double C=C bonds.

What is the significance of LDL and HDL cholesterol?

LDL is considered 'bad' cholesterol, while HDL is 'good' cholesterol.

What is DNA replication?

The process by which genetic information is copied from one generation of cells to the next.

What is semiconservative replication?

A method where each daughter DNA molecule consists of one original strand and one newly synthesized strand.

What are DNA polymerases?

Essential enzymes that catalyze the addition of nucleotides during DNA synthesis.

What is the role of Polymerase III in DNA replication?

It is the primary enzyme involved in elongation during DNA synthesis.

What does Polymerase III require to initiate DNA synthesis?

A template strand and a primer with a free -OH group.

What byproduct is released during the synthesis of DNA by Polymerase III?

Pyrophosphate (PPi).

What is the role of DNA polymerase I in DNA replication?

It has proofreading function to remove mismatched nucleotides through exonuclease activity.

What is the function of helicases in DNA replication?

They unwind the DNA double helix to allow access for DNA polymerases.

How do topoisomerases assist in DNA replication?

They alleviate torsional strain caused by unwinding, preventing supercoiling.

What is the role of single-stranded binding proteins (SSBs)?

They stabilize unwound DNA strands, preventing re-annealing or degradation.

What is the function of DNA ligase?

It joins Okazaki fragments on the lagging strand to form a continuous DNA molecule.

What initiates the DNA replication process?

Helicase binding to the origin of replication and breaking hydrogen bonds between base pairs.

What is the significance of RNA primers in DNA synthesis?

They provide the necessary starting point for DNA polymerases, as they cannot initiate synthesis de novo.

In which direction does DNA polymerase III synthesize new DNA strands?

In the 5' to 3' direction.

What are Okazaki fragments?

Short segments of DNA synthesized on the lagging strand during DNA replication.

What is the error rate of DNA synthesis due to proofreading mechanisms?

Approximately one mistake per billion nucleotides added.

What is the role of telomeres in eukaryotic chromosomes?

They protect the ends of linear chromosomes and prevent degradation and fusion.

What enzyme maintains telomere length?

Telomerase.

What are substitution mutations?

Mutations involving the replacement of one base in the DNA sequence with another.

What are frameshift mutations?

Mutations that occur when nucleotides are inserted or deleted from the DNA sequence, altering the reading frame.