Biochem Exam 2 Study Guide

Covalent Bonds

Strongest type of chemical bond formed by the sharing of electron pairs between atoms.

Hydrogen Bonds

Weak electrostatic attraction between a hydrogen atom and another electronegative atom, important for protein structure and DNA base pairing.

Ionic Bonds

Electrostatic interactions that occur between positively and negatively charged amino acid side chains.

Van der Waals Interactions

Weak interactions due to transient electric dipoles, contributing to protein folding.

Hydrophobic Interactions

Nonpolar molecules group together to minimize exposure to water, crucial for protein folding.

Peptide Bond

Covalent bond formed between the carboxyl group of one amino acid and the amino group of another.

Primary Structure

Linear sequence of amino acids in a protein.

Secondary Structure

Local folding of amino acids into α-helices and β-sheets.

Tertiary Structure

Three-dimensional folding of a single polypeptide.

Quaternary Structure

Assembly of multiple polypeptide chains into a protein complex.

Nucleotide Structure

A nucleotide consists of a nitrogenous base, pentose sugar, and phosphate group.

Purines

Nitrogenous bases with a double-ring structure, including Adenine (A) and Guanine (G).

Pyrimidines

Nitrogenous bases with a single-ring structure, including Cytosine (C), Thymine (T), and Uracil (U).

DNA Polymerases

Enzymes that catalyze DNA replication by adding nucleotides to a growing DNA strand.

RNA Polymerases

Enzymes that synthesize RNA using ribonucleoside triphosphates without requiring a primer.

Ribosomes

Cellular structures made of rRNA and proteins, crucial for protein synthesis.

Restriction Enzymes

Enzymes that recognize specific palindromic sequences and cut DNA.

DNA Ligase

Enzyme that forms phosphodiester bonds to join DNA fragments.

Sanger Sequencing

Method that uses dideoxy-NTPs to generate DNA fragments of different lengths, causing chain termination.

PCR (Polymerase Chain Reaction)

Technique used to amplify specific DNA fragments through a series of temperature cycles.

Hemoglobin Mutation

Mutation in β-subunit of hemoglobin causing sickle cell disease due to abnormal hemoglobin polymerization.

Michaelis-Menten equation

Mathematical description of enzyme kinetics illustrating the rate of enzymatic reactions.

Allosteric Regulation

The binding of a molecule at a site other than the active site, influencing enzyme activity.

Steps of PCR

1. Denaturation: DNA is heated to separate strands. 2. Annealing: Primers bind to target sequences. 3. Extension: DNA polymerase synthesizes new DNA strands.

Applications of PCR

1. Gene cloning. 2. Disease diagnosis. 3. Forensic analysis. 4. Environmental monitoring. 5. Genetic research.

Plasmid Vectors

Circular DNA molecules used to clone, transfer, or express genes in bacteria.

Transcriptional Signals

Sequences in DNA that indicate where transcription should start, often including promoters.

Translational Signals

Sequences in mRNA that guide ribosomes to initiate protein synthesis, including start codons.

Protein Separation Techniques

Methods such as chromatography, electrophoresis, and centrifugation used to isolate and purify proteins.

Enzyme Kinetics

Study of the rates of enzyme-catalyzed reactions, often described by the Michaelis-Menten equation.

Differential Solubility

Principle used in protein purification where solubility of proteins varies with changes in salt concentration or pH.

Size-Exclusion Chromatography

Technique that separates proteins based on their size, allowing smaller molecules to pass through porous beads while larger molecules elute first.

Ion-Exchange Chromatography

Method of separating proteins based on their electrical charge, involving a stationary phase with charged groups binding oppositely charged proteins.

Affinity Chromatography

Technique that separates proteins based on their specific binding interactions with ligands attached to a stationary phase.

Ribosome Structure

Ribosomes consist of two subunits: the small subunit and the large subunit, composed of rRNA and proteins.

Role of Ribosomes

Ribosomes are the cellular machinery responsible for synthesizing proteins from amino acids.

Binding Sites of Ribosomes

Ribosomes have three binding sites for tRNA: the A site (aminoacyl), P site (peptidyl), and E site (exit).

Translation Process

The process of translation occurs in ribosomes, where mRNA is decoded to produce polypeptides.

Prokaryotic vs Eukaryotic Ribosomes

Prokaryotic ribosomes have two subunits (50S and 30S), while eukaryotic ribosomes have two subunits (60S and 40S), reflecting differences in size and composition.

Polysomes

Polysomes are clusters of ribosomes that translate a single mRNA strand simultaneously.

A Site

The aminoacyl site on the ribosome where the incoming tRNA carries an amino acid during translation.

P Site

The peptidyl site on the ribosome where the tRNA holding the growing polypeptide chain is located.

E Site

The exit site on the ribosome where empty tRNA molecules leave after delivering their amino acid.

X-Ray Crystallography

A technique used to determine the atomic and molecular structure of a crystal by diffracting X-ray beams through the crystal lattice.

Meselson-Stahl Experiment

An experiment that demonstrated the semiconservative model of DNA replication using isotopes of nitrogen to trace the incorporation of nucleotides.

Types of DNA Polymerases

There are several DNA polymerases in eukaryotes, including Polymerase α, β, γ, δ, and ε, each with distinct roles in DNA replication and repair.

Role of DNA Polymerase I

DNA Polymerase I is involved in DNA repair and replacing RNA primers with DNA during DNA replication.

Proofreading Activity

Many DNA polymerases have proofreading ability, enabling them to correct errors by excising incorrectly paired nucleotides.

Processivity of DNA Polymerases

Refers to the number of nucleotides added by a DNA polymerase before it dissociates from the template strand, with some polymerases, like Polymerase δ, showing high processivity.

Template Strand Requirement

DNA polymerases require a template strand to synthesize a new DNA strand, ensuring that the correct complementary nucleotides are added.

DNA Polymerase Proofreading

The mechanism by which DNA polymerases check and correct errors during DNA synthesis by removing incorrectly paired nucleotides.

Glycosidic Bonds

Covalent bonds formed between a sugar (like ribose or deoxyribose) and a nitrogenous base, crucial for forming nucleotides.

Phosphodiester Bonds

Covalent bonds that link the 5' phosphate group of one nucleotide to the 3' hydroxyl group of another, creating a sugar-phosphate backbone in nucleic acids.

Hydrogen Bonds in DNA

Hydrogen bonds between the nitrogenous bases hold the two strands of DNA together, ensuring stable double helical structure.

Hydrogen Bonds in RNA

In RNA, hydrogen bonds between complementary bases help stabilize the structure of molecules such as tRNA and rRNA, influencing their functions.

Importance of Hydrogen Bonds

Hydrogen bonds play a critical role in the specificity of base pairing during DNA replication and transcription.

Base Numbering in DNA

Base numbering in DNA starts from the 5' end of the strand, with the first nucleotide designated as position 1.

Base Numbering in RNA

Similar to DNA, in RNA, the base numbering also starts from the 5' end, reflecting the sequence of nucleotides.

Sugar Numbering in Nucleotides

In nucleotides, the sugar ring is numbered with carbon atoms labeled from 1' to 5', with the 1' position connected to the nitrogenous base.

5' and 3' Ends of Nucleotides

The orientation of nucleotides in nucleic acids is described by the 5' phosphate group and the 3' hydroxyl group.

Bonding in DNA

Covalent phosphodiester bonds connect nucleotides in a DNA strand, while hydrogen bonds hold the complementary bases of the two strands together.

Bonding in RNA

In RNA, covalent bonds form the sugar-phosphate backbone, with hydrogen bonds stabilizing base pairing as in DNA.

Importance of Bond Angles

Bond angles in nucleotides affect the overall 3D structure of nucleic acids, influencing their biological function.

Glycosidic Bond Formation

Glycosidic bonds form between the sugar of a nucleotide and the nitrogenous base, crucial for forming nucleotides.

Stability of Phosphodiester Bonds

Phosphodiester bonds provide stability to the nucleic acid backbone, essential for maintaining the integrity of genetic material.

Base Pairing and Bonding

Base pairing in DNA involves specific hydrogen bonding between adenine and thymine (A-T) and cytosine and guanine (C-G).

Alanine (A)

A nonpolar amino acid known for its beta-alanine form, contributing to protein structure.

Arginine (R)

Positively charged amino acid involved in urea cycle and protein synthesis.

Asparagine (N)

Polar amino acid that plays a key role in nitrogen transport and metabolism.

Aspartic Acid (D)

Negatively charged amino acid, important for neurotransmission and enzyme function.

Cysteine (C)

A sulfur-containing amino acid, crucial for disulfide bond formation in proteins.

Glutamic Acid (E)

Negatively charged amino acid, serves as a neurotransmitter and is involved in metabolism.

Glutamine (Q)

Polar amino acid that functions as a nitrogen donor in biosynthetic processes.

Glycine (G)

The simplest amino acid, providing flexibility to protein structures and being nonpolar.

Histidine (H)

A polar amino acid important for enzyme active sites and histamine production.

Isoleucine (I)

An essential branched-chain amino acid important for muscle metabolism.

Leucine (L)

An essential branched-chain amino acid critical for protein synthesis and recovery.

Lysine (K)

Positively charged essential amino acid important for protein synthesis and immune function.

Methionine (M)

An essential amino acid that contains sulfur, serving as the starting amino acid for protein synthesis.

Phenylalanine (F)

An essential aromatic amino acid, precursor of neurotransmitters like dopamine.

Proline (P)

An amino acid that introduces kinks in protein structures, enhancing stability.

Serine (S)

A polar amino acid that contributes to active sites of enzymes and protein phosphorylation.

Threonine (T)

An essential polar amino acid important for protein structure and function.

Tryptophan (W)

Essential amino acid that serves as a precursor for serotonin and melatonin.

Tyrosine (Y)

A polar amino acid that is a precursor for neurotransmitters and hormones, including adrenaline.

Valine (V)

An essential branched-chain amino acid important for muscle metabolism and tissue repair.

Asparagine (N)

A polar amino acid that plays a key role in nitrogen transport and metabolism.