Biochemistry Test 1 Flashcards

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Questions and Answers

What is biochemistry?

The study of chemical reactions in plants

A discipline in biochemistry; is the description of molecules in biology/chemistry of proteins (correct)

The study of molecules in biology

A discipline in chemistry

What is molecular biology?

A discipline in biochemistry; the manipulation of DNA, genetics.

What does cell biology study?

A discipline in biochemistry; larger scale, functions and mechanisms within a cell/cell energetics.

What is cellulose?

A natural polymer; found in plants for storage. Signup and view all the answers

What is glycogen?

A natural polymer; found in animals for storage. Signup and view all the answers

What is a protein?

A natural polymer; tightly linked bonds. Signup and view all the answers

What does nucleotide refer to?

A natural polymer; covalent bonds. Signup and view all the answers

What are the chemical elements commonly found in biochemistry?

C, H, N, O, S. Signup and view all the answers

What is the significance of carbon in biochemistry?

An element commonly found in biochemistry, creates strong single or double bonds with very little rotation. Signup and view all the answers

What is a covalent bond?

A chemical bond in biology; a pair of shared electrons, very strong, bonds between polymers. Signup and view all the answers

What characterizes a non-covalent bond?

A chemical bond in biology; weaker bonds, but additive, creates specificity, highly dynamic/transient bonds. Signup and view all the answers

Match the following types of non-covalent interactions:

Electrostatic = Like charges repel Hydrogen = A H is shared between two electronegative atoms Van der Waals = Temporary dipoles from fluctuating electrons Hydrophobic = Clustering of non-polar molecules in polar substances Signup and view all the answers

The H bond _ becomes more tightly linked, the H bond _ becomes less tightly linked.

donor acceptor Signup and view all the answers

What types of non-covalent interactions are there?

Electrostatic, hydrogen, van der Waals, hydrophobic. Signup and view all the answers

What role does water play in biological systems?

Roles of water; many organic and biological materials are able to dissolve in water. Signup and view all the answers

What is the ideal temperature of water with the highest heat capacity?

37°C. Signup and view all the answers

What is the pH of blood?

7.4. Signup and view all the answers

Which of the following statements about amino acids is true?

The side chains of amino acids are known as R-groups. Signup and view all the answers

What is the function of peptidases?

Specialized proteins that break peptide bonds. Signup and view all the answers

Define hydrolysis in the context of amino acids.

The name of the reaction when 2 amino acids break their amino and carboxyl terminus. Signup and view all the answers

What is SDS?

Sodium dodecyl sulfate, a negatively charged detergent. Signup and view all the answers

What is a gel used to determine the molecular size and purity of a protein?

SDS-PAGE. Signup and view all the answers

Study Notes

Biochemistry Fundamentals

Biochemistry: Study of biological and chemical molecules, primarily proteins.
Molecular Biology: Focuses on DNA manipulation and genetics.
Cell Biology: Examines functions and mechanisms within cells.

Natural Polymers

Cellulose: Found in plants, critical for structural storage.
Glycogen: Storage form of energy in animals.
Proteins: Comprised of tightly linked peptide bonds.
Nucleotides: Building blocks of nucleic acids, linked by covalent bonds.

Chemical Elements in Biochemistry

Common elements: Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), Sulfur (S).
Carbon: Forms strong single or double bonds, allows for structural complexity.

Chemical Bonds

Covalent Bonds: Strong bonds formed by sharing electron pairs between atoms, allowing flexibility.
Non-Covalent Bonds: Weaker, transient interactions crucial for molecular recognition, include:
- Electrostatic interactions (ionic bonds)
- Hydrogen bonds
- Van der Waals forces
- Hydrophobic interactions

Non-Covalent Interactions

Electrostatic Interaction: Ionic connections like Na⁺ and Cl⁻ in NaCl.
Hydrogen Bonds: Form when H is shared between electronegative atoms (N, O, F).
Van Der Waals Forces: Temporary dipole-based interactions; weak but contribute cumulatively.
Hydrophobic Interaction: Non-polar molecules clustering in polar environments, e.g., water.

Water in Biochemistry

Acts as a biological solvent, dissolving many organic and biological materials.
In reactions, it participates in bond cleavage.
Critical for temperature and pH regulation; optimal at 37°C.
Hydrophilic substances bond via dipole-dipole and hydrogen bonding.
Hydrophobic aliphatic compounds lack affinity for water, typically consist of long chains of C and H.

Acid-Base Chemistry

pH: Measures hydrogen ion concentration, calculated as -log[H⁺].
Acids release protons, while bases accept protons.
Ka & pKa: Reflect acidity, with pKa = -log[Ka].
Monoprotic Acids: Release one proton; polyprotic acids release multiple.
Buffer Solutions: Resist changes in pH, crucial for biochemical stability (e.g., acetate, citrate, phosphate).

Amino Acids

Composed of amino, carboxyl, alpha carbon, and R-group.
Chirality: Alpha carbon binds four different groups, yielding enantiomers.
Commonly known forms of amino acids are L (notable for biological processes).
Isoelectric pH: pH at which an amino acid has no net charge, calculated from average pKa values.

Protein Structure and Composition

Peptides and Proteins:
- 1-10 amino acids = multiple
- 10-100 amino acids = polypeptide
- 100 amino acids = protein.
Protein Composition:
- Monomeric: Single polypeptide chain.
- Multisubunit: Multiple polypeptide chains (oligomeric).
- Simple: Only made of amino acids; Conjugated: includes non-amino acid components.
Globular vs Fibrous Proteins: Globular proteins are soluble in water, while fibrous proteins contribute to structural integrity.

Protein Purification Techniques

Assay Development: Initial step in purification process.
Fractional Centrifugation: Separates supernatant (liquid) from pellet (solid).
Chromatography Methods: Such as:
- Gel Filtration: Based on size; larger proteins elute first.
- Ionic Exchange: Separates by charge, utilizing agarose or cellulose.
- Affinity Chromatography: Based on ligand interactions.

Molecular Weight and Analysis

Specific Activity: Ratio of total activity to total protein; helps in assessing enzyme concentration.
Yield: Total activity during the process over original activity.
Purification Level: Measures the effectiveness of purification based on specific activity.

Gel Electrophoresis

SDS-PAGE: Assesses molecular size and purity; smaller proteins migrate faster.
Sodium Dodecyl Sulfate (SDS): Anionic detergent used to coat proteins.
Polyacrylamide Gel (PAGE): Used in size and purity assays; contains acrylamide, a neurotoxic component that forms pore structures.

Summary of Key Characters and Processes

Cysteine & Cystine: Cysteine is reduced; cystine features oxidized disulfide bonds.
Condensation and Hydrolysis Reactions: Join or split amino acids, respectively.
Peptidases: Proteins that cleave peptide bonds (e.g., trypsin).
Reducing Agents: Such as beta-mercaptoethanol, break disulfide bonds.

Essential Terminology

Residue: Refers to the side chain of an amino acid; directionality denoted as left (N-terminus) and right (C-terminus).
Isoelectronic Point: pH where net charge of an amino acid is neutral; average of pKa values.

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Description

Explore key concepts in biochemistry through these flashcards. This quiz covers essential terms such as biochemistry, molecular biology, and cell biology. Perfect for students preparing for exams or anyone interested in the foundational principles of biochemistry.