Biochem exam 1 study guide module 1 and 2

Three domains of life

bacteria, archaea, and eukarya

bacteria

single-celled organisms that inhabit various environments

archaea

single-celled organisms known for thriving in extreme environments

Eukarya

encompasses all eukaryotic organisms, including plants, animals, fungi, and protists

While bacteria and archaea are prokaryotes…

eukarya is more closely related to archaea than bacteria

gram-positive bacteria

have thick peptidoglycan layer outside their plasma membrane and lack and outer membrane

gram-negative bacteria

have a thinner peptidoglycan layer and possess and outer membrane composed of a lipid bilayer

What leads to differential staining properties in the gram staining technique

difference in cell envelope structure betweeb gran-positive and gram-negative bacteria

Cytosol

the fluid portion of the cytoplasm, a highly concentrated solution containing enzymes, RNA, amino acids, nucleotides, metabolites, coenzymes, and inorganic ions. It serves as the site for many metabolic reactions.

Cytoplasm

the entire internal volume enclosed by the plasma membrane, consisting of the cytosol and suspended particles like mitochondria, ribosomes, and the cytoskeleton.

Dynamic steady state

refers to the state in living organisms where molecules are constantly synthesized and broken down, maintaining a stable internal environment despite constant exchange with the surroundings. This state is maintained through a continuous input of energy and is far from equilibrium.

the four major classes of biomolecules

proteins, nucleic acids, polysaccharides, and lipids

Proteins

composed of amino acids, and perform various functions like catalysis, structural support, and signaling.

Nucleic acids

including DNA and RNA, store and transmit genetic information.

Polysaccharides

polymers of simple sugars, serve as energy sources and structural components.

Lipids

diverse in structure, are crucial for membrane formation, energy storage, and signaling

Configuration

refers to the fixed spatial arrangement of atoms in a molecule, determined by the presence of double bonds or chiral centers, and cannot be changed without breaking bonds.

Conformation

the spatial arrangement of substituent groups that are free to rotate around single bonds, leading to different three-dimensional shapes without altering the connectivity of atoms.

Enthalpy (H)

the heat content of a system, reflecting the number and types of bonds

Entropy (S)

a measure of the system's randomness or disorder.

Free energy (G)

combines enthalpy and entropy, representing the energy available to do work.

G= H-TS where T is absolute temperature

standard free-energy change (∆G°)

indicates the tendency of a rxn to proceed spontaneously under standard conditions

A negative ∆G° vs positive

negative= exergonic (spontaneous) reaction

positive= endergonic (non-spontaneous) reaction

Energy coupling

links endergonic reactions, requiring energy input, with exergonic reactions, releasing energy. For example, the breakdown of ATP (adenosine triphosphate) is highly exergonic, releasing energy that can be used to drive endergonic reactions like muscle contraction or biosynthesis.

The central dogma of molecular biology

describes the flow of genetic information: DNA is transcribed into RNA, and RNA is translated into proteins. This process ensures the transmission and expression of genetic information, ultimately dictating cellular structure and function

Relationship between the 20 common amino acids and protein structure

The 20 common amino acids serve as the building blocks of proteins, much like letters in an alphabet form words. The unique sequence of these amino acids determines the protein's three-dimensional structure and ultimately, its function.

Describe the four substituents attached to the alpha-carbon of an amino acid

a carboxyl group (-COOH), an amino group (-NH2), a hydrogen atom (-H), and a variable R group (side chain) that distinguishes each amino acid.

Differentiate between L and D stereoisomers in amino acids, and state which one is prevalent in proteins

L and D stereoisomers are mirror images of each other, like left and right hands. Proteins

exclusively utilize L-amino acids

What distinctive characteristics of aromatic R groups allows for the detection of certain proteins

Aromatic R groups absorb UV light at wavelengths of 270-280 nm, which enables the

detection and quantification of proteins containing these amino acids using

spectrophotometry

Which class of amino acids can form disulfide bonds, and what is the significance of this

bond in protein structure?

Cysteine contains a sulfhydryl group (-SH) in its R group that can form disulfide bonds (S-S) with other cysteine residues. Disulfide bonds contribute to the stability of protein structure.

Describe how the chemical environment can affect the pKa values of an amino acid's

functional groups.

The chemical environment, particularly the pH, influences the ionization state of functional

groups. For example, a lower pH will favor the protonated form of an amino acid's carboxyl group, while a higher pH will favor the deprotonated form.

Define the isoelectric point (pI) of an amino acid and explain its relevance.

The isoelectric point (pI) is the pH at which an amino acid has no net charge. At this pH, the amino acid is the least soluble and does not migrate in an electric field.

Explain the difference between polypeptides and proteins.

A polypeptide is a chain of amino acids linked by peptide bonds. A protein is a larger, more

complex polypeptide with a defined three-dimensional structure and biological function.

Generally, a polypeptide with a molecular weight greater than 10 kDa is considered a

protein.

Describe two common methods used to separate proteins based on their properties.

Two common protein separation methods are:

a) Ion-exchange chromatography: separates proteins based on their net charge.

b) Size-exclusion chromatography: separates proteins based on their size.

Explain how the technique of electrophoresis is used to analyze proteins

Electrophoresis utilizes an electric field to separate proteins within a gel matrix based on

their charge and size. This technique allows visualization of protein bands, estimation of

protein size, and assessment of purity.