BioE002- Fundamentals of Molecular Biology Chapter 2

Covalent Bonds

Formed by 2 atoms sharing electrons. A common bond is formed with peptide bonds, between 2 amino acids. Atoms are free to rotate around a single bond but not a double bond.

Ionic bonds

Formed from attraction between charged ions

First law of thermodynamics

Energy can’t be created or destroyed, it can only change form

Second law of thermodynamics

Degree of disorder (entropy) in a system increases over time

Exergonic

Chemical reactions that entail a decrease in free energy (ΔG < 0) are energetically favorable

Endergonic

Reactions with an increase in free energy (ΔG>0) are unfavorable because they require an input of free energy

Examples of Noncovalent bonds

Thermal energy, Van der Waals, H-bonds. They are increasing in strength in that order

Examples of covalent bonds

Hydrolysis of ATP phosphoanhydride bond, C-C, C=C. Increasing in strength in this order

Organic molecules of cells

carbohydrates, glucose, polysaccharides, glycosidic bond, oligosaccharide

Carbohydrate

Body’s primary source of energy. It is broken down into glucose by cells for use as ATP

Glucose

A monosaccharide and major nutrients of cells/starting material for synthesis of all constituents

Polysaccharide

Storage form of sugars and form structural components of cells. Hundreds of thousands of sugars joined together

Glycosidic bond

covalent bonding of monosaccharide

Oligosaccharide

Few sugars joined together

Lipids

Fatty acids. Major roles include energy storage, being the major component of cell membrane, cell signaling. Fatty acids are stored as tryglycerides or fats. Fats allow energy to be stored in less than half the body weight than would be required to store the same amount of energy in carbohydrates.

Phospholipids

Principal components of cell membranes, consisting of 2 fatty acids joined to a polar head group.

Glycolipids

2 hydrocarbon chains linked to polar head groups that contain carbohydrates

Cholesterol

4 hydrocarbon rings that are highly hydrophobic

Nucleic acids

Informational molecules of cells. Contains nitrogenous bases and sugars

Nitrogenous bases

Purines and pyrimidines

purines

Nitrogenous bases with a double ring structure and are key components of DNA and RNA. Adenine and Guanine

pyrimidines

Cytosine and thymine/uracil

sugars

deoxyribose DNA (ATCG) and ribose RNA (AUCG)

Nucleotides

Organic molecules that are the building blocks of DNA and RNA. Phosphates + nitrogenous bases + sugars

RNA

Composed of an extra hydroxyl group instead of hydrogen

DNA

Has a H bond instead of a hydroxyl group

Polymerization of nucleotides

Involves formation of phosphodiester bonds between 5’ phosphate of one nucleotide and the 3’ hydroxyl of another nucleotide. Sequences of bases in DNA and RNA are written in the 5’ to 3’ direction.

Double helix advantages

Allows tight packing of DNA into chromosomes, facilitates proper self-replication, facilitates proper transcription to RNA, makes DNA more stable, doesn’t allow rapid mutation of dna structure, makes DNA water soluble in nature

mRNA

Messenger RNA, carries info from DNA to ribosomes. mRNA code determines amino acid sequence in protein that is produced

rRNA

Ribosomal RNA. Incorporates into the ribosomes. Makes part of the ribosome which does translations.

Transfer RNA

Transfers amino acids to polypeptide chains at ribosomal cite of protein synthesis during translation.

miRNA

Micro RNA. Regulates gene activity.

Carbohydrates

Biomolecule consisting of carbon, hydrogen, and oxygen

Hydrocarbon

Biomolecule consisting of carbon and hydrogen

proteins

Polymers synthesized from 20 different amino acids. They carry out instructions contained in nucleic acids. They are folded into distinct 3D shapes.

Enzyme

Increases the rate of chemical reactions without being consumed themselves. They also increase the reaction rate without interfering in the equilibrium between the reactants and the products

Substrate

Binds to the active site of an enzyme.

Induced fit

Alters configurations of both the enzyme and the substrate

Coenzymes

Sites of enzymes bind other small molecules that participate in catalysis. They work together with enzymes to enhance reaction rates.

Catalytic Activity

Increased rate of chemical reactions without being consumed or permanently altered by reaction. It also increases reaction rates without altering chemical equilibrium between reactants and products.

Inhibition

Enzyme regulation by small molecules occurs through competitive and noncompetitive inhibition.

Competitive Inhibition

Binds active site of enzymes and blocks binding of the substrate. Can out compete the inhibitor by adding more substrate

Noncompetitive inhibition

Binding of small molecules to regulatory site on enzyme distinct from active site. Changes conformation of a protein which alters the shape of the active site. AKA allosteric regulation

Cell membrane

AKA plasma membrane. Defines the shape of the cell. In eukaryotes, it defines intracellular organelles such as the nucleus, mitochondria, and lysosomes. Consists of selectively permeable lipid bilayer and regulates transport of materials entering/exiting the cell. Each organelle has a plasma membrane

Phospholipid bilayers

Basic structures of cell membranes. They are amphipathic molecules consisting of 2 hydrophobic fatty acid chains linked to phosphate containing a hydrophilic head group. It plays a major role in energy transport. Uses cell-cell signaling to communicate

Fluid mosaic model

Very fluid and flexible structure. Allows organelles to assume typical shapes and enables membranes budding and fusion/fission

Budding

Allows for materials to come in/out parts of the cell

Hydrophobic core of phospholipid bilayer

Prevents most water-soluble substances from crossing one side of the membrane to the other.

Transport proteins

Mediate passage of most molecules across membranes

Channel proteins

Form open pores through the membrane whereas carrier proteins bind the molecules to be transported then undergo a conformational change to release molecules on the other side of the membrane

Passive transport

Molecules transported in energetically favorable direction

Active transport

Uses energy derived from ATP hydrolysis to transport molecules in the energetically unfavorable direction

Confocal microscopy

A pinpoint of light is focused on the specimen at a particular depth, and emitted fluorescent light is collected by a detector

Multiphoton excitation microscopy

Alternative to confocal microscopy that is especially useful for visualizing cells positioned
deeper within living tissue.

• The specimen is illuminated with a wavelength of light that is twice the excitation
wavelength of the fluorophore.

• Excitation of the fluorophore
requires the simultaneous
absorption of two or more
photons

• Simultaneous absorption of
two photons is required to
excite the fluorescent dye