Bio 202 Section 1

Ionic bonding

Transfer of electrons

Covalent bonding

Sharing of electrons

Electronegativity

The tendency of an atom to attract electrons

Adhesion

Water molecules that adhere to the glass and pull upwards at the perimeter

Cohesion

Water molecules at the surface form hydrogen bonds with nearby water molecules and resist the upward pull of adhesion

pH scale

Determines level of acidity

Buffers

Chemicals that minimize changes in pH by either absorbing protons from solution or releasing protons into the solution to keep the pH at a particular point

Potential energy

Stored/chemical energy

Energy of motion

Kinetic/thermal energy

Gibbs free energy (G)

Energy associated with a system

Change in Gibbs free energy (ΔG)

Free energy change associated with a chemical reaction (ΔG = ΔH - TΔS)

ΔH

Change in enthalpy

ΔS

Change in entropy

Cellular respiration

The complete breakdown of glucose under aerobic conditions

Chemical evolution

The processes that could have taken place on a prebiotic earth (before life had formed) that created the molecules necessary for life to arise

Stanley Miller

Scientist who performed the first simulations showing that carbon reduction would have been possible on the early earth

Prebiotic soup model of chemical evolution

Proposes that early Earth's oceans, rich in simple organic compounds and energized by lightning or UV radiation, formed a soup from which life spontaneously emerged

Surface metabolism model of chemical evolution

Proposes that life originated on mineral surfaces at hydrothermal vents where inorganic catalysts, such as iron and nickel sulfides, facilitated the formation of complex organic molecules from simpler precursors before self-replicating genetic molecules (RNA/DNA) emerged

Proteins

Most abundant biological macromolecules, composed of 20 amino acids with unique side chains

Amino acids

Composed of a central carbon connected to a hydrogen, amino group, carboxyl group, and R group; form proteins

R group

Side chain on amino acids that is different between them

Ionized form of an amino acid

In aqueous solution and at about neutral pH, the amino group will pick up a proton, giving it a positive charge, and the carboxyl group will lose a proton to the solution and have a negative charge; charges cancel out, so only the R group determines if an amino acid has a charge

Nonpolar amino acids

Amino acids whose R groups are nonpolar; no polar covalent bonds that would allow them to hydrogen bond with water

Polar amino acids

Amino acids whose R groups are not charged but have some electronegative atoms in their periphery with polar covalent bonds with partial positive and negative charges; interact with water through hydrogen bonding

Charged amino acids

R group either has a negative (acidic) or positive (basic) charge; either give up or take a proton/positive charge from solution

Chiral

Molecules that have four different functional groups attached to them; able to be found in mirror images of one another

Isomers

Molecules with the same chemical formula but different chemical structures

Optical isomers

Molecules that are mirror images of each other (chiral)

What form of amino acids are used by organisms?

Left-handed form

What is the only non-chiral amino acid?

Glycine; R group is a proton

Polymer

Long chain molecules that are composed of repeated subunits

Condensation reactions

Reactions that generate water as a byproduct

Hydrolysis

Reactions when water is used to split something

Peptide bonds

The covalent bonds formed by condensation reactions that link amino acids together

Peptide

A short chain of unfolded amino acids

N-terminus/amino terminus

The first amino acid in a peptide that still has a free amino group (+)

C-terminus/carboxyl terminus

The last amino acid in a peptide that still has a free carboxyl group (-)

Polarity

One side is different from another

Primary structure

The linear structure of amino acids in a peptide

Secondary structure

Protein folding structure stabilized by the hydrogen bonds between the carboxyl oxygen and the amino hydrogen of different amino acids

Alpha helix

Type of secondary structure where the protein coils around itself

Beta-pleated sheets

Secondary protein structure shaped like an accordion where the protein is wrapped around itself

Tertiary structure

Protein folding structure when regions of the secondary structure interact with each other through hydrogen bonding, ionic bods, Van der Waals interactions, and disulfide bonds

Hydrogen bonding

Tertiary structure where hydrogens between R groups of polar amino acids, or the amino group of one amino acid and the carboxyl or R group of another, interact

Ionic bonds

Tertiary protein structure where R groups of an acidic and a basic amino acid interact

Van der Waals interactions

Tertiary protein structure where the R groups of non-polar amino acids interact

Van der Waals forces

Very weak attractive forces that primarily play a role in interaction between hydrophobic molecules

Disulfide bonds

Tertiary protein structure where the sulfhydryl groups on cysteines in a protein form a covalent disulfide bonds linking the two sulfur groups together

Quaternary structure

Proteins where the final functional form of the protein is composed of two different peptides that folded up independently into their tertiary structures and then came together

Molecular complementary

Two molecules can only interact if:

• They have enough noncovalent interactions to stabilize their association

• They have shapes that fit together in a way that they come into close contact

Denaturation

Unfolding of proteins caused by the introduction of a chemical or a change in environmental conditions

Oil drop model of protein folding

Proteins fold by burying hydrophobic (non-polar) amino acid side chains in their core, shielded from water, while placing polar/charged amino acid side chains on the surface

Chaperones

Protein complexes that help other proteins fold properly by grabbing unfolded polypeptides and folding them

Chaperonins

Protein complexes that help other proteins fold properly by creating an enclosed space for unfolded polypeptides to fold within

Proteinopathies

Diseases caused by miss-folded proteins

Prion diseases

Diseases that arise when a type of protein called a prion misfolds an binds to the correctly folded form of another prion protein, causing it to misfold as well

Nucleotide

5-carbon sugar (ribose or deoxyribose) with a nitrogenous base attached to carbon 1 and 1-3 phosphate groups attached to carbon 5

Purines

Nitrogenous bases with larger two-ring structures (cytosine, uracil, and thymine)

The ribose problem

It is difficult to get 5-carbon sugars to form in conditions that mimic the prebiotic earth

The pyrimidine problem

It is much easier for purines to arise than pyrimidines in pre-biotic earth conditions

Nucleic acids

Polymers of nucleotides

Phosphodiester bond/linkage

Covalent bond that forms between nucleotides in nucleic acids when a hydroxyl group in the five-prime phosphate of the next nucleotide that’s about to be added to the chain interacts with the hydroxyl group on the three-prime carbon of the last nucleotide in the chain

Gel electrophoresis

Separates DNA fragments by length by using a magnetic field to interact with their negative charges

Five-prime end

End of DNA that has a phosphate group in its five-prime carbon that isn’t attached to anything else, giving it a positive charge

Three-prime end

End of DNA that has a hydroxyl group on its three-prime carbon that isn’t attached to anything else, giving it a negative charge

Chargaff’s Rules

Discovered by Erwin Chargaff; found that the ratio of purines to pyrimidines was 1:1, the ratio of adenine to thymine was 1:1, and the ratio of guanine to cytosine was 1:1

X-ray crystallography

Crystalizes the molecule being studied and X-rays it, so the refraction pattern can be used to determine the original structure of the crystal

Rosalind Franklin and Maurice Wilkins

Used X-ray crystallography to discover that DNA is helical and determine its width and the length of one turn

James Watson and Francis Crick

Used models to determine that DNA is an antiparallel, double stranded helix with purines and pyrimidines opposite one another

Sugar-phosphate backbone

All of the sugar phosphates lining up on top of one another within DNA’s double helix

Minor groove

The narrow face of a DNA double helix

Major groove

The wide face of a DNA double helix; where proteins bind to DNA because they have the most access to bases

What is the difference between RNA and DNA?

• RNA uses ribose as its five-carbon sugar instead of deoxyribose, which has a hydroxyl group on the 2’ carbon instead of a hydrogen\

• More reactive and adopts a wider range of shapes

• Uracil used instead of thymine

Information carrier RNAs

Intermediaries from genetic information in DNA to final protein structure

Structural RNAs

RNAs that fold up into a shape and that molecule then carries out a structural role within the cell

Ribozymes

RNAs that serve as catalysts for biochemical reactions

Catalyst

Something that speeds up the rate of a reaction by lowering the activation energy

Living molecule

A molecule that has the capability of copying itself

Ribosome

Macromolecular structure in a cell that is responsible for making proteins; composed of small proteins and small ribosomal RNAs

RNA world hypothesis

Idea that during the transition from chemical evolution to the first true living organism, there was an intermediary period dominated by RNA

Carbohydrates

Biological macromolecules characterized by having the chemical formula (CH₂O)_n

Monosaccharides

Simple sugars

Polysaccharides

Polymers of monosaccharides

Carbonyl group

Carbon double bonded to an oxygen

Aldose

Monosaccharide with a carbonyl group at the end of the chain

Ketose

Monosaccharide with a carbonyl group in the middle of the carbon chain

Glucose

Six-carbon sugar with a hydroxyl group on carbon 4 pointing below the plane of the molecule

Galactose

Six-carbon sugar with a hydroxyl group on carbon 4 pointing above the plane of the molecule

Alpha glucose

Glucose that has formed a ring with the hydroxyl group on carbon 1 pointing below the plane of the molecule, in the opposite direction of carbon 6

Beta glucose

Glucose that has formed a ring with the hydroxyl group on carbon 1 pointing above the plane of the molecule, in the same direction of carbon 6

Glycosidic linkage

Bond formed between monosaccharides by a condensation reaction between hydroxyl groups