Chapter 3: Macromolecules

Merged flashcards from Chapter 3 of Principles of Life, 3rd Edition.

Polymers

Molecules made of smaller molecules called monomers; in macromolecules, these contain carbohydrates, nucleic acids, and proteins as they form long chains

Residues

The name for monomers when inside a polymer

Lipids

Non-monomers characterized by insolubility and aggregation in water, formed out of C—C and C—H bonds

• Have variable melting points due to size and packing

Fatty acid

A non-polar hydrocarbon chain with a polar terminal carboxyl functional group, thus giving it amphipathic traits

Phospholipid

Fatty acids bound to glycerol that also contain an amphipathic phosphate; these help form water-excluding bilayers as a result of aggregation and can transport materials with proteins

Lipoproteins

Structures with hydrophobic interiors and hydrophilic exteriors to transport lipids like triglycerides and cholesterol in water

Glycerol

A three-carbon molecule with three hydroxyl groups

Saturation

• Possessing this gives a lipid a straight, long chain with only single bonds for hydrogen and carbon, allowing for higher melting points

• Without this, lipids can have double bonds with carbons and be more loosely packed, giving it lower melting points

Triglycerides

Lipids with 3 fatty acids linked to glycerol via condensation; these are the most common and are best for energy storage

Wax

A lipid with a long-chain alcohol bound to a fatty acid; these are very hydrophobic

• This coats the leaves of plants to reduce water loss and protect against pathogens

Carotenoid

Lipids with a repeating, branched five-carbon unit; these enable light absorption

Steroid

Lipids with a 17-carbon atom core in four fused rings

• Some hormones are a type of these, functioning as signals

White fat

This type of fat stores energy and provides insulation in mammals

Brown fat

This type of fat gets its color from iron-rich mitochondria and regulates temperature in infants

Carbohydrates

A group of molecules varying in size, properties, and functions, with the chemical formula C_m(H₂O)_n and a hydroxyl group connected to C atoms

• Those with less than 12 carbons are simple sugars

• Can be small or joined together

Monosaccharides

The simplest carbohydrates, with a linear or ring formation formed by 5 or 6 carbons

• Comprised of structural or stereoisomers, differing in arrangement for binding

• Polymer structures depend on these

Disaccharides

Two monosaccharides joined in a condensation reaction

• Linked by a glycosidic bond formed by two hydroxyl groups that form water and oxygen

• Like monosaccharides, these can be broken down for energy or bonded to other macromolecules

Oligosaccharides

Three to ten monosaccharides, modified by their functional groups

• Often covalently bonded to proteins or lipids for functions or solubility, and can be found on the outsides of cells as signals

Polysaccharides

Hundreds to thousands of monosaccharides, joined by glycosidic bonds and arranged in chains or branches

• Branching depends on function and location, often for energy storage

• Hydrogen bonds can form in parallel groups, creating strength (as in cellulose)

• Joined via 1,4 glycosidic bonds for linear forms or 1,6 glycosidic bonds for branching forms (number denotes carbon order)

Starch

The principal energy storage compounds for plants

Glycogen

The principal energy storage compounds for animals, fungi and bacteria

• These are insoluble, but can have glucose ends hydrolyzed and broken down

• Grouping of these prevent osmotic pressure from building up

Nucleic acids

Polymers that store and express genetic information via nucleotide monomers, grouped into DNA (with deoxyribose) and RNA (with ribose)

• DNA encodes for RNA, which encodes for protein types

Nucleotide

A single unit of a nucleic acid, made of a monosaccharide, a nitrogen-containing base (linked to the 1’ carbon), and one to three phosphate groups (linked to the 5’ carbon)

• Can be joined in oligonucleotides for basic regulation as RNA (3 to 20 monomers) or polynucleotides for heredity in DNA (hundreds of millions of monomers)

Base

Nitrogen-containing molecules that form the genetic code for DNA and RNA, classified as pyrimidines (single rings) or purines (double rings)

• Linked to the 1’ carbon

Nucleoside

A nitrogenous base and ribose without a phosphate group

Phosphodiester bond

This is formed to create the “sides” in the sugar-phosphate bond, where the 3’ carbon atom on the previous nucleotide is linked to the triphosphate on the next 5’ carbon atom

• Requires more than one phosphate due to an increase in free energy

Complimentary base pairing

When two nitrogenous bases in DNA or RNA pair with their complimentary parts through hydrogen bonds; bonds between guanine and cytosine are stronger than those between adenine, thymine, or uracil with more bonds

• These bonds across millions of bases collectively create an attraction that is strong enough to remain together but can be separated with some energy

• Required for transcription and translation, which are performed in opposite direction

Deoxyribonucleic acid (DNA)

A double-stranded molecule with informational and complimentary base pairs in the middle, twisting into a helical structure

• The expression of this is determined by its function and position in the body despite each cell containing all of this molecule’s instructions

Ribonucleic acid (RNA)

A single-stranded molecule that can fold back, stabilized by complimentary base pairing

• Created as a result of transcription from DNA to signal for protein production in translation in smaller groups

DNA replication

The process where DNA is copied onto new DNA molecules for transmission to daughter cells and offspring

Proteins

Polymers made up of tens to tens of thousands of monomers called amino acids, essential to the functioning of life due to their numerous abilities

Amino acid

A single monomer of a protein that contains an amino and carboxyl group; these can be classified into twenty different types with charge, polarity, size, shape, and functional differences

• Like nucleotides, these form proteins sequentially, with carboxyl groups chaining with incoming amino groups to form peptide bonds

• Some are required to be obtained from the diet

Peptide bond

The bond between amino acids in a protein, formed by a carboxyl and amino group with a water molecule loss

Alpha carbon

The central carbon in an amino acid that can form four covalent bonds

• Two are occupied by the carboxyl and amino groups

• A third is occupied by a hydrogen atom

• The fourth is occupied by the differing R group

R group

A functional group unique to each of the twenty amino acids

• Ten are hydrophilic, with five having an electric charge attracting ions and another five having polarity attracting hydrogen bonds

• Seven have nonpolar hydrocarbon chains, which can cluster together in the protein’s interior or interact with lipids

• Three remain in a special category due to structural features

Glycine

A special R group consisting of a hydrogen atom

• This allows for tight corners and flexibility in proteins

Cysteine

A special R group with a terminal SH group

• Can react with another side chain or molecule to form a stabilizing covalent disulfide bridge

Oligopeptides

Short polymers of 20 or fewer amino acids; includes some hormones and other signaling molecules

Polypeptides

Very long polymers with a unique sequence of amino acids that ultimately comprise proteins

Primary structure

The precise sequence of amino acids in a protein; there are many of these due to the 20 amino acids available

• Determined by covalent peptide bonds

Secondary structure

The stage of a protein’s structure that consists of regular, repeated spatial patterns in different regions of a polypeptide chain; the most common patterns are the alpha helix and beta pleated sheet

Alpha helix

A right-handed helical shape formed in secondary structures, with R groups coiling and extending from the peptide backbone to form hydrogen bonds within the coil

Beta pleated sheet

A secondary structure shape formed by extended and aligned amino acids, stabilized by hydrogen bonds between amino and carboxyl groups on the two chains

Tertiary structure

The stage of a protein’s structure that arises from the bending and folding of polypeptide chains, resulting in a three-dimensional structure with an interior and exterior capable of molecular interactions

Side chain interactions

These determine the shape of tertiary and quaternary structures, and include:

• Cystine covalent disulfide bridges

• Ionic interactions and bonds between charged side chains to ensure correct formations

• Hydrogen bonds

• van der Waals interactions between hydrophobic side chains

Subunits

Two or more polypeptide chains folded into a unique tertiary structure, these affect quaternary structure folding

Quaternary structure

These result from subunit binding and interactions as well as side chain interactions

• May form beta pleated sheets between separate polypeptide chains, which can lead to abnormalities if overly aggregated

Denaturing

Occurs when a protein is heated or has its molecular structure disrupted

• Can often be reversed if cooled or the disruptive force is removed, requiring the primary structure to remain intact and unbonded from unoriginal polypeptides

• May also occur due to pH, polar solutes, ionic bonds, and nonpolar substances that affect chemical reactions

Enzymes

Catalytic molecules that increase the rate of biochemical reactions by lowering the activation energy needed

• These can bind to reactants to participate in the reaction yet maintain their chemical form

• Generally specialized to bind to only one or a few closely related reactants in one reaction

• Produced and regulated according to needs of environment and system

Structural and motor proteins

Proteins that provide physical stability and enable movement in the cell

Signal and regulatory proteins

Proteins that control the rates of numerous biological processes

Receptor proteins

Proteins that receive and respond to molecular signals from inside and outside the organism

Protein bonding

This occurs at specific sites on the protein determined by its three-dimensional shape, where side chains bond with molecules or ions

Ligand

A molecule or ion that binds to another molecule, like a protein, through numerous weak bonds that determine binding affinity

• Addition of these can cause conformational changes which affect protein functions

Binding affinity

The interaction strength between a ligand and protein molecule

Conformational change

A change in the shape of a protein following the binding of a ligand, affecting its function

Side chain modification (R group modification)

Protein structure modifications through amino acid and chemical group bonds

Cofactor

An additional molecule that some proteins require to function, varying in bond strength either for tight or loose bonds

• Seen with ATP as it is converted to and from ADP

Prosthetic groups

Cofactors that are tightly bound to a protein with covalent bonds

Coenzymes

Cofactors that are loosely bound to enzymes

Proteolysis

The breaking apart of a bond in a protein for a change in activation state as needed

Reaction rate

This can be affected by temperature, concentrations, free energy, and activation energy

Activation energy (E_a)

The energy needed to successfully start and complete a reaction

• This can be met with higher temperatures or molecular reorganization for higher interaction likelihood

• Most common way of meeting this in living systems is lowering it via enzymes

Catalysis

The ability to increase reaction rates without chemical changes; enzymes can do this repeatedly and rapidly up to a 10³ to 10⁸ speedup

Substrates

The reactants in an enzyme-catalyzed reaction

Active site

The site on the enzyme where specific substrate molecules bind

• Typically only a small part of the protein

• Relies on hydrogen bonds, van der Waals interactions, and charged groups for binding

Conformation

The three-dimensional shape of an enzyme

• With its chemical properties, one enzyme is made to be highly specific

• This may change during a reaction as an example of induced fit

Enzyme-substrate complex (ES)

This is created by the binding of substrates to the active site of an enzyme, held together by chemical bonds, in order to give rise to products

Induced strain

Method of inducing change through an enzyme by stretching bonds in the substrate, making them easier to break with greater potential energy

Substrate orientation

Method of inducing change through an enzyme by orienting two substrates to facilitate reactions

Chemical modification

Method of inducing change via an enzyme via the involvement of the side chains (R groups) in the reaction for manipulation of products

Metabolic pathway

A series of reactions in which the product of one reaction is a substrate for the next for the breakdown or synthesis of molecules

Catabolic pathway

A metabolic pathway that breaks down molecules and releases energy

Anabolic pathway

A metabolic pathway that synthesizes molecules from simpler ones, building up potential energy

Inhibitor

A molecule that prevents the entry of a molecule into the active site, lowering the rate of reaction

Irreversible inhibition

When an inhibitor covalently binds to an active site of an enzyme and fails to leave, disabling the enzyme

• Rare in nature but used in medicines

Competitive inhibitor

An inhibitor of an enzyme that binds to the active site and prevents substrate binding normally, decreasing the rate of reaction as none occur

• These are reversible and can be countered with greater substrate concentration

Uncompetitive inhibitor

An inhibitor of an enzyme that binds to the complete enzyme-substrate complex, preventing the release of products

• Cannot be countered with greater substrate concentration due to attraction to already-bound enzyme

• Can be unbound, allowing for occasional formation of products

Noncompetitive inhibitor

An inhibitor of an enzyme that binds outside of the active site, changing the enzyme structure so that normal binding cannot occur

• Cannot be countered with greater substrate concentration due to attraction to enzyme itself (requires greater enzyme concentration)

• Can be unbound with reversible effects

• Is a type of allosteric regulation

Allosteric regulation

Type of regulation where molecules bind to an enzyme outside of the active site and modify the enzyme’s shape, allowing for a change in activity

• This can be done non-covalently and reversibly

• Seen with noncompetitive inhibitors

Allosteric site

The binding location of molecules involved in the allosteric regulation of enzymes

• These are typically on different peptides of the protein

Phosphorylation

The process of modifying an amino acid by the addition of a phosphate group

• Can induce changes like increased hydrophilicity

• Is reversible

Kinase

A class of enzymes that catalyzes the addition of phosphate groups to proteins

Phosphatase

A class of enzymes that catalyzes the removal of phosphate groups from proteins