Claude Unit 2 vocab

Ion

An atom or molecule with a net electric charge because it has gained or lost electrons

Molecule

Two or more atoms held together by covalent bonds

Covalent bond

Strong bond in which two atoms share one or more pairs of electrons

Polar covalent bond

Covalent bond with unequal sharing of electrons, giving partial positive (δ+) and partial negative (δ−) ends

Ionic bond

Attraction between oppositely charged ions

Noncovalent bond

Weak attraction that does not involve sharing electrons (ionic/electrostatic, hydrogen bonds, van der Waals); many together stabilize molecular shape

Hydrogen bond

Weak attraction between a partially positive hydrogen (attached to O or N) and a partially negative atom such as O or N

Van der Waals forces (London dispersion force)

Weak, short-range attractions between atoms caused by temporary fluctuations in electron distribution

Hydrophilic force

Attraction of polar or charged groups to water; they form hydrogen bonds with water

Hydrophobic force

Tendency of nonpolar groups to avoid water and cluster together

Condensation reaction

Reaction that joins two molecules by removing a water molecule (dehydration synthesis); builds polymers from monomers

Hydrolysis

Reaction that breaks a bond by adding water; breaks polymers into monomers

Carboxyl group

–COOH; acidic functional group found in amino acids and fatty acids

Hydroxyl group

–OH; polar functional group found in alcohols and sugars

Amino group

–NH2; basic functional group found in amino acids

Glycosidic bond

Covalent bond joining two sugars in a carbohydrate; formed by a condensation reaction

Fatty acid

Long hydrocarbon chain with a carboxyl group at one end; hydrophobic building block of many lipids

Proteins are polymers of what? (and how many standard types)

Polymers of amino acids; there are 20 standard amino acids

Amino acid

Monomer of proteins; a central α carbon bonded to an amino group, a carboxyl group, a hydrogen, and a variable R group

R group (side chain)

The variable part of an amino acid that gives it its chemical properties; the part not involved in peptide bond formation

Hydrophobic (nonpolar) amino acids (per slides)

Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Methionine (Met, M), Phenylalanine (Phe, F), Tryptophan (Trp, W), Tyrosine (Tyr, Y)

Polar hydrophilic amino acids

Asparagine (Asn, N), Glutamine (Gln, Q), Serine (Ser, S), Threonine (Thr, T)

Basic hydrophilic amino acids

Lysine (Lys, K), Arginine (Arg, R), Histidine (His, H)

Acidic hydrophilic amino acids

Aspartic acid (Asp, D), Glutamic acid (Glu, E)

Special amino acids

Glycine (Gly, G), Proline (Pro, P), Cysteine (Cys, C)

Glycine (Gly, G)

Special amino acid whose R group is just a hydrogen (the smallest amino acid)

Proline (Pro, P)

Special amino acid whose side chain loops back to bond with the amino group, forming a ring

Cysteine (Cys, C)

Special amino acid with an –SH (sulfhydryl) side chain (CH2–SH)

Polar R groups vs nonpolar R groups

Polar R groups are hydrophilic and form hydrogen bonds with water; nonpolar R groups are hydrophobic and cluster away from water

Essential amino acids (as listed on slide)

Arginine, Histidine, Isoleucine, Lysine, Valine, Methionine, Phenylalanine, Threonine, Tryptophan

Primary structure

The linear sequence of amino acids in a polypeptide

Proteins are determined by the ______ of amino acids

Sequence

Polypeptide

A chain of amino acids linked by peptide bonds

Peptide bond

Covalent bond between the carboxyl carbon of one amino acid and the amino nitrogen of the next, formed by a condensation reaction (releases H2O)

How is a peptide bond formed?

Condensation (dehydration) reaction between the N end and C end of neighboring amino acids

N-terminus

End of a polypeptide with a free amino group

C-terminus

End of a polypeptide with a free carboxyl group

Polypeptide backbone

The repeating chain of atoms of the peptide bond and α carbon (N–Cα–C) running the length of the polypeptide

Side chains (R groups) of a peptide

The parts of the amino acids not involved in peptide bond formation

Polypeptide chain properties

Long and flexible

Conformation

Another way to describe a protein's 3D shape

What drives protein folding?

The hydrophobic/hydrophilic nature of amino acids: nonpolar side chains cluster in the core, polar side chains sit on the outside and hydrogen bond with water

Noncovalent interactions in protein conformation

Electrostatic attractions, hydrogen bonds, and van der Waals attractions between side chains and backbone help hold the 3D shape

Secondary structure

Local folding of the polypeptide backbone into α helices and β sheets, stabilized by hydrogen bonds between backbone groups

α helix

Coiled secondary structure; each backbone carbonyl group hydrogen bonds to an amide group four residues away, with side chains pointing outward and not involved in H bonds

β sheet

Secondary structure made of β strands from different parts of a single polypeptide chain, held together by backbone hydrogen bonds; two orientations (parallel and antiparallel)

Antiparallel β sheet

Adjacent strands run in opposite directions; narrowly spaced H-bond pairs alternate with widely spaced pairs

Parallel β sheet

Adjacent strands run in the same direction; evenly spaced H bonds bridge at an angle

Topology diagram

Simplified diagram of secondary structure (cylinders for α helices, arrows for β strands running N to C) that makes folds and motifs easy to identify

Motif

A recurring folding pattern made of a combination of secondary structure elements (α helices and β strands)

Tertiary structure

The overall 3D shape of a single polypeptide, formed by interactions among side chains and the backbone

Quaternary structure

Arrangement of two or more polypeptide subunits in one protein; involves binding sites for other proteins

Subunit

A single polypeptide chain that is part of a larger multi-chain protein

Binding site

Region of a protein where another molecule (such as another protein) binds

Protein domain

A compact, semi-independent folded unit within a single polypeptide chain; proteins often have one or more domains

Protein family

Group of related proteins with similar amino acid sequences and 3D structures

Molecular chaperones

Proteins that help other proteins fold correctly and prevent misfolding and aggregation

Levels of protein structure (in order)

Primary (amino acid sequence), secondary (α helix/β sheet), tertiary (folded polypeptide), quaternary (assembled subunits)

Denaturation

Loss of a protein's native 3D shape and biological activity (caused by agents like pH, temperature, ionic strength, solubility); example: cooking an egg white

Renaturation

A denatured protein regains its native shape and activity

Protein aggregates and neurodegeneration

Misfolded proteins clump together; linked to Alzheimer's, Parkinson's, and Mad Cow disease (amyloid β, tau protein, α-synuclein, prions)

How do cells regulate proteins?

Gene expression, compartmentalization, and interactions with other molecules

Protein phosphorylation

Attaching a phosphate group to an R group (side chain) of a protein, causing a conformational change

Protein kinase

Enzyme that adds a phosphate group (from ATP) to a protein; turns it ON or OFF

Protein phosphatase

Enzyme that removes a phosphate group from a protein

Motor proteins

Proteins that use ATP (binding, hydrolysis, release) to produce movement

GTP-binding proteins

Active when bound to GTP; GTP hydrolysis to GDP + Pi makes them inactive; exchanging GDP for GTP reactivates them

DNA (deoxyribonucleic acid)

Macromolecule (polymer of nucleotides) that stores genetic information

Is DNA a molecule or a macromolecule?

Both, but it is a macromolecule because it is a large polymer of nucleotides

Nucleotide

Monomer of nucleic acids: a phosphate, a sugar, and a nitrogenous base

Sugar (in nucleotides)

5-carbon sugar: ribose in RNA, deoxyribose in DNA

Nitrogenous base (base)

Nitrogen-containing ring in a nucleotide that carries genetic information (A, C, G, T in DNA; U replaces T in RNA)

Purine

Double-ring nitrogenous base: adenine and guanine

Pyrimidine

Single-ring nitrogenous base: cytosine and thymine (uracil in RNA)

5' end

End of a nucleic acid strand with a free phosphate group on the 5' carbon of the terminal sugar

3' end

End of a nucleic acid strand with a free hydroxyl (–OH) group on the 3' carbon of the terminal sugar

Phosphodiester bond

Covalent bond linking nucleotides: joins the 3' hydroxyl of one sugar to the phosphate on the 5' carbon of the next; forms the sugar-phosphate backbone

Complementary base pair

Bases that pair through hydrogen bonds: A with T (2 H bonds) and G with C (3 H bonds); in RNA, A pairs with U

Double helix

DNA structure of two strands twisted around each other, bases inside and sugar-phosphate backbone outside

How many strands are in a DNA molecule?

2

What holds the two DNA strands together?

Hydrogen bonds between the bases

Sugar-phosphate backbone

Outer part of the DNA double helix made of alternating sugar and phosphate groups

Scientists in the controversy over discovery of DNA structure

Watson and Crick, Rosalind Franklin, and Maurice Wilkins

Antiparallelism

The two DNA strands run in opposite directions: one runs 5' to 3' while the other runs 3' to 5'

Why are DNA strands antiparallel?

Nucleotides are bonded so each strand is polar (has a 5' end and a 3' end), and the two strands are oriented in opposite directions

Genetic information code

The sequence of nucleotides in DNA

Gene expression

The process of using the information in a gene to make a product, usually a protein (DNA to RNA to protein)

Genome

The complete set of genetic information (all the DNA) in a cell or organism

Gene

A segment of DNA that codes for a functional product (a protein or functional RNA); a unit of heredity

Chromatin

Complex of DNA and proteins (mainly histones) that makes up chromosomes in the eukaryotic nucleus

How is DNA packaged in eukaryotes?

The DNA helix is wrapped into chromatin, using histones to wrap the DNA

Chromosome (x-some)

A single long DNA molecule packaged with proteins as chromatin

Interphase chromosome

Extended, less condensed chromosome in the nucleus during interphase, when gene expression and chromosome duplication occur

Mitotic chromosome

Highly condensed, compact chromosome during mitosis (visible); the mitotic spindle attaches to distribute DNA to daughter cells

Interphase

Phase of the cell cycle in which chromosomes are duplicated

Mitosis

Phase in which the duplicated chromosomes are distributed to the newly formed daughter nuclei

Nucleolus

Region of the nucleus where ribosomal RNAs are synthesized

Euchromatin

Less condensed chromatin that contains genes undergoing gene expression

Heterochromatin

Most highly condensed chromatin; has few genes or genes that are not expressed

Histone

Positively charged protein responsible for the first level of DNA coiling; DNA wraps around histones