unit 1 bio

Element:

A distinct type of substance or matter. Each element has atoms that contain a unique number of protons in the nucleus.

Atom

Smallest unit of matter. The fundamental unit of an element, made of protons, neutrons, and electrons.

Ion

An atom or molecule that carries a full charge—positive if it contains more protons than electrons, and negative if it contains more electrons than protons.

Molecule

A structure made of two or more atoms held together by covalent bonds.

Covalent bond

An attraction between two atoms based on shared electrons.

Electronegativity

The tendency for an atom's nucleus to attract the shared electrons in a covalent bond.

Polar covalent bond

An asymmetry in the position of shared electrons, due to differences in the electronegativities of the atoms involved, that creates a partial positive charge on one atom and a partial negative charge on the second atom.

Nonpolar covalent bond

Equal sharing of electrons, due to equal or roughly equal electronegativities of the atoms involved.

Hydrogen bond

An attraction between a partial positive charge on a hydrogen atom and a partial negative charge on another atom

Hydrophilic molecule

a molecule that can readily interact with the partial charges on water.

Hydrophobic molecule

a molecule that contains mostly nonpolar covalent bonds and cannot readily interact with the partial charges on water.

Ion

an atom or molecule that carries a full charge.

Acid

an ion or molecule that releases a proton.

Base

an ion or molecule that acquires a proton.

pH scale

a method for expressing the concentration of protons in a solution—specifically, the negative of the base 10 logarithm of the proton concentration

Monosaccharide

an organic molecule that includes a carbon chain, a C=O group, and C-OH groups. The carbon chain can be linear or form a ring structure. Also called a simple sugar.

Glycosidic linkage

a covalent bond that links monosaccharides together to form polymers.

Glycan

a polymer made up of many monosaccharides joined by glycosidic linkages. (Synonymous with 'polysaccharide.')

Carbohydrates

a family of molecules that includes both monosaccharides and glycans.

Nucleotide

A molecule made up of a phosphate group and a nitrogenous base bonded to a 5-carbon sugar.

Nucleic acid

A molecule made up of nucleotides linked to form a chain or strand.

Phosphodiester bond

Covalent bonds between the phosphate group on the 5′ carbon of one nucleotide and the -OH group on the 3′ carbon of a second nucleotide.

Complementary base pairing

Hydrogen bonding between A-T or A-U and G-C pairs in a nucleic acid.

Primary structure

The sequence of nucleotides in a nucleic acid, read 5′ to 3′.

Secondary structure

Formation of a double helix in DNA or a stem-and-loop structure in RNA, based on complementary base pairing.

Sugar-phosphate backbone

The "spine" of 5-carbon sugars and phosphate groups in a nucleic acid (the nitrogenous bases project from this backbone).

Antiparallel strands

Strands of DNA or RNA that align in opposite 5′ to 3′ orientation.

Monomer

A small "subunit" molecule that can be linked to another, via a covalent bond, to form a larger molecule called a polymer.

Polymer

A large molecule made up of strings of covalently bonded small molecules (monomers).

DNA polymerase

An enzyme that catalyzes the formation of phosphodiester linkages between deoxyribonucleotides, forming the primary structure of DNA.

DNA ligase

An enzyme that catalyzes the formation of phosphodiester linkages in gaps between two existing nucleotides in double-stranded DNA.

Origin of replication

A location (a point) where enzymes open the DNA double helix so replication can begin.

Replication fork

The y-shaped structure visible in micrographs of DNA during replication. This is the site where the replisome works, synthesizing the leading and lagging strands.

Primase

An enzyme that adds a short RNA primer to single-stranded DNA, so DNA polymerase can start adding complementary bases.

Replisome

The multi-molecular machine that works at the replication fork, copying DNA.

Helicase

An enzyme in the replisome that opens the DNA double helix, creating single-stranded template DNA that become the leading and lagging strand during synthesis.

Topoisomerase

An enzyme that is important in DNA replication. It breaks and rejoins DNA to relieve the tension created when helicase continuously opens the double helix.

Leads

It describes the newly synthesized Dna strand that into the replication fork

Primed (Primase; RNA; Primer)

A bare DNA template needs to be ___ for synthesis, by adding a short stretch of RNA

Replication Bubble

Micrographs, an oval-shaped structure that looks like ___

Forks (replication Form)

looks like a road that…

RNA polymerase

An enzyme that catalyzes the formation of phosophodiester linkages between ribonucleotides, forming an RNA product that is complementary to the sequences of bases in a DNA template.

Template strand

The strand in a DNA double helix that is “read” by RNA polymerase during transcription.

Non-template strand (coding strand)

The strand in a DNA double helix that matches the sequence of bases in the RNA product of transcription, except that the DNA contains thymine (T) and the RNA contains uracil (U).

Promoter

The regulatory sequence in a gene or operon where RNA polymerase initiates transcription.

Genetic code

The set of relationships between the 64 possible codons in mRNA and the amino acids that are added to a newly synthesized protein.

Codon

A group of three bases in an mRNA that codes for an amino acid.

Start codon

The codon that signals where translation and thus protein synthesis begins. Usually AUG and also codes for the amino acid methionine (Met).

Stop codon

A codon that signals where translation and thus protein synthesis ends. Usually UAA, UAG, and UGA.

Anticodon

A sequence of three bases found at one end of a tRNA that binds to a codon in mRNA during translation via complementary base pairing.

Release factor

A protein that fits into the A site of a ribosome, binds to a stop codon, and interacts with the ribosome to terminate translation.

Reading frame

The sets of three-base codons in RNA or DNA that specify the primary sequence of amino acids in a protein; is set by the start codon, and identifies the subsequent sequence of codons.

Ribozyme

An RNA molecule that catalyzes a chemical reaction, analogous to enzymes, which are protein catalysts.

Amino acids

the building blocks that connect together via covalent bonds to form proteins

Amino group

a group of NH2 atoms; can pick up a proton to form NH3+

Carboxyl group

a group of COOH atoms; can lose a proton to form COO-

R-group

a highly variable group of atoms bonded to the central carbon of an amino acid

Hydrophilic

can readily interact with the partial charges on water

Hydrophobic

cannot readily interact with the partial charges on water

Protein Primary structure

Specifically, the carboxyl group on one amino acid links with the amino group on a second amino acid

Peptide bond

the covalent bond that forms between the carboxyl group of one amino acid and the amino group of another

Protein primary structure

the sequence of amino acids, linked via peptide bonds

Protein secondary structure

formation of ⍺-helices and β-pleated sheets, stabilized by hydrogen bonds between backbone atoms

Protein tertiary structure

folding into a 3-D shape stabilized by hydrogen bonds, ionic bonds, S-S bridges, and hydrophobic interactions

Ionic bond

an interaction that occurs when a positively charged ion is attracted to a negatively charged ion

Hydrophobic interactions

interactions that stabilize hydrophobic regions of molecules by minimizing their contact with water

Protein quaternary structure

assembly of multipart proteins from folded subunits, stabilized by hydrogen bonds, ionic bonds, S-S bridges, and hydrophobic interactions

Denaturing

"unfolding" or loss of 3-dimensional shape (secondary, tertiary, and quaternary structure), often via heating or changes in pH

The cell membrane

This is a structure comprised of a lipid bilayer and membrane proteins with short carbohydrates attached to both. This is the structure that regulates which ions and molecules come into the cell and which get sent out.

Genetic material

In organisms, heritable information is always present in the form of one or more DNA molecules called chromosomes. Although DNA is always present as a double helix, other aspects of DNA structure vary. For example, chromosomes can be linear or circular depending on the species. In many species, specialized proteins bind to the DNA double helix