Cells to Ecosystems and DNA Replication

Flashcards covering key vocabulary from lecture notes on hierarchical organization, chemical bonds, atomic properties, molecular polarity, functional groups, nucleotides, protein structure, and DNA replication.

Chemical bond

A force that holds atoms together to form molecules and compounds, usually to achieve stability by filling their valence shell.

Ionic Bond

A chemical bond formed by the transfer of electrons from one atom to another, resulting in ions with opposite charges that attract.

Covalent Bond

A chemical bond formed by the sharing of electrons between atoms.

Nonpolar Covalent Bond

A type of covalent bond where electrons are shared equally between atoms.

Polar Covalent Bond

A type of covalent bond where electrons are shared unequally between atoms, leading to partial positive and negative charges.

Hydrogen Bond

A weak intermolecular attraction between polar molecules, especially when hydrogen is bonded to oxygen, nitrogen, or fluorine.

Van der Waals Forces

Weak, temporary intermolecular attractions due to fluctuating electron clouds.

Metallic Bond

A type of chemical bond in metals where electrons are shared as a 'sea of electrons,' explaining conductivity and malleability.

Valence Electrons

Electrons in the outermost shell of an atom that determine how atoms bond.

Electronegativity

How strongly an atom attracts electrons; its difference between atoms determines bond type.

Molecular Polarity

The distribution of electrical charge across a molecule, dependent on bond polarity and molecular geometry.

Hydrophilic

Describes polar or charged molecules that are 'water-loving,' form hydrogen bonds with water, and are soluble in it.

Hydrophobic

Describes nonpolar molecules that are 'water-fearing,' do not dissolve in water, and tend to cluster together.

Functional Group

A specific cluster of atoms in a molecule that gives it distinct chemical properties, such as reactivity, polarity, or solubility.

Methyl Group (–CH₃)

A functional group that is nonpolar and hydrophobic, reducing water solubility, and can regulate gene expression.

Amino Group (–NH₂)

A functional group that is polar and basic, capable of accepting H⁺, found in amino acids.

Carboxyl Group (–COOH)

A functional group that is polar and acidic, capable of donating H⁺, found in amino acids and fatty acids.

Hydroxyl Group (–OH)

A functional group that is polar and hydrophilic, forming hydrogen bonds, common in alcohols and sugars.

Phosphate Group (–PO₄²⁻)

A functional group that is very polar, acidic, negatively charged, contributes to solubility, and is involved in high-energy bonds in ATP and nucleic acids.

Carbon (tetravalent)

An atom with 4 valence electrons that can form up to 4 covalent bonds, allowing for diverse structures like chains and rings, forming the basis of macromolecules.

Lewis Formula

A scientific model of organic molecules that shows all atoms, bonds, and lone pairs, good for visualizing valence electrons.

Space-Filling Model

A scientific model that shows the actual relative sizes of atoms and how they pack together, illustrating the volume occupied by a molecule.

Nucleotide

The monomer of nucleic acids, composed of a nitrogenous base, a pentose sugar, and one or more phosphate groups.

Nitrogenous Base

A component of a nucleotide (purine or pyrimidine) that provides specificity for base pairing through hydrogen bonds.

Pentose Sugar

A five-carbon sugar (deoxyribose in DNA, ribose in RNA) that forms the backbone of nucleic acids and links to the base and phosphate.

Phosphodiester Bond

A covalent bond that links the 3' hydroxyl group of one nucleotide's sugar to the 5' phosphate group of the next nucleotide, forming the sugar-phosphate backbone of DNA/RNA.

5' End (DNA)

The end of a DNA strand that has a free phosphate group attached to the 5' carbon of the pentose sugar.

3' End (DNA)

The end of a DNA strand that has a free hydroxyl group attached to the 3' carbon of the pentose sugar.

Antiparallel

The orientation of the two complementary strands in a DNA double helix, where one strand runs 5' to 3' and the other runs 3' to 5'.

DNA as an Organic Acid

DNA's property of being acidic at physiological pH due to the negatively charged phosphate groups, which release protons (H⁺).

Primary Protein Structure

The unique, linear sequence of amino acids in a polypeptide chain.

Secondary Protein Structure

Localized, regular folding patterns of the polypeptide backbone, primarily alpha-helices and beta-sheets, stabilized by hydrogen bonds.

Tertiary Protein Structure

The overall three-dimensional shape of a single polypeptide chain, resulting from interactions among R groups (side chains).

Quaternary Protein Structure

The arrangement and interaction of multiple polypeptide chains (subunits) to form a functional protein complex.

Amino Acid

The monomer building block of proteins, consisting of a central carbon, an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group).

Peptide Bond

A covalent bond formed between the carboxyl group of one amino acid and the amino group of another amino acid during dehydration synthesis, linking them in a polypeptide chain.

DNA Replication

The biological process of producing two identical replicas of DNA from one original DNA molecule, occurring during the S-phase of the cell cycle.

Semi-conservative Replication

The mechanism of DNA replication where each new DNA molecule consists of one original (template) strand and one newly synthesized strand.

DNA Helicase

An enzyme that unwinds the DNA double helix at the replication fork by breaking hydrogen bonds between bases.

Primase

An enzyme that synthesizes short RNA primers, providing a starting point for DNA polymerase to add new nucleotides.

DNA Polymerase III

The primary enzyme responsible for synthesizing new DNA strands in the 5' to 3' direction during replication, extending from the RNA primer.

Leading Strand

The new DNA strand that is synthesized continuously in the 5' to 3' direction, towards the replication fork.

Lagging Strand

The new DNA strand that is synthesized discontinuously, in short segments called Okazaki fragments, in the direction away from the replication fork.

Okazaki Fragments

Short DNA segments synthesized discontinuously on the lagging strand during DNA replication.

DNA Polymerase I

An enzyme that removes RNA primers during DNA replication and replaces them with DNA nucleotides.

DNA Ligase

An enzyme that seals the nicks (gaps) in the sugar-phosphate backbone, particularly joining Okazaki fragments on the lagging strand.

Proofreading (DNA replication)

The 3' to 5' exonuclease activity of DNA polymerase that checks for and corrects mismatched bases during DNA synthesis, enhancing accuracy.

Independent Variable (IV)

The factor manipulated or changed by the researcher in an experiment; 'what you change'.

Dependent Variable (DV)

The factor measured or observed in response to changes in the independent variable; 'what you observe'.

Control Treatment

A baseline group in an experiment that does not receive the experimental manipulation or receives a standard condition, used for comparison.

Confounding Variables

Factors other than the independent variable that could influence the dependent variable and must be held constant to avoid bias.

Replication (experiment)

Repeating an experiment or having multiple samples in each group to reduce random variation and increase the reliability of results.