Chapter 2 Biology Notes: Atoms, Elements, and Biomolecules Flashcards

100 question-and-answer flashcards covering fundamental concepts in biology including atomic structure, isotopes, chemical bonding, water chemistry, functional groups, ATP, and macromolecular structures (proteins, nucleic acids, carbohydrates, lipids).

What element is described in the lecture notes as essential for life?

Water

What element is described as the backbone of life?

Carbon

According to the notes, how many man-made elements exist?

24 man-made elements

What three subatomic particles make up an atom?

Protons, neutrons, and electrons

What charge does a proton carry?

Positive charge

What charge does a neutron carry?

Neutrally charged

What charge does an electron carry?

Negative charge

Which subatomic particles are located in an atom's nucleus?

Protons and neutrons

Where are an atom's electrons located and how do they move?

In orbitals around the nucleus

How is an element's atomic number determined?

By the number of protons

An atom that contains 6 protons is always which element?

Carbon

How is atomic mass calculated?

The number of protons plus the number of neutrons

What are the atomic number and atomic mass of Boron?

Atomic Number = 5, Atomic Mass = 10.811

In isotopes of an element, how do proton and neutron counts compare?

The proton number stays the same, but the neutron number is different

What are carbon isotopes used for?

Carbon dating

What substance is used in PET scans to illuminate cancer cells?

Fludeoxyglucose

How many neutrons does Carbon 12 have, and is it an isotope?

6 neutrons; it is the non-isotope form of carbon

How many neutrons are in Carbon 13?

7 neutrons

How many neutrons are in Carbon 14?

8 neutrons

How does an atom acquire a net electric charge?

By gaining or losing an electron

What is a positively or negatively charged atom called?

An ion

What are the regions of space called that electrons occupy?

Orbitals

How many orbitals do atoms with more than two electrons have?

At least two orbitals

How many electrons are required in the 1st orbital/shell to achieve valency?

2 electrons

How many electron spots are in the 2nd orbital/shell and beyond to achieve valency?

8 electron spots

What does valency mean for an atom?

The outermost orbital of an atom is at capacity

What effect does achieving valency have on an atom?

The atom becomes more stable

Which element is given as an example of achieving valency and being relatively stable?

Helium

In an atom, which part is constantly moving and which part remains relatively still?

Electrons are always moving, while the nucleus is relatively still

How are elements organized when reading across the rows of the periodic table?

By their specific chemical properties

What do elements in the same column or group share?

The same number of electrons in their outermost shell

What do elements in the same row share?

Similar properties

What holds atoms together when they combine to form molecules?

Chemical bonds

When does molecule stability occur?

When atoms of the molecule share enough electrons to occupy the outermost energy level

What determines the number of chemical bonds an atom can form?

The number of valence electrons

What occurs during the formation of a covalent bond?

Two atoms share electrons

What defines a non-polar covalent bond?

Equal sharing of electrons between atoms

What defines a polar covalent bond?

Non-equal sharing of electrons across the molecule

What specific type of bond exists within a single $H_2O$ molecule?

Polar covalent bond

Why are shared electrons closer to oxygen than hydrogen in a water molecule?

Because the electronegativity of oxygen is greater than that of hydrogen

What partial charges result from unequal electron sharing in a water molecule?

Partial negative charges on oxygen and partial positive charges on hydrogen

What occurs when an ionic bond forms between sodium and chlorine?

Chlorine takes an electron from sodium, resulting in a negatively charged chlorine atom and a positively charged sodium atom

Why do sodium and chlorine ions interact after an electron transfer?

Because opposite charges attract one another

Which song and singer are referenced to describe ionic attraction?

"Opposites Attract" by Paula Abdul

Why do salts dissolve in water?

Partial positive charges on hydrogen associate with negative chloride ions, and partial negative charges on oxygen associate with positive sodium ions

What are reactants in a chemical reaction?

The substances being added together

What is a product in a chemical reaction?

What comes out of the reaction

What do the terms hydrophilic and hydrophobic mean?

Hydrophilic means water loving; hydrophobic means scared of water

What is the pH of pure water?

7

What does pH measure?

The concentration of hydrogen ions (protons) in a solution

How much does the hydrogen ion concentration change between each unit on the pH scale?

There is a 10x buffer (tenfold difference) between each number

What are the ion concentration characteristics and pH of acidic solutions?

Elevated $[H^+]$, reduced $[OH^-]$, and pH < 7

What are the ion concentration characteristics and pH of basic solutions?

Elevated $[OH^-]$, reduced $[H^+]$, and pH > 7

How does adding an acid affect the $H^+$ concentration of a solution?

It increases the $H^+$ concentration

How does adding a base affect the $H^+$ concentration of a solution?

It decreases the $H^+$ concentration

How do strong acids and bases behave in water compared to weak ones?

Strong acids and bases completely dissociate in water; weak ones reversibly release and accept hydrogen ions

What is the biological function of buffers?

Buffers are substances that minimize changes in concentrations of $H^+$ and $OH^-$ in a solution

What is the internal pH of most living cells?

Close to 7

How does a hydrogen bond form between two water molecules?

The partial positive charge of a hydrogen atom is attracted to the partial negative charge of an oxygen atom

What are the four emergent properties of water that facilitate life?

Cohesive behavior, ability to moderate temperature, expansion upon freezing, and versatility as a solvent

What is cohesion in water?

Hydrogen bonds collectively holding water molecules together

How does cohesion benefit plants?

It helps transport water against gravity in plants

What is adhesion?

An attraction between different substances, such as between water and plant cell walls

Are plant cell walls and tubes described as hydrophilic or hydrophobic?

Hydrophilic

What is the chemical structure and polarity of a carbonyl group?

Structure: Carbon double-bonded to oxygen ($C=O$); Polarity: Polar

What is the chemical structure and polarity of a carboxyl group?

Structure: Carbon double-bonded to oxygen plus a hydroxyl group ($C=O + OH$); Polarity: Polar

On what specific monomer is a carboxyl group found without exception?

Found on every single amino acid

What is the chemical structure and stated polarity of an amino group?

Structure: Nitrogen with two hydrogens attached ($-NH_2$); Polarity: Nonpolar (according to lecture notes)

What is the chemical structure and polarity of a sulfhydryl group?

Structure: Sulfur with hydrogen ($-SH$); Polarity: Nonpolar

Why are sulfhydryl groups important in protein structure?

They can form disulfide bonds in proteins

What is the chemical structure, charge, and polarity of a phosphate group?

Structure: Phosphorus double-bonded to one oxygen and attached to three additional oxygens (carrying negative charges); Polarity: Polar

What is the chemical structure and polarity of a methyl group?

Structure: Carbon with three hydrogens attached ($-CH_3$); Polarity: Nonpolar

Why are methyl groups biologically important?

They are important for recognizing molecular structures

What three molecular components make up ATP?

Adenine, ribose sugar (a pentose sugar), and three phosphate groups

When specifically does a cell obtain usable energy from ATP?

When a phosphate group is removed from ATP

What equation represents the breakdown of ATP to release cellular energy?

$$ATP \rightarrow ADP + \text{phosphate} + \text{energy}$$

What do the abbreviations ATP and ADP stand for?

ATP = adenosine triphosphate; ADP = adenosine diphosphate

Which phosphate group is removed from ATP when releasing energy?

The terminal phosphate group

What are the roots and definition of the term hydrolysis?

Hydro = water, Lysis = breaking; hydrolysis means breaking something down using water

If you see a molecule with three phosphate groups on an exam, how should you identify it?

As ATP

What are the four major organic molecules?

Proteins, Nucleic Acids, Carbohydrates, and Lipids

What are four biological functions of proteins?

Structural support, transport across cell membranes, cellular functions, and acting as enzymes

What are enzymes and how do they function?

Enzymes are catalysts that speed up chemical reactions, allowing them to happen faster than they would naturally

What are the primary functions of nucleic acids?

Encode and transmit genetic information

What are two main functions of carbohydrates?

Provide structural support and provide sources of energy

Which specific monosaccharide do cells primarily use for energy?

Glucose

How do animals and plants store carbohydrates?

Animals store carbohydrates as glycogen; plants store carbohydrates as starch

What are the key properties and functions of lipids?

Generally nonpolar, do not interact well with water, make up cell membranes (phospholipids), store energy, and play a role in cell communication

Why do cells rely more on glucose than lipids for energy despite potential speed?

There are more chemical pathways for using glucose

What is the difference between hydrolysis and condensation/dehydration synthesis?

Hydrolysis breaks molecules down using water; condensation/dehydration synthesis builds larger molecules from smaller ones with an overall loss/release of water

What four groups are attached to the central alpha carbon of an amino acid?

An amino group, a carboxyl group, a hydrogen, and an R group

What component determines the unique properties of different amino acids?

The R group

What type of chemical bond links amino acids together to form a protein?

Peptide bonds

How does a peptide bond form between two amino acids?

The carboxyl group loses its hydroxyl group ($-OH$), resulting in a carbonyl group within the protein through dehydration synthesis/condensation

How is the number of peptide bonds in a single chain calculated?

It is one less than the total number of amino acids ($\text{number of amino acids} - 1$)

What three main components make up all nucleic acids?

A pentose sugar, a nitrogenous base, and one or more phosphate groups

How do the pentose sugars in DNA and RNA differ structurally?

The sugar in DNA (deoxyribose) is missing an oxygen on the second carbon; the sugar in RNA (ribose) has the hydroxyl group/oxygen on the second carbon

Which nitrogenous bases are purines and how many cyclic structures do they possess?

Adenine (A) and Guanine (G); they have two cyclic structures ("AGGIES ARE PURE")

Which nitrogenous bases are pyrimidines and how many cyclic structures do they possess?

Cytosine (C), Thymine (T), and Uracil (U); they have one cyclic structure

What type of bond forms the backbone of DNA and RNA by linking a phosphate group to a sugar?

Phosphodiester bonds