Biomolecular Structure & Function Flashcards

Identify the structure and function of major biological macromolecules (carbohydrates, lipids, proteins, nucleic acids) and describe how water supports life processes. (101 cards)

1
Q

What is an atom?

A

The smallest unit of matter that still holds the properties of an element.

Elements are types of matter that have specific chemical and physical properties and cannot be broken down into other substances.

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2
Q

How are atoms created?

A

Atoms originate via nucleosynthesis—light elements (H, He, trace Li) formed in the Big Bang.

Heavier elements were forged in stars and supernovae/neutron-star mergers.
Nuclear fission splits heavy nuclei and is not a primary atom-creation process.

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3
Q

How many elements are there?

A

118

Most elements occur naturally, but some are synthesized in a laboratory.

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4
Q

What are the three main subatomic particles in an atom?

A
  • Protons
  • Electrons
  • Neutrons

Subatomic particles are the particles that when put together, create an atom. These are measured using Atomic Mass Units (amu).

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5
Q

What are electrons?

A

Negatively charged subatomic particles.

Found in the electron cloud of an atom.

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6
Q

What is the electron cloud?

A

The space surrounding the nucleus where electrons can be found.

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7
Q

What are neutrons?

A

Subatomic particles that have no charge.

They are found in the nucleus of an atom and have a mass of 1 amu.

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8
Q

What is a proton?

A

Positively charged subatomic particles.

Protons are found in the nucleus of an atom and have a mass of 1 amu.

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9
Q

What is the difference between atoms and molecules?

A
  • Atoms are the most basic units of elements.
  • Molecules are the most basic units of compounds.

Atoms build molecules.

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10
Q

What is the atomic number?

A

The number of protons in an atom, defining it as a specific element.

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11
Q

What are atoms with a charge called?

A
  • Cations
  • Anions

Cations are positively charged ions; anions are negatively charged ions.

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12
Q

What is the term for a charged atom?

A

Ion

An ion is an atom or molecule that has a net electric charge due to the loss or gain of electrons.

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13
Q

What is the term for a positively charged ion?

A

Cation

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14
Q

What is the term for a negatively charged ion?

A

Anion

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15
Q

What type of bond is formed when positively and negatively charged ions are brought together by their electrostatic charge?

A

Ionic bond

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16
Q

What are isotopes?

A

Atoms that have a different number of neutrons than the average number.

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17
Q

What is the purpose of the periodic table?

A

To organize elements based on their properties.

An element’s physical and chemical properties correspond directly to their atomic number (the number of protons in an atom).

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18
Q

What is the atomic mass unit a measure of?

(AMU)

A

Mass

1 amu is defined as 1/12 the mass of a carbon-12 atom; protons/neutrons ≈1 amu; an electron ≈0.00055 amu.

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19
Q

What is an element defined as?

A

A pure substance consisting of only one type of atom.

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20
Q

What are molecules made up of?

A

Atoms chemically bond together to form molecules.

The most basic units of compounds.

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21
Q

What are chemical bonds and how do they occur in molecules?

A
  • They are forces that hold atoms together in molecules.
  • They form by sharing or transferring electrons.
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22
Q

What is the ball-and-stick model used for in chemistry?

A

To represent atoms and the bonds between them in molecules.

Used to study the exact shape of the molecule and how the atoms connect to each other.

Best for modeling small to medium molecules.

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23
Q

What does the space-filling model represent in molecules?

A

The amount of space occupied by an atom’s electron cloud.

Looks like blobs and are used to understand how molecules interact.

Best for modeling small to medium molecules.

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24
Q

When is a line-angle model used in chemistry?

A

To show the structure of a molecule, minus the details.

Best when modeling small and medium molecules in two dimensions.

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25
How do scientists determine **macromolecular** structures?
* X-ray crystallography * NMR spectroscopy * cryo-electron microscopy
26
What determines the **stability** of an atom's outer electron shell?
The **number of electrons** in the outer shell. ## Footnote The outer electron shell typically needs 8 electrons to be stable. This need to have 8 electrons in the outer shell is known as the octet rule.
27
What is **electronegativity**?
* It is an atom’s tendency to **attract shared electrons** in a covalent bond. * It generally **increases** across a period and **decreases** down a group due to effective nuclear charge and atomic radius. ## Footnote Determines the type of bond formed between 2 atoms. Atoms of different elements have different amounts of electron orbitals or shells leading to different electronegativities.
28
What is a **nonpolar** covalent bond?
A bond that occurs between atoms where electrons are shared **equally**. ## Footnote A bond that occurs between atoms with an electronegativity difference of \<0.4. Compounds formed from these types of bonds have a neutral charge.
29
What is a **polar** covalent bond?
A bond that occurs between atoms where electrons are shared **unequally**. ## Footnote Different sides of the molecule will exhibit positive and negative charges Occurs with an electronegativity difference between 0.4 - 1.7. The more electronegative atom will be slightly negative, and the less electronegative atom will be slightly positive.
30
What kind of models are used for **macromolecules** and very large molecules like proteins or DNA?
Blob or Ribbon models ## Footnote These models focus on the overall shape of the molecule, not the exact structure or number of atoms.
31
What are the **models** used for studying the molecular structure of molecules?
* Ball-and-stick model * Space-filling model * Line-angle model * Blob or ribbon model
32
What type of bonds occur when atoms **share an electron pair**?
Covalent bonds ## Footnote Atoms share electrons to try to achieve the octet rule. Generally very strong and very stable. Examples: Oxygen (O2), Water (H2O), Methane (CH4)
33
What are atoms and molecules **mainly composed of** in biology?
Organic molecules made with **carbon**, often bonded to other common elements like oxygen, nitrogen, and hydrogen.
34
What are the two main types of **bonding** between atoms in molecules?
* **Covalent bonds** where atoms **share** an electron pair. * **Ionic bonds** when atoms with positive and negative charge are **attracted** to each other.
35
How do chemists know what a molecule **looks like**?
By observing them through **noncontact atomic force microscopy** and using **chemistry mathematics** to predict shapes based on electronegativity.
36
Why is **learning** about molecular structures important?
* To **predict** chemical reaction outcomes. * **Create** useful substances like drugs. * **Determine** the composition of unknown substances.
37
What is a **diatomic element**?
Elements whose atoms **bond to each other** and share their electrons equally. ## Footnote Examples: Hydrogen, Oxygen, Nitrogen
38
What are **double and triple** covalent bonds collectively known as?
Multiple bonds
39
What are the unique properties of **covalent bond** molecules?
* Held together by weak van der Waals forces. * Not conductors of electricity. * Easily dissolve in organic solvents. * Have low density. * Have low boiling and melting points. * Are usually in a gaseous, soft solid, or volatile liquid state.
40
What is the **outermost shell** of an atom referred to as?
Valence shell ## Footnote Electrons found here are known as valence electrons.
41
What are electrons in the outermost shell **not involved in bond formation** called?
Lone pairs
42
When can an atom form **multiple bonds** with the same partner?
If that atom has enough valence electrons. ## Footnote Double Bond: 2 sets of electrons are shared between 2 atoms. Triple Bond: 3 sets of electrons are shared between 2 atoms.
43
How many **valence electrons** does carbon have and how many **covalent bonds** can it form?
* Four valence electrons. * Four covalent bonds.
44
How are the bonds between atoms in a **covalent** bond often represented?
with a **line** ## Footnote Instead of a dot representation, the bond between atoms in a covalent bond is often abbreviated with a line.
45
What is **predictable** about the structure of a molecule?
The **bond length** and **bond angle**.
46
What are **ionic bonds**?
Electrostatic interactions between two **oppositely charged** ions. ## Footnote Generally stable bonds. Occurs when the difference in electronegativity between atoms is greater than 2.0. Example: Sodium Chloride (NaCl)
47
How do atoms with **incomplete valence levels** deal with instability?
* Share electrons. * Take or donate electrons.
48
What does the lowercase Greek letter **Delta** followed by a plus or minus sign represent in terms of charges?
The **slightly positive and slightly negative** charges on atoms in a polar covalent bond.
49
What is the term used to describe the **difference in charge** within a polar covalent bond?
Polarity
50
What is a **dipole**?
An electrically asymmetrical molecule that is **oppositely charged** at two points. ## Footnote Formed due to the presence of a polar bond and the shape or geometry of the molecule.
51
What is a **hydrogen bond**?
An **intermolecular force** between a hydrogen atom in one polar molecule and a small and very electronegative atom of another polar molecule.
52
How are hydrogen bonds **formed**?
Between polar molecules with one molecule serving as a **hydrogen bond donor** and the other as a **hydrogen bond acceptor**. ## Footnote Molecule with a relatively large positive charge at one end (donor). Molecule with an atom containing a lone pair of electrons (acceptor).
53
What is the strength of a **hydrogen bond** compared to **covalent bonds**?
A hydrogen bond is usually only **2-5%** as strong as a typical covalent bond. ## Footnote Despite being weak compared to covalent bonds, hydrogen bonds play important roles in various applications such as the formation of liquids like water and surface tension.
54
Give an example of a **daily application** of hydrogen bonds.
* Hydrogen bonds form liquids like water. * Provide surface tension for water striders to move across. * Important for the formation of paper products. ## Footnote Hydrogen bonds are crucial in various everyday applications, despite being weaker than covalent bonds.
55
What is the **difference** between intramolecular and intermolecular forces?
* **Intramolecular** forces are bonds holding a molecule together. * **Intermolecular** forces are forces of attraction between molecules. ## Footnote Examples of intramolecular forces include covalent bonds, while hydrogen bonds are examples of intermolecular forces.
56
What are **macromolecules**?
**Large molecules** that contain key nutrients necessary for survival that are consumed from other organisms. ## Footnote Macromolecules are composed of carbon, hydrogen or oxygen in different arrangements.
57
Define **inorganic molecules**.
Inorganic molecules are compounds that lack carbon-hydrogen (C-H) bonds. They may contain carbon or hydrogen individually but not both in a C-H bond. Examples include water (H₂O), salts, and carbon dioxide (CO₂).
58
What are **monomers**?
**Smaller molecules** or subunits that compose macromolecules. ## Footnote 'Mono-' means 1. Monomers are individual pieces that are put together to create polymers.
59
What is **polymerization**?
The process of chemically **linking monomers together** to form polymers. ## Footnote 'Poly-' means many.
60
What is **catabolism**?
The **chemical breakdown** of molecules, such as macromolecules, through hydrolysis.
61
What is **anabolism**?
The process of **building molecules**, particularly macromolecules, through dehydration synthesis.
62
Name the **four classes** of macromolecules.
* Carbohydrates * Proteins * Lipids * Nucleic acids
63
What are **carbohydrates** primarily used for?
quick energy ## Footnote Examples: Sugar, starches
64
What are **lipids** used for in the body?
**Store** energy for future use and **protect** internal organs. ## Footnote They are also known as fats, waxes, steroids, membranes. Lipids are utilized when carbohydrates are low or the body's energy demands exceed those provided by carbohydrates.
65
What are **phospholipids** major constituents of?
cellular membrane ## Footnote Phospholipids are the main components of cell membranes, forming a bilayer with hydrophilic heads and hydrophobic tails.
66
What are **proteins** used for in the body?
* Movement * Cellular protection * Structural components * Signaling ## Footnote Can also be used as an energy source in the body when the body has depleted its stores of carbohydrates and lipids.
67
What are **nucleic acids** responsible for?
They contain **genetic information** and direct the production of proteins. ## Footnote Common examples include DNA or RNA.
68
What is the **chemical formula** of a water molecule?
H₂O
69
How many **hydrogen atoms** are in a water molecule?
two
70
What causes the **bent structure** of a water molecule?
Extra **unpaired** electrons of oxygen. ## Footnote Water is bent (~104.5°) because two lone pairs on oxygen repel the two O–H bonding pairs, giving a tetrahedral electron geometry and bent molecular shape.
71
What property of water allows ice to **float**?
Ice is less dense than liquid water. ## Footnote When water freezes, crystalline structures form within the ice leaving space between the molecules.
72
What is the **specific heat capacity** of water?
1 cal/g°C | (4186 J/kg°C) ## Footnote Water's high specific heat capacity makes it challenging to heat or cool. 1 calorie of energy must be added to 1 gram of water in order to increase the temperature of the water 1°C.
73
What is the **heat of vaporization** of water?
540 cal/g | (41 kJ/mol) ## Footnote The high heat of vaporization enables water to have a significant cooling effect on the environment.
74
What are the cohesive and adhesive **properties** of water?
* **Cohesion**: attraction between water molecules due to hydrogen bonds. * **Adhesion**: attraction of water molecules to molecules of other substances. ## Footnote Cohesion and adhesion are essential for transporting water and nutrients in plants.
75
What is **surface tension** in water?
Water's ability to **resist being stretched or broken**. ## Footnote Surface tension in water enables small objects to float and insects to walk on its surface.
76
What property of water allows it to **move up** a narrow plastic tube against gravity?
Capillary action ## Footnote Water's cohesive and adhesive properties contribute to capillary action. * Cohesion: Water molecules-hydrogen bonding to each other. * Adhesion: Water molecules-hydrogen bonding to other substances.
77
Why is water considered one of the **essential requirements** for Earth to be habitable?
* Regulates planet's temperature. * Allows for the hydration and survival of plants and animals.
78
What is **density** a measure of?
Mass of an object per unit volume. ## Footnote Density indicates how much matter occupies a given volume.
79
Why can bodies of water help **cool** the surrounding area?
Water has a **high specific heat** and requires extra energy to heat, creating a more temperate climate.
80
What are **polymers**?
chains of monomers
81
What are the **monomers** of carbohydrates?
Monosaccharides ## Footnote Monosaccharides are simple sugars.
82
What is the **combination** that creates a lipid?
A glycerol backbone bonded to hydrocarbon tails (fatty acids). ## Footnote This combination creates a nonpolar, hydrophobic structure, meaning that lipids will not dissolve in water. Note: Not all lipids follow this pattern—steroids and terpenes, for example, lack glycerol backbones and fatty acid tails.
83
Why are lipids **not** considered polymers?
They are not composed of **repeating** monomer subunits. ## Footnote Many lipids are assembled from glycerol and fatty acids, while others (e.g., steroids) lack repeating units altogether.
84
What are the **monomers** of nucleic acids?
Nucleotides ## Footnote Nucleic acids are polymers of nucleotides, each composed of a nitrogenous base, a pentose sugar, and a phosphate group. DNA Bases: * Adenine * Thymine * Cytosine * Guanine RNA Bases: * Adenine * Uracil * Cytosine * Guanine
85
What are the three **subcomponents** of a nucleotide?
* Sugar * Phosphate * Base
86
What is the **difference** between DNA and RNA in terms of sugar content?
* DNA has **deoxyribose** sugar * RNA has **ribose** sugar ## Footnote DNA is double-stranded. RNA is single-stranded.
87
What are **proteins** made of?
Amino acids
88
What determines the **function** of a protein?
final shape ## Footnote The protein’s final 3D shape determines its function.
89
What are some **healthy carbohydrate** choices you can introduce to your students?
* Brown rice * Carrots * Broccoli * Whole grain bread
90
What is a common choice for **healthy lipids** you can introduce to your students?
* Salmon * Nuts * Avocados
91
What can the body **reuse** lipid components for?
energy and cell membranes ## Footnote Fatty acids are oxidized for ATP through β-oxidation, while glycerol enters glycolysis as glycerol-3-phosphate; both also act as precursors for membrane phospholipids.
92
What molecule provides **instructions** for building proteins?
Proteins carry out **growth and repair functions** encoded by **DNA**.
93
What are some examples of foods rich in **protein**?
* Meat * Seafood * Eggs * Dairy
94
What is the function of **RNA** in cells?
To carry the genetic information from **DNA to build proteins**.
95
What are **polysaccharides**?
Macromolecules made up of many monosaccharides.
96
What properties of water are attributed to **hydrogen bonds**?
* Cohesion and adhesion * Solubility * Low density when frozen * Surface tension ## Footnote Excellent solvent (high polarity and hydrogen bonding) for ionic and many polar substances.
97
What is the **function** of DNA in cells?
To carry the genetic information that is responsible for **inheritable traits**.
98
Is the molecule pictured **organic** or **inorganic**?
organic ## Footnote The molecule contains carbon.
99
Is the molecule pictured **organic** or **inorganic**?
inorganic ## Footnote There is no carbon present in the molecule.
100
What **property of water** is described as water being attracted to other water molecules?
Cohesion
101
What **property of water** describes its attraction to other substances?
Adhesion