CELL BIOLOGY - CLUTCH CH. 2 - CHEMICAL COMPONENTS OF...

! www.clutchprep.com

!

CELL BIOLOGY - CLUTCH

CH. 2 - CHEMICAL COMPONENTS OF CELLS

CONCEPT: SMALL MOLECULES

● The properties of water are crucial for cell activity □ Water is a universal solvent, which means it can _______________________ many types of molecules

- Water makes up >70% of the cell’s weight

- In water hydrophilic molecules dissolve, hydrophobic molecules do not dissolve

□ Water (H2O) is polar, which is an uneven distribution of _____________________ within the water molecule

- Oxygen draws electrons towards it giving it a slight negative charge and hydrogens a slight positive

□ Water molecules are cohesive because the polar nature allows for water molecules to stick together

- Cohesion allows water to act as a temperature stabilizing molecule

- has high specific heat = amount of absorbed heat per gram to raise temperature by 1oC

EXAMPLE: Water molecule demonstrating polarity

● The properties of carbon are also crucial for cell activity □ The carbon atom can bind up to four molecules at once

- Most likely to bond with Oxygen, Hydrogen, Nitrogen, and Sulfur

□ Carbon bonds through covalent bonds and these are extremely ____________________________

- Bond energy measures the amount of energy needed to break a bond (calories/mole)



□ Carbon molecules can have multiple configurations as carbon can bind to __________________ molecules

- Stereoisomers are carbon molecules with the same chemical nature but are mirrored structures

- Two stereoisomer conformations are possible for an asymmetric carbon atom (chiral center)

□ Functional groups found on large carbon molecules confer particular characteristics onto the molecule

EXAMPLE: Carbon stereoisomers

PRACTICE

1. Which of the following is not a property of water? a. It is a universal solvent b. It is polar c. It dissolves hydrophobic molecules d. It has a high specific heat



2. Which type of molecule dissolves in water? a. Hydrophobic b. Hydrophilic c. Amphipathic

3. A carbon atom can bind how many independent molecules at once? a. 1 b. 2 c. 3 d. 4



CONCEPT: IMPORTANT CHEMICAL BONDS AND ATTRACTIONS

Properties of Atoms

● The properties and structure of atoms allow for the _________________________________ of chemical bonds □ An atom has a core of neutrons and protons, which is surrounded by a negatively charged electron cloud

- Electron shells contain the orbiting electrons circling the atom’s core

- Incomplete electron shells are less stable, therefore supporting a chemical bond

□ There are 90 naturally occurring atoms, but are found in cells (Carbon, Hydrogen, Nitrogen, Oxygen = 95%)

- In cells, these elements do not exist by themselves, but instead form bonds

- Carbon can form four bonds, and serves as a foundational element of biological chemistry in cells

EXAMPLE: Electron shells of two bonded carbon atoms

Covalent Bonding ● Covalent bonds are formed through sharing electrons □ Occurs when the outer electron shells of two molecules “want” to be complete, so they _____________ electrons

- Can share two electrons (single bond), four electrons (double bond) or six electrons (triple bond)

□ Molecule polarity occurs through the unequal sharing of electrons (nonpolar molecules share electrons equally)

- Concentration of negative/positive charges on different atoms in a molecule

- Electronegativity describes atoms with an ability to attract electrons

□ Covalent bonds have a high bond strength, defined as the amount of _____________ needed to break the bond

- The bond strength required to break a single Carbon-Oxygen bond is 84 kcal/mol



EXAMPLE: Formation of water through covalent bonding results in the polarity of the water molecules

Noncovalent Bonding ● Noncovalent bonds (intermolecular forces) are bonds that ______________________ involve the sharing of electrons ● Ionic bonds (salt bridges) are a formed by donating or accepting electrons □ Occurs when the outer electron shells donate or take in an electron in order to be complete

□ After the electron moves between the molecules they become charged

- Cations are positively charged (Na+) and Anions are negatively charged (Cl-)

- These ions are then attracted to each other by their charges (NaCl)

□ Ionic bonds are __________________________ (1-5 kcal/mol) and are easily dissolved in water

EXAMPLE: Ionic bond formation between Sodium and Chloride

● Hydrogen bonds are formed through attractions between a hydrogen atom and an electronegative atom □ The partial positive charge of the hydrogen attracts electronegative atoms



□ Hydrogen bonds are extremely important in providing water it’s important properties

- ________________________________ in water depends on the ability to create hydrogen bonds

- Result in attraction between water molecules

□ Hydrogen bonds are weak (1-2 kcal/mol)

EXAMPLE: Hydrogen bonds form between water molecules

● Van der Waals attractions are nonspecific attractive forces that occur as two atoms approach each other □ Can occur in polar or nonpolar molecules

□ Strength of bond ________________________________ with distance of the atoms

- Very weak bonds (1kcal/mol)

EXAMPLE: Van der waals forces are responsible for the sticky nature of geico toes



Attractive Forces ● The hydrophobic effect explains attractions between _______________________________ molecules □ Attraction that explains the aggregation of fat molecules in water

- Hydrophilic molecules dissolve in water, hydrophobic molecules do not dissolve in water

□ Hydrophobic molecules have a neutral charge, and therefore cannot form hydrogen bonds in water

- Therefore, the hydrophobic molecules are surrounded by hydrogen bonding water molecules

□ Hydrocarbons are _______________________, hydrophobic molecules made up of Hydrogen and Carbon

- Because they do not dissolve in water, they are able to form important cellular structures in water

EXAMPLE: Hydrophobic molecules cluster together in water due to the hydrophobic effect

● Certain characteristic features of these bonds allow for the formation of important biological structures □ Noncovalent bonds are weak individually, but can be ______________ together to create a strong effective force

- DNA molecules are held together by a series of weak noncovalent interactions

□ Some molecules fit together like a “lock and key”

- Molecular complementarity describes the nearly perfect fit between properties of two molecules

- Affinity is determined by the fit of the molecule; the higher the fit the the higher the affinity

EXAMPLE: Lock and key fit between two molecules



PRACTICE: 1. Which of the following bonds form through the sharing of electrons

a. Ionic bonds b. Hydrophobic effect c. Van der Waals attractions d. Covalent bonds

2. Which of the following bonds form through the donating and receiving of electrons? a. Ionic bonds b. Hydrophobic effect c. Van der Waals attractions d. Covalent bonds



3. Which of the following bonds form through nonspecific attractive forces that arise when two molecules approach each other?

a. Ionic bonds b. Hydrophobic effect c. Van der Waals attractions d. Covalent bonds



CONCEPT: ACIDS, BASES, AND BUFFERS

● Acids and bases are molecules found in cellular aqueous solutions □ Acids are substances that release positively charged ___________________________ ions into solution

- The hydrogen gives up its electron, leaving a positively charged proton in the solution

- The hydrogen ions form with water to create H3O (hydronium ions)

- Weak acids do not completely disassociate in solution

□ Bases are substances that ____________________________ positively charged hydrogen ions - Combine directly with hydrogen ions to form OH (hydroxide) or water

- Weak bases only partially associate in solution

□ Water can act as an acid or base EXAMPLE: Acids and Bases dissolve in water

● The pH scale measures the concentration of Hydrogen ions (H+)/Hydronium ions (H3O+) on a logarithmic scale EXAMPLE: pH scale: Red=acidic; Blue = basic

□ Aqueous solutions in cells have H+ and OH- molecules in different concentrations

Cytosol = 7.2 ________________; Lysosome = 4.5 _________________



● Buffers are solutions that limit ________________________________ in pH of a solution □ Composed of both weak acids and bases

- These adjust the pH of the solution by releasing or accepting protons

□ Buffers are crucial in cell biology to keep cellular compartments at a specific pH EXAMPLE: Blood pH is balanced by the weak carbonic acid (H2CO3) and the weak conjugate base (HCO3-)



PRACTICE: 1. Choose which of the following is false.

a. Acids are proton acceptors b. Buffers work to neutralize the pH of a solution c. The pH scale is a measure of the acidity of a solution d. Bases are proton acceptors

2. A substance with a pH of 3 is considered what? a. Acidic b. Basic c. Neutral



3. True or False: Bases release positively charged ions into a solution? a. True b. False



CONCEPT: FOUR CLASSES OF MACROMOLECULES

● Polysaccharides are sugars (carbohydrates) that are responsible for cellular energy storage and support

□ Monosaccharides are the building blocks that make up ________________________ polysaccharides

- Covalent glycosidic bonds between a carbon and hydroxyl (OH) attach two monosaccharides together

- Can form into linear or ring structures – (CH2O)n

□ Aldose and Ketose are the two _______________________ of polysaccharides

- The class is determined based on the position of the carbonyl group (C=O)

EXAMPLE: Ketose (C=O in middle) vs. Aldose structure (C=O on end)

□ Starch, Cellulose, and Glycogen are the three main storage and structural polysaccharides in cells

- In plant cells, energy is stored as starch and structural support is provided by cellulose

- In animal cells, glycogen stores surplus chemical energy

□ Sugars are named by the ______________________________ of subunits they contain

- Mono- = 1 subunit; Di- = 2 subunits; Oligo- = up to 10 subunits, Poly- = 11+ subunits

- Common sugars include: Glucose (mono); Sucrose (Di); Lactose (Di); Amylose (Poly)

□ Glycolipids are sugars attached to lipids; Glycoproteins are sugars attached to proteins

EXAMPLE: Amylose is a linear polysaccharide made up of α(1→4) bonds



● Nucleic acids are the subunits of DNA and RNA which are responsible for storing and transmitting genetic information

□ Each nucleotide contains a base, a five carbon sugar (deoxyribose or ribose), and a phosphate group

- There are two classes of bases: Purines with a pair of fused rings and Pyrimidines with a single ring

- Adenine (A) and Guanine (G) = purines; Cytosine (C), Thymine (T), and Uracil (U) = pyrimidines

□ Phosphodiester bonds are responsible for ____________________________ nucleic acids together

- Linear sequence of nucleic acids is important because it encodes genetic information

□ Nucleotides can also store energy

- Adenosine tri-phosphate (ATP) is a nucleotide that supplies energy for numerous cellular reactions

EXAMPLE: Complementary nucleotides bound in a DNA molecule



● Proteins are macromolecules responsible for carrying out cellular __________________________________

□ Amino acids are subunit building blocks used to build polypeptide chains that form proteins

- Amino acids have an alpha carbon, a carboxyl group (COOH), an amino group (NH3), and a “R” group

- Amino acids (called residues) are linked by peptide bonds between the carboxyl group and amino group

EXAMPLE: Amino acid structure

□ Proteins function is determined by _______________________________ properties

- The 20 amino acids are arranged in a specific formation to provide the protein its function

- The properties of the side chain (R group) gives the protein unique structural and functional properties

- Can be classified as polar, charged, nonpolar or “other”

- Forms stabilizing disulfide bridges between sulfhydryl groups (SH) on the amino acid cysteine

EXAMPLE: Polypeptide chain made up of single amino acids – add extra image on structure of amino acid up!



● Lipids are macromolecules responsible for the formation of cellular barriers; They are nonpolar = do not dissolve in H2O

□ Phospholipids are one main class of lipids responsible for the formation of bilayer membranes

- Composed of two fatty acids (long unbranched hydrocarbon chains with carboxyl group) and polar group

- They are amphipathic, which means they contain both hydrophilic and hydrophobic parts

EXAMPLE: A free fatty acid compared to a phospholipid

□ Fats are a second class of lipids responsible for energy _____________________________

- Triglycerides are composed of three fatty acids, linked by an ester bond to a glycerol molecule

- Can be saturated if they do not contain double bonds, or unsaturated if they contain chemical bonds

- 1 gram of fat stores twice the energy of 1 gram of carbohydrate

EXAMPLE: Triglyceride structure

□ Steroids are a class of lipids responsible for hormone signaling and membrane structure

- Composed of a ringed hydrocarbon skeleton

- Cholesterol is a common example found in cellular membranes that provided rigidity

EXAMPLE: Structure of cholesterol



PRACTICE 1. Which of the following is false?

a. Polysaccharides are responsible for energy storage and cellular support b. Nucleic acids are linked via Phosphodiester bonds c. Amino acid sequence and structure provide proteins with unique physical attributes d. Fatty acids are composed of branched hydrocarbon chains

2. Which of the following macromolecules does the cell use for structure and support? a. Polysaccharides b. Nucleic Acids c. Lipids d. Proteins



3. Animal cells store excess sugar in the form of what? a. Starch b. Cellulose c. Amylose d. Glycogen

4. True or False: Polysaccharides are the macromolecules that act as a source of energy storage. a. True b. False



CONCEPT: PROPERTIES OF MACROMOLECULES

Macromolecule Polymerization

● Linear polymerization forms the structures of polysaccharides, nucleic acids, and proteins (NOT lipids!) □ Condensation reactions form the _________________________ between monomers (subunits)

- Monomer H + molecule OH group react and release water

- Repetition of condensation reactions sequentially add monomers to the macromolecule’s end

□ Hydrolysis reactions degrades long polymer chains through the addition of a water molecule

□ For proteins and amino acids, biological function depends on the specific sequence of subunits

EXAMPLE: A condensation reaction connects amino acid monomers together and results in the loss of water

Stereoisomers

● Macromolecules can be created as stereoisomers (mirror images) due to an asymmetric carbon atom (chiral center) □ Stereoisomers are two molecules with the same chemical formula, but with different physical structures

□ Come in __________________ main forms: D- and L- forms

- Amino acids, monosaccharides, nucleic acids and steroid lipids have stereoisomer forms

- Certain biological functions only use one form (Proteins are only made up of L-amino acids)

EXAMPLE: Two amino acids stereoisomers displayed on hands to show the D- (right) and L- (left) forms



Role of Noncovalent Bonds ● Noncovalent bonds are crucial for macromolecule formation and function □ Although weak individually, the strength of noncovalent bonds is __________________ (more bonds = stronger)

□ Macromolecule conformation depends on placement and formation of noncovalent bonds

- Allows for a close and strong fit between two interacting molecules (Ex: multi-protein complexes)

- Macromolecule functional groups are groups of atoms that act as a unit to provide unique properties

EXAMPLE: Two potential noncovalent bonds between lysine and glutamic acid

PRACTICE:

1. Which of the following is not a property of macromolecules? a. They are formed through linear polymerization of individual subunits b. They have the ability to form stereoisomers c. Noncovalent bonds allow for the formation of complex functions d. Covalent interactions allow for stable conformations of macromolecules



2. Which of the following reactions connects individual monomers together?

a. Hydrolysis Reactions b. Condensation Reactions c. Glycolyic Reactions d. Monomeric Reactoins

3. True or False: Proteins are most often found in the D form. a. True b. False



CELL BIOLOGY - CLUTCH CH. 2 - CHEMICAL COMPONENTS OF...

Documents

Transcript of CELL BIOLOGY - CLUTCH CH. 2 - CHEMICAL COMPONENTS OF...