Biological Molecules and Functional Groups

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Questions and Answers

What four kinds of molecules are characteristic of living things?

Carbohydrates, lipids, proteins, and nucleic acids.

Which are considered polymers? of which monomers do they consist?

Carbohydrates, proteins, and nucleic acids are polymers. Carbohydrates consist of monosaccharides, proteins consist of amino acids, and nucleic acids consist of nucleotides.

What are the eight functional groups introduced in lecture?

Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl, and ethyl

What are their names, chemical formulas, and important properties? i.e., which are polar? nonpolar? charged? acidic? basic?

<p>This question refers to the eight functional groups: Hydroxyl (OH), Carbonyl (C=O), Carboxyl (COOH), Amino (NH2), Sulfhydryl (SH), Phosphate (PO4), Methyl (CH3). Methyl is nonpolar. Carboxyl is acidic. Amino is basic.</p> Signup and view all the answers

What is an isomer?

<p>Isomers are molecules with the same molecular formula but different structural arrangements of atoms.</p> Signup and view all the answers

What are the three types of isomers presented in lecture?

<p>Structural isomers, geometric isomers (cis-trans isomers), and enantiomers (stereoisomers).</p> Signup and view all the answers

What occurs in a condensation reaction? a hydrolysis reaction?

<p>Condensation reaction: monomers join to form polymers by losing a water molecule. Hydrolysis reaction: polymers are broken down into monomers by adding a water molecule.</p> Signup and view all the answers

Proteins are polymers composed of which type of monomer?

<p>Amino acids.</p> Signup and view all the answers

Which two functional groups are present in all amino acids?

<p>Amino group (-NH2) and carboxyl group (-COOH).</p> Signup and view all the answers

In which forms do these groups exist in amino acids found inside cells?

<p>The amino group is typically protonated (-NH3+) and the carboxyl group is typically deprotonated (-COO-) at cellular pH.</p> Signup and view all the answers

Which isomer form of amino acids do we observe in organisms?

<p>L-isomers.</p> Signup and view all the answers

Which amino acids are positively charged?

<p>Lysine, arginine, and histidine.</p> Signup and view all the answers

What does their charge mean for the chemical reactivity?

<p>Their positive charge allows them to form ionic bonds with negatively charged molecules or regions of molecules.</p> Signup and view all the answers

Which amino acids are uncharged but polar?

<p>Serine, threonine, cysteine, asparagine, and glutamine.</p> Signup and view all the answers

What does their polarity mean for the chemical reactivity?

<p>Their polarity allows them to participate in hydrogen bonding and dipole-dipole interactions, influencing protein structure and interactions with other molecules.</p> Signup and view all the answers

Which amino acids are nonpolar?

<p>Glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, and proline.</p> Signup and view all the answers

Which amino acids are exceptional and do not fall into the above three groups?

<p>There are no amino acids that do not fall into the above three groups (positively charged, negatively charged, uncharged polar, and nonpolar).</p> Signup and view all the answers

What is a disulfide bridge? which amino acid can form them?

<p>A disulfide bridge is a covalent bond between the sulfur atoms of two cysteine residues. Cysteine can form them.</p> Signup and view all the answers

How do the size and shape of glycine and proline affect their location within a folded polypeptide?

<p>Glycine, being small, can fit into tight spaces or allow for flexibility in the polypeptide chain. Proline, with its cyclic structure, introduces kinks and rigidity.</p> Signup and view all the answers

What distinguishes a "polypeptide" from a "peptide"?

<p>A polypeptide is a longer chain of amino acids than a peptide. The terms are often used interchangeably, but peptide generally refers to a shorter sequence.</p> Signup and view all the answers

How is a peptide bond formed?

<p>A peptide bond is formed through a dehydration reaction between the carboxyl group of one amino acid and the amino group of another amino acid.</p> Signup and view all the answers

What comprises the primary structure of a protein?

<p>The primary structure of a protein is its linear sequence of amino acids.</p> Signup and view all the answers

Which type(s) of bond is/are involved?

<p>Covalent (peptide) bonds.</p> Signup and view all the answers

What comprises the secondary structure of a protein?

<p>The secondary structure of a protein consists of local folding patterns, such as alpha helices and beta sheets, stabilized by hydrogen bonds.</p> Signup and view all the answers

What comprises the quaternary structure of a protein?

<p>The quaternary structure of a protein is the arrangement of multiple polypeptide subunits into a functional complex.</p> Signup and view all the answers

Which levels of protein structure are affected by slow moderate heating of the molecule?

<p>Secondary, tertiary, and quaternary structures are affected by heating.</p> Signup and view all the answers

How does a denatured protein differ from a "native" protein

<p>A denatured protein has lost its proper three-dimensional structure, while a native protein has its functional conformation.</p> Signup and view all the answers

How do shape and surface chemistry contribute to protein function?

<p>Shape and surface chemistry determine how proteins interact with other molecules, such as substrates, ligands, or other proteins.</p> Signup and view all the answers

How can protein structure be affected by environmental conditions?

<p>Protein structure can be affected by temperature, pH, salt concentration, and the presence of denaturing agents.</p> Signup and view all the answers

How can interaction with other molecules affect protein structure?

<p>The binding of ligands or other molecules can induce conformational changes in a protein, affecting its structure and function.</p> Signup and view all the answers

Broadly speaking, what characterizes the structure of carbohydrates? i.e., which elements in what combination are found in all carbohydrates? which functional groups are present?

<p>Carbohydrates are composed of carbon, hydrogen, and oxygen atoms in a ratio of 1:2:1 (CH2O)n. They contain hydroxyl (-OH) and carbonyl (C=O) functional groups.</p> Signup and view all the answers

What are the four major biochemical roles of carbohydrates?

<p>Energy storage, structural support, cell-cell recognition, and precursors for biosynthesis of other molecules.</p> Signup and view all the answers

How do we define: monosaccharide

<p>A monosaccharide is a simple sugar containing one sugar unit.</p> Signup and view all the answers

What is an example of a six-carbon sugar? a five-carbon sugar?

<p>Six-carbon sugar: glucose. Five-carbon sugar: ribose.</p> Signup and view all the answers

What does the alpha orientation of a glucose molecule look like? the beta orientation?

<p>In the alpha orientation, the hydroxyl group on carbon-1 is on the same side as the carbon-6. In the beta orientation, the hydroxyl group on carbon-1 is on the opposite side as the carbon-6.</p> Signup and view all the answers

What occurs during glycosidic bond formation?

<p>A glycosidic bond forms between two monosaccharides through a dehydration reaction, releasing a water molecule.</p> Signup and view all the answers

How do we characterize an alpha bond? a beta bond?

<p>An alpha bond has the glycosidic linkage oriented downwards relative to the plane of the sugar ring, while a beta bond has the glycosidic linkage oriented upwards.</p> Signup and view all the answers

How do we use the numbered carbons and orientation of the monosaccharides that are bonding to name a glycosidic bond?

<p>The glycosidic bond is named by specifying the carbons involved and the orientation; for example, α-1,4-glycosidic bond.</p> Signup and view all the answers

Which three polysaccharides did we highlight in lecture?

<p>Starch, glycogen, and cellulose.</p> Signup and view all the answers

How are they arranged?

<p>Starch is a mixture of amylose (linear) and amylopectin (branched). Glycogen is highly branched. Cellulose is linear chains that form rigid structures.</p> Signup and view all the answers

Where do we find them?

<p>Starch is found in plants, glycogen in animals, and cellulose in plant cell walls.</p> Signup and view all the answers

What is their function?

<p>Starch and glycogen function as energy storage molecules. Cellulose provides structural support.</p> Signup and view all the answers

Why do we not refer to lipids as polymers?

<p>Lipids are not composed of repeating monomeric units linked together by covalent bonds, unlike carbohydrates, proteins, and nucleic acids.</p> Signup and view all the answers

Why are lipids hydrophobic?

<p>Lipids are hydrophobic because they consist predominantly of nonpolar hydrocarbon chains, which do not interact favorably with water.</p> Signup and view all the answers

What is the structure of a triglyceride? i.e., what are its molecular components?

<p>A triglyceride consists of a glycerol molecule esterified to three fatty acids.</p> Signup and view all the answers

Which bond holds together the components?

<p>Ester bonds.</p> Signup and view all the answers

Which reaction yields these bonds?

<p>Esterification, a type of dehydration reaction, yields these bonds.</p> Signup and view all the answers

What is the structural difference between a saturated and unsaturated fatty acid?

<p>Saturated fatty acids have no carbon-carbon double bonds, while unsaturated fatty acids have one or more carbon-carbon double bonds.</p> Signup and view all the answers

How does this affect triglycerides in terms of their state at room temperature?

<p>Triglycerides with saturated fatty acids are typically solid at room temperature, while triglycerides with unsaturated fatty acids are typically liquid.</p> Signup and view all the answers

What are the molecular components of a phospholipid?

<p>A phospholipid consists of a glycerol molecule esterified to two fatty acids and a phosphate group, which is often modified with a polar head group.</p> Signup and view all the answers

Why do we refer to this molecule as amphipathic?

<p>A phospholipid is amphipathic because it has both a hydrophobic (fatty acid tails) and a hydrophilic (phosphate head) region.</p> Signup and view all the answers

How do phospholipids behave in an aqueous solution?

<p>Phospholipids spontaneously form bilayers in aqueous solutions, with the hydrophobic tails facing inward and the hydrophilic heads facing outward, interacting with water.</p> Signup and view all the answers

Flashcards

Four main biomolecules

Carbohydrates, lipids, proteins, and nucleic acids.

What is an isomer?

Isomers are molecules with the same molecular formula but different structural arrangements and properties.

Condensation vs. Hydrolysis

A reaction where two molecules combine to form a larger molecule, with the loss of a small molecule (like water). Hydrolysis is the reverse, adding water to break a bond.

Monomer of Proteins

Amino acids.

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Amino acid functional groups

Amino (-NH2) and Carboxyl (-COOH).

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Amino Acid Isomer Form

L-isomers.

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Positively charged amino acids

Arginine, histidine, and lysine.

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Negatively charged amino acids

Aspartic acid and glutamic acid.

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Uncharged polar amino acids

Serine, threonine, cysteine, tyrosine, asparagine, and glutamine.

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Nonpolar amino acids

Glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, and proline.

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Study Notes

  • The four kinds of molecules characteristic of living things should be noted.
  • Identify which molecules are considered polymers and specify their respective monomers.
  • List the eight functional groups
  • Provide their names, chemical formulas, and important properties
  • Identify which are polar, nonpolar, charged, acidic and basic
  • Define what an isomer is.
  • Describe the three types of isomers.
  • Explain what occurs during a condensation reaction and a hydrolysis reaction.
  • The type of monomer of which proteins are composed should be identified.
  • Identify the two functional groups present in all amino acids.
  • Note the forms in which these groups exist within amino acids found in cells.
  • The isomer form of amino acids commonly observed in organisms should be known.
  • The amino acids that are positively charged.
  • Explain what their charge indicates for chemical reactivity.
  • The amino acids that are negatively charged.
  • Explain the meaning of their charge regarding chemical reactivity.
  • State which amino acids are uncharged but polar.
  • Note what their polarity means for chemical reactivity.
  • List the amino acids that are nonpolar.
  • Explain what their nonpolarity indicates for chemical reactivity.
  • Identify the exceptional amino acids that don't fall into the previous three categories.
  • Define what a disulfide bridge is and state which amino acid can form one.
  • Explain how the size and shape of glycine and proline impact their location in a folded polypeptide.
  • Note the difference between a "polypeptide" and a "peptide".
  • Explain how a peptide bond is formed.
  • Identify what comprises the primary structure of a protein and the bond types involved.
  • Describe what comprises the secondary structure of a protein and the bond types involved.
  • Explain what comprises the tertiary structure of a protein and the bond types involved.
  • Describe what comprises the quaternary structure of a protein and the bond types involved.
  • Note which levels of protein structure are affected by slow moderate heating.
  • Explain how a denatured protein differs from a native protein.
  • Explain how shape and surface chemistry affect protein function.
  • Describe how protein structure can be altered by environmental conditions.
  • Explain how interaction with other molecules can affect protein structure.
  • Broadly describe the structure of carbohydrates, including the elements and functional groups present.
  • List the four major biochemical roles of carbohydrates.
  • Define monosaccharide, disaccharide, oligosaccharide, and polysaccharide.
  • Provide an example of a six-carbon sugar and a five-carbon sugar.
  • Show what the alpha and beta orientations of a glucose molecule entail.
  • Describe what occurs during glycosidic bond formation.
  • Explain how we characterize alpha and beta bonds.
  • Describe how the numbered carbons and monosaccharide orientations name a glycosidic bond.
  • List three polysaccharides.
  • Describe how these three polysaccharides are arranged.
  • State where to find these three polysaccharides.
  • State the function of these three polysaccharides.
  • Explain why lipids are not referred to as polymers.
  • Explain why lipids are hydrophobic.
  • Describe the structure and molecular components of a triglyceride.
  • Identify the bond that holds the components together.
  • Note the reaction that yields these bonds.
  • Describe the structural difference between saturated and unsaturated fatty acids.
  • Explain how this difference affects triglycerides in terms of their state at room temperature.
  • List the molecular components of a phospholipid.
  • Explain why phospholipids are referred to as amphipathic.
  • Describe how phospholipids behave in an aqueous solution.

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