note from Mr. W: 6/21/19: I’m in the process of modifying these to add questions about nucleic acids

1. Biochemistry Flashcards

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[h]biochemistry flashcards

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2. New Unit 1 Biochemistry Flashcards for AP Bio

Note from Mr. W: 9/8/21. This is a new set of flashcards that aim to cover all of the core content of unit 1 (and link to these objectives from the College Board). These haven’t yet been linked up to the learn-biology.com grading system (because the year is in progress, and I don’t want to cause confusion). But for AP Bio students, these are highly recommended. 

Also, I’ve deliberately left out the objectives connected to directionality. We’ll cover issues related to DNA’s 5′ to 3′ directionality when we cover DNA replication in AP Bio Unit Six.

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[h] Unit 1 Biochemistry Review Flashcards

[q]Describe water’s molecular structure, and the intermolecular bonds that result from this structure.

[a]Water is a polar covalent molecule. Because of unequal electron sharing between oxygen and hydrogen, the oxygen side of water has a partially negative charge, and the hydrogen side of water has a partially positive charge. As a result of this polarity, water can form hydrogen bonds with other water molecules, and with other polar substances.

[q]What are the key physical and chemical properties that result from water’s structure.

[a]As a result of water’s polarity

  • Water is a great solvent for polar and ionic substances, but can’t dissolve non-polar substances.
  • What has a high heat of vaporization, and a high specific heat.
  • Water will stick to other substances (adhesion) and to itself (cohesion)
  • Bodies of water have high surface tension.
  • Water is a liquid between 0 and 100 degrees C (despite its light molecular weight)
  • Water is less dense as a solid than as a liquid (one of the only substances in the universe for which this is true).

[q] In terms of hydrogen ions, hydroxide ions, and pH, describe the difference between an acidic and a basic solution.

[a] Acidic solutions have more hydrogen ions (protons or H+) than hydroxide ions (represented by OH) The pH of an acidic solution is below 7. Bases are substances that have more hydroxide ions than hydrogen ions, and their pH is above 7.

[q]Explain the importance of carbon in all biological molecules.

[a]Carbon has six electrons, and four valence electrons. That enables carbon atoms to form four covalent bonds, both with other carbon atoms and with atoms of other elements. In addition to single bonds, carbon can also form double bonds and triple bonds. This allows carbon-based molecules to form chains, rings, and branched structures, creating the kind of complex molecules that can carry out the information and energy storage and transfer functions that make like possible.

[q]Describe the biological importance of nitrogen and phosphorus in the molecules that make up living things

[a]Nitrogen is found in amino acids, the monomers of proteins, and in the nitrogenous bases that make up nucleotides (the monomers of nucleic acids). Phosphorus is found in the sugar-phosphate backbone of nucleic acids, in phospholipids, and in the energy transfer molecule ATP.

[q] List the four families of biomolecules, and briefly describe each one.

[a]

  • Carbohydrates include sugars and their polymers, starches and plant fiber.
  • Lipids are mostly hydrophobic molecules, and include fats and oils; phospholipids; steroids, and waxes.
  • Proteins are the most diverse molecules: their functions include enzymes; motor proteins; structural molecules that make up hair and fingernails; and antibodies (just to name a few).
  • Nucleic acids are the molecules of genetics and heredity, and includes DNA and RNA. One nucleic acid monomer, ATP, is also life’s key energy currency.

[q] What’s the difference between a monomer and a polymer?

[a] A monomer is a molecular building block. Monomers are combined to form polymers, which are monomers that are chemically linked together.

[q] Briefly explain how monomers are assembled into polymers, and how polymers are disassembled back into monomers.

[a]

  • Monomers are assembled into polymers by dehydration synthesis, during which enzymes catalyze bonds between monomers as they remove an “—OH” from one monomer and an “—H” from another. As a result, as monomers are linked to one another, a water molecule is released.
  • Polymers are taken apart through hydrolysis, during which enzymes break the bonds between the monomer residues in a polymer by jamming in a water molecule, which becomes an “—OH” on one monomer and an “—H” on the second.

[q] What are the three categories of carbohydrates? Briefly describe each one, and list examples of each.

[a]

  • Monosaccharides are the monomers of carbohydrates. They have a formula of (CH2O)n. In addition to acting as building blocks for other carbohydrates, monosaccharides, such as glucose, are sources of quick energy, fueling cellular respiration.
  • Two linked monosaccharides form a disaccharide. These molecules, such as sucrose and lactose, are generally used for energy transfer.
  • Three or more monosaccharides make a polysaccharide. These include energy storage molecules, like starch and glycogen, and also fibers, like cellulose, which makes up the primary component of plant cell walls.

[q] ADVANCED TOPIC: Both starch and cellulose are polysaccharide polymers of glucose. But their nutritional value is very different. Explain.

[a] Starch is an energy-rich food while cellulose is calorie-free fiber. This is because the bonds that connect the glucose monomers in starch can be hydrolyzed by the enzymes in our digestive tract. The released glucose can power cellular respiration in our cells, or can be used as building blocks for making other molecules. By contrast, the bonds that connect the glucose monomers in cellulose have a different shape, and can’t be hydrolyzed by our enzymes. As a result, the cellulose just passes through our system, useful for fiber, but useless as energy.

[q] ADVANCED TOPIC: Describe some of the biochemical and evolutionary issues connected with lactose tolerance and intolerance.

[a] Lactose is a disaccharide. It’s the key sugar in milk. Milk-drinking mammals can digest lactose when they’re babies, but most stop producing the lactose-digesting enzyme lactase once they’re weaned. In other words, most mammals are lactose intolerant (except when they’re babies). If these mammals, as adults, ingest lactose, they’d experience diarrhea and flatulence.

In a few populations of humans, domestication of ruminants (mammals like cows, goats, and camels) was accompanied by the spread of a mutation that allowed humans to continue to produce lactase throughout their lifespan, enabling them to digest milk products. But other populations (the majority of humanity) are lactose intolerant (as are many individuals within the cultures that descend from the ancestral milk-drinkers).

[q] What are the four categories of lipids, and what are the functions of each?

[a]

  1. Fats and oils, are triglycerides. They’re made of three fatty acids connected to a glycerol. Their functions are storing energy, providing insulation, and providing buoyancy (in marine mammals).
  2. Steroids consist of four fused carbon rings. They include steroid hormones, and the molecule cholesterol, which is important in stabilizing cell membranes.
  3. Phospholipids consist of a “tail” of two fatty acids and a polar “head” which contains a phosphate group. Phospholipids form bilayers, which make up the key structure of the cell membrane.
  4. Waxes consist of two long fatty acids. They’re used for waterproofing, and are found on the upper and lower surface of leaves.

[q]Explain the structure of phospholipids, and their biological importance.

[a]Phospholipids consist of a nonpolar “tail” of two fatty acids and a polar “head” which contains a phosphate group. The tail is hydrophobic and the head is hydrophilic. As a result, when phospholipids are mixed with water they spontaneously form a structure called a phospholipid bilayer — the main structural component of the cell membrane.

[q] Compare and contrast fats and oils.

[a] Both fats and oils are triglycerides, consisting of three fatty acids connected to glycerol (a 3-carbon alcohol). In fats, the three fatty acids are saturated, meaning that they have no double bonds in their hydrocarbon chains. As a result, these fatty acids are straight, and form weak bonds with one another, and with saturated fatty acids in adjacent fat molecules. These bonds, weak as they are, make fats solid at room temperature.

Oils, by contrast, have at least one fatty acid that is unsaturated. This causes the hydrocarbon chain to bend, preventing bonding between the fatty acids within the molecule or between adjacent oil molecules. The result, at room temperature, is a liquid.

[q] Describe the structure of an amino acid. Explain how amino acids can differ from one another.

[a] Amino acids are built around a central carbon. On one side of that carbon is an amino group (—NH2). On the other side is a carboxylic acid (—COOH). Above the central carbon is a hydrogen atom, and below it is a side chain or R-group. There are 20 different side chains found in nature, and they can be non-polar, polar, acidic (negatively charged) or basic (positively charged).

[q]What are peptide bonds? How do they work?

[a]Amino acids bond with one another through peptide bonds. These bonds form through a dehydration synthesis reaction that’s catalyzed by ribosomes during protein synthesis. In a peptide bond, the carboxyl group of one amino acid binds to the amino group of the next, resulting in a bond between a carbon atom and a nitrogen atom. The carbon is double bonded to an oxygen, making a carbonyl group. The nitrogen is bonded to a hydrogen. 

[q] Describe the four levels of protein structure.

[a]

  • Primary structure is the genetically determined sequence of amino acids in the polypeptide chain.
  • Secondary structure involves hydrogen bonds between the carbonyl and amino functional groups within the polypeptide backbone. These result in two shapes: an alpha helix (a corkscrew), or a beta pleated sheet (a series of folds).
  • Tertiary structure involves bonds between side chains. These can be hydrogen bonds between polar side chains, hydrophobic clustering involving non-polar side chains, ionic bonds, and disulfide bridges.
  • Quaternary structure involves multiple folded polypeptide chains bonding together (through any of the interactions just listed at the tertiary level)

[q]What are the two types of nucleic acids? In terms of function, how are they different?

[a]The two nucleic acids are DNA and RNA.

DNA’s main function is storing genetic information in cells, and “telling” cells what proteins they should make.

RNA’s main function in cells is to bring genetic information from DNA to ribosomes, and to translate that genetic information into protein. In some viruses, RNA is the genetic information.

[q]Describe the monomers of nucleic acids. How are these monomers different in DNA and RNA?

[a]The monomers of nucleic acids are nucleotides. Each nucleotide consists of a 5 carbon sugar, a phosphate group, and one of 4 nitrogenous bases. In DNA, the sugar is deoxyribose, and the four bases are A, T, C, and G (adenine, thymine, cytosine, and guanine). In RNA, the sugar is ribose, and the four bases are A, U, C and G (adenine, uracil, cytosine, and guanine).

[q]Nucleic acids are life’s key information molecule. How do they store information?

[a]Nucleic acids store information in their sequence of nucleotides. That sequence can be translated into the primary structure of a protein, allowing information to become molecular structures that carry out specific functions (as in enzymes and other protein molecules).

[q]What are the base pairing rules in DNA? Why are these rules important?

[a]The base pairing rules allow for DNA to be accurately copied from one generation of organisms or cells to the next. The rules are A bonds with T, and C bonds with G.

[q]Describe DNA’s overall structure.

[a]DNA is a double helix. The double helix consists of two anti-parallel strands, which means that each strand is upside down relative to the other. Each strand consists of a sugar-phosphate backbone on the outside, with nitrogenous bases facing inward. Each strand connects to the other through hydrogen bonds between nitrogenous bases with complimentary shapes (with A bonding with T, and C bonding with G).

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3. Biochemistry Cumulative Quiz

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[h]Biochemistry Cumulative Quiz

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 Next Steps

  • This ends this unit about biochemistry. Use the choices above to choose your next unit. Typically Cell Structure and Function  is the next unit in most biology curricula.
  • Or, if you want a musical break (that’s still educational), listen to my song “DNA, Fantastic!”