Biochemical Basics Flashcards

Question

Name the four levels of protein structure.

Answer 1

* Primary structure * Secondary structure * Tertiary structure * Quaternary structure

Answer 2

It is simply its linear amino acid sequence. ## Footnote Primary structure is often written using either a one- or a three-letter abbreviation for each amino acid (for example, "Gly-Pro-Ile-Cys..." or "GPIC...").

Answer 3

Refers to the folding of the amino acid chain into repetitive structures due to hydrogen bonding between backbone groups.

Answer 4

amides ## Footnote In fact, they are sometimes alternatively known as amide linkages. A peptide bond forms when the amine group of one amino acid attacks the carbonyl carbon of another.

Answer 5

Refers to its large-scale three-dimensional shape. ## Footnote Tertiary structure is determined by interactions between side chains and by hydrophobic interactions (the tendency for nonpolar groups to avoid facing the watery environment).

Answer 6

It is present only in proteins that are composed of multiple subunits. This level of structure refers to interactions between subunits. ## Footnote For example, hemoglobin (shown here) consists of four separate subunits, held together by various interactions and attractive forces.

Answer 7

A class of organic macromolecule characterized by their nonpolar (non-water-soluble) nature. ## Footnote Most notably, lipids include triglycerides (fats), oils, steroids, waxes, and phospholipids.

Answer 8

triglyceride ## Footnote A triglyceride is commonly known simply as a fat. It consists of three fatty acid molecules attached to a three-carbon glycerol backbone.

Answer 9

polyunsaturated ## Footnote Saturated fatty acids have carbon chains that include only single bonds, while unsaturated fatty acids include one or more double bonds in their chains. Since this fatty acid contains three carbon-carbon double bonds, it is **polyunsaturated**. (To be monounsaturated, a fatty acid must include only one double bond in its carbon chain.)

Answer 10

A **carboxylic acid (COOH)** group attached to a **hydrocarbon chain**. ## Footnote Fatty acids can combine with glycerol to form triglycerides, or fat. Fatty acids can also be broken down to provide cells with energy.

Answer 11

phospholipids ## Footnote The cell membrane (in both eukaryotes and prokaryotes) is composed mainly of phospholipids in the form of a "bilayer," or double layer.

Answer 12

amphipathic ## Footnote Specifically, the polar "head" region includes phosphate, which is charged; this charge is what gives the head group its polarity. The two "tails" consist of fatty acids, which are largely nonpolar due to their long hydrocarbon chains.

Answer 13

steroid hormones ## Footnote Steroid hormones are derived from cholesterol (shown here). These lipid molecules can be easily spotted due to their structures, which include four fused rings.

Answer 14

Nucleic acids ## Footnote The structure pictured here is a nucleotide, as is evident from its nitrogenous base, sugar, and phosphate group. Nucleotides are the monomers ("building blocks") that form nucleic acids, including DNA and RNA.

Answer 15

Nucleic acid ## Footnote All four of the main classes of organic macromolecule include covalent bonds, so that piece of information is unhelpful. However, only nucleic acids and (some) lipids can contain phosphorus. Since we are told that this molecule is not a lipid, it must be a nucleic acid.

Answer 16

A class of organic macromolecule, which consists of long chains of nucleotide monomers and are involved in the storage and transmission of genetic material.

Answer 17

It collectively refers to the biological processes that occur within cells. Specifically, these processes either generate energy through the breakdown of molecules or use energy to build molecules. ## Footnote Metabolism is also known as "cellular respiration."

Answer 18

It is the biological breakdown of molecules into smaller units. Catabolic processes are accompanied by the generation of energy. ## Footnote The opposite of this class of metabolic reactions is **anabolism**.

Answer 19

It is the creation of larger biomolecules from smaller units. Anabolic processes require energy input. ## Footnote The opposite of this class of metabolic reactions is **catabolism**.

Answer 20

Aerobic respiration requires oxygen, while anaerobic respiration does not require oxygen. ## Footnote As part of metabolism, both processes involve the breakdown of biological molecules and the eventual release of energy.

Answer 21

Glycolysis ## Footnote Glycolysis is a biochemical process that forms pyruvate from the breakdown of glucose. The pathway produces 2 NADH and a net total of 2 ATP per glucose molecule.

Answer 22

C₆H₁₂O₆ + 2NAD⁺ + 2 P_i + 2 ADP ⇒ 2 pyruvate + 2 ATP + 2 NADH + 2 H₂O + 2 H⁺ ## Footnote While glycolysis only produces a net of two ATP molecules, it generates a total of four. However, two molecules of ATP are used as reactants in early glycolytic steps.

Answer 23

Fermentation ## Footnote This process takes place when O₂ is too scarce to facilitate the entry of glycolytic products into the Krebs cycle. Fermentation can produce either ethanol or lactic acid, depending on the species.

Answer 24

Fermentation **regenerates NAD⁺** by oxidizing NADH and reducing pyruvate. ## Footnote NAD⁺ is necessary for glycolysis, but cannot be regenerated by the electron transport chain under anaerobic conditions. Fermentation serves to produce NAD⁺, reducing buildup of NADH and allowing glycolysis to continue.

Answer 25

**Pyruvate**, a three-carbon molecule, is the substrate. **CO₂**, **NADH**, and **acetyl-CoA** are the ultimate products.

Answer 26

4 NADH molecules ## Footnote During glycolysis, the initial two glucose molecules will be converted into four molecules of pyruvate. For every molecule of pyruvate that is decarboxylated by pyruvate dehydrogenase, one molecule of NADH is formed.

Answer 27

The **Krebs cycle** produces the electron carriers NADH and FADH₂, as well as an ATP equivalent (either ATP or GTP). ## Footnote The Krebs cycle, also known as the citric acid cycle, involves the cyclic transformation of organic molecules. It occurs in the mitochondrial matrix.

Answer 28

One full cycle produces 3 NADH molecules and 1 FADH₂. ## Footnote Other products include carbon dioxide, which is released as waste, and one molecule of GTP.

Answer 29

The **electron transport chain (ETC)** uses a series of complexes along the inner mitochondrial membrane. These molecules support a chain of oxidation-reduction reactions, ultimately resulting in the oxidization of NADH and FADH₂ and the reduction of O₂. ## Footnote The transport of electrons through the chain creates a proton gradient that provides the energy to convert ADP to ATP.

Answer 30

ATP synthesis ## Footnote After establishment of the gradient, proton concentration in the intermembrane space is high. When possible, these protons will move down their gradient and reenter the matrix; this can only occur if they pass through ATP synthase, an enzyme. As this process occurs, ATP synthase uses this energy to convert ADP to ATP.

Answer 31

**NADH** is a required substrate, and **O₂** must be present as the final electron acceptor in the chain. ## Footnote Glucose and pyruvate, though linked to NADH production, are not directly necessary for the electron transport chain. CO₂ is a waste product of cellular respiration.

Answer 32

* Pyruvate * NADH ## Footnote Ethanol, lactate, and NAD⁺ are all products of fermentation.

Answer 33

* ATP * pyruvate ## Footnote NADH, though not listed here, is another glycolytic product. Glucose and NAD⁺ are consumed in glycolysis, while O₂ is not involved. Remember that glycolysis is an anaerobic process.

Answer 34

The Krebs cycle produces **NADH** and **FADH₂**, which are electron carriers that are later used. ## Footnote Acetyl-CoA and NAD⁺ are consumed in the Krebs cycle, while pyruvate is not directly involved.

Answer 35

1. Glycolysis 2. Fermentation ## Footnote Note that fermentation only takes place in anaerobic conditions. All other processes take place in the mitochondria.

Answer 36

1. The Krebs cycle 2. Pyruvate decarboxylation ## Footnote The electron transport chain is also a mitochondrial process, but occurs along the inner membrane, not within the matrix itself.

Answer 37

Proteases | also called peptidases ## Footnote Proteins are cleaved into amino acids. Depending on their identity, these amino acids can be converted to acetyl-CoA, pyruvate, or other metabolic intermediates.

Answer 38

Acidosis | or low pH ## Footnote This is the result of excess CO₂and the buildup of lactic acid in muscles during anaerobic respiration. Note that normal plasma pH is 7.4.

Answer 39

facilitated diffusion ## Footnote This occurs with the assistance of a family of transport proteins. This process is promoted by high plasma glucose levels, which creates a concentration gradient that drives glucose into the cells. It is also promoted by the activity of insulin, which increases the number of glucose transporters on the membranes of certain cell types.

Answer 40

The phosphorylation of fructose 6-phosphate. ## Footnote This reaction is catalyzed by the enzyme phosphofructokinase-1 (PFK-1). For this reason, PFK-1 is sometimes called the rate-limiting enzyme of glycolysis.

Answer 41

AMP ## Footnote The other two molecules are inhibitors. You can figure this out logically: "activate" means "stimulate." Glycolysis should be stimulated when available energy is low (to make more) and inhibited when it is high. High AMP concentrations imply that cellular ATP is low.

Answer 42

C₆H₁₂O₆ ## Footnote Broadly, glucose is a carbohydrate; specifically, it is a monosaccharide.

Answer 43

* ethanol * lactate ## Footnote Alcohol fermentation, which takes place in yeast and certain bacteria, involves the reduction of pyruvate to ethanol. Lactic acid fermentation, which takes place in human muscle cells as part of anaerobic respiration, involves the reduction of pyruvate to lactate.

Answer 44

Pyruvate decarboxylation ## Footnote Under aerobic conditions, pyruvate (a three-carbon molecule) is converted to a two-carbon acetyl group. This group then attaches to coenzyme A.

Answer 45

**Acetyl-CoA**, a two-carbon compound, is the substrate entering the cycle. It immediately reacts with oxaloacetate to form a six-carbon compound (citrate). ## Footnote Coenzyme A is released in this process and can be used again.

Answer 46

Protons are pumped from the mitochondrial matrix to the intermembrane space.

Answer 47

A molecule that increases the rate of a reaction without being consumed itself. ## Footnote Catalysts change the kinetics of a reaction, not the thermodynamics. In other words, they lower the activation energy without altering the equilibrium or free energy change of a reaction.

Answer 48

A biological catalyst that structurally facilitates a chemical reaction. Like all catalysts, enzymes increase the rate of a chemical reaction without being consumed. ## Footnote Most enzymes are proteins, but RNA molecules called **ribozymes** also have enzymatic activity.

Answer 49

Enzymes must be at a certain optimal temperature to maintain their structure. ## Footnote The structure of an enzyme, especially in relation to its active site, is essential to its function as a catalyst. Like other proteins, enzymes denature, or lose their original conformations, above a certain temperature. However, reactions generally progress more slowly at low temperatures, further narrowing the range of optimal activity.

Answer 50

A lowered activation energy increases the reaction rate. ## Footnote Each reaction must overcome an activation energy barrier to progress from reactants to products. When this barrier is lower, reactants are more likely to collide with sufficient energy, speeding up the reaction.

Answer 51

Enzymes can only maintain their functional structure at a certain optimal pH. ## Footnote The structure of an enzyme, especially in relation to its active site, is essential to its function as a catalyst. The active site often contains positively or negatively charged groups, which contribute to the specificity of the site. Changes in pH can affect these sites, reducing enzyme activity.

Answer 52

At higher-than-optimal temperatures, most human enzymes lose function and cannot support necessary biological processes. ## Footnote Most human enzymes function most efficiently at an optimal temperature of 37 ºC. While these enzymes can remain active at slightly higher temperatures, their function is impaired.

Answer 53

Specificity ## Footnote The substrate(s) that can be accommodated by an enzyme are determined by the shape of its active site. For example, proteases are specific to protein substrates, while lipases act on lipid-based substrates.

Answer 54

It wrongly portrays all enzymes as being rigid and inflexible. ## Footnote In reality, the active site of an enzyme can change its conformation to facilitate binding to the substrate.

Answer 55

* **Cofactors** are a broad group of compounds that are required for the proper functioning of enzymes. * **Coenzymes** are a class of small, organic cofactors. ## Footnote Cofactors can also be inorganic substances, such as ions.

Answer 56

Vitamins ## Footnote Vitamins are often used to synthesize coenzymes, which are non-protein organic compounds that are essential for proper enzyme function.

Answer 57

This is an example of **negative feedback**. In such processes, increased concentration of a product decreases the rate of the reaction that forms that product. ## Footnote Glycolysis involves the breakdown of glucose to form ATP, among other products. If increased amounts of ATP are already present, glycolysis will slow.

Answer 58

This is the study of energy transformations within organisms. Specifically, it concerns the energy released and used during the formation and breaking of chemical bonds. ## Footnote Bioenergetics is closely related to thermodynamics, especially Gibbs free energy.

Answer 59

The change in Gibbs free energy, or **ΔG**, determines reaction spontaneity. ## Footnote A negative ΔG means the reaction will be spontaneous, while a positive ΔG denotes a nonspontaneous reaction.

Answer 60

exergonic ## Footnote In such reactions, ΔG is always negative, meaning that free energy is released. The opposite type of reactions are **endergonic**. In these processes, ΔG is positive and the reaction will not proceed spontaneously.

Answer 61

The catalyzed reaction will have a lower activation energy. ## Footnote Note that the overall change in free energy will be the same for the catalyzed and uncatalyzed reactions.

Answer 62

A specific molecule that an enzyme acts upon, usually via interactions with the enzyme's active site. ## Footnote For example, starch is the substrate of salivary amylase. This means that amylase, an enzyme, catalyzes a reaction involving starch as a reactant.

Answer 63

It is the structural component where enzyme-substrate interactions take place. ## Footnote In other words, the active site is the catalytic region of an enzyme. It is structured to facilitate the binding of its substrate, often through the presence of certain amino acid residues.

Answer 64

it posits that a substrate will fit perfectly into the active site of its corresponding enzyme, without any conformational changes taking place. ## Footnote In this model, the active site is the "lock" and its complementary substrate is the "key."

Answer 65

It posits that active sites are flexible. When a substrate approaches the enzyme, the conformation of the active site will change to better fit the substrate. ## Footnote The induced fit model is a more recent adaptation of the lock-and-key model.

Answer 66

A region of an enzyme, separate from the active site, where molecules can bind and affect enzyme function. ## Footnote Allosteric binding can either facilitate or inhibit the binding of substrate to the active site.

Answer 67

It binds to an enzyme on its active site, inhibiting the reaction. ## Footnote Specifically, these inhibitors compete with the substrate and block it from binding the active site.

Answer 68

It binds to an enzyme on a region outside of its active site, inhibiting the reaction. ## Footnote Specifically, these inhibitors bind an allosteric site, inducing a structural change in the enzyme that decreases its efficiency. Substrates can still enter the enzyme's active site.

Answer 69

disaccharides ## Footnote Maltase breaks down maltose into two glucose molecules. Sucrase cleaves sucrose into glucose and fructose, and lactase breaks down lactose into glucose and galactose.

Answer 70

This molecule is **adenosine triphosphate (ATP)**, the major form of cellular energy. ## Footnote ATP consists of three phosphate groups bound to the ribonucleoside adenosine. The cleavage of the third phosphate bond facilitates the release of energy, which the cell harnesses to drive biological processes.

Answer 71

phosphoanhydride bonds ## Footnote These phosphoanhydride bonds exist between phosphate groups on molecules like ATP (shown) and ADP. The name of these bonds comes from the reaction that forms them: dehydration (removal of H₂O). Predictably, they can be broken by the reverse reaction, hydrolysis (addition of H₂O).