Biochemistry

Task 1 Vocabulary1: match the words with their meanings.

1 carbohydrates	A the process in which cells build protein
2 lipids	B any process by which a cell converts one kind of signal or stimulus into another.
3 cell metabolism	C large organic compounds made of amino acids arranged in a linear chain and joined by peptide bonds
4 endocrine system	D a class of hydrocarbon-containing organic compounds essential for the structure and function of living cells. They are categorized by the fact that they are soluble in nonpolar solvents (such as ether and chloroform) and are relatively insoluble in water
5 protein biosynthesis	E the process (or really the sum of many ongoing individual processes) by which living cells process nutrient molecules and maintain a living state
6 cell membrane	F any molecule that contains both amine and carboxyl functional groups
7 signal transduction	G relatively complex carbohydrates (sometimes called glycans)
8 proteins	H molecules that contain oxygen, hydrogen, and carbon atoms
9 amino acid	I a selectively permeable lipid bilayer coated by proteins which comprises the outer layer of a cell
10 polysaccharides	J a control system of ductless glands that secrete chemical "instant messengers" called hormones that circulate within the body via the bloodstream to affect distant cells within specific organs

Task 2 Vocabulary 2: Read the following introduction. Some of the words are missing. Put them in the correct place. The missing words are -

monomers, alternate, organisms, catalyzed, terrestrial, endocrine system, ancestor

Biochemistry is the study of the chemical processes and chemical transformations in living __________ (1). This article only discusses __________ (2) biochemistry (carbon- and water-based), as all the life forms we know are on Earth. Since life forms alive today are believed to have descended from the same common __________ (3), they naturally have similar biochemistries, even for matters which would appear to be essentially arbitrary, such as the genetic code or handedness of various biomolecules. It is unknown whether __________ (4) biochemistries are possible or practical. Biochemistry is the study of the structure and function of cell (biology) components, such as proteins, carbohydrates, lipids, nucleic acids, and other biomolecules. Chemical biology aims to answer many questions arising from biochemistry by using tools developed within synthetic chemistry. Although there are a vast number of different biomolecules, they tend to be composed of the same repeating subunits (called ''__________ (5) ''), in different orders. Each class of biomolecules has a different set of subunits. Recently, biochemistry has focused more specifically on the chemistry of enzyme- __________ (6) reactions, and on the properties of proteins. The biochemistry of cell metabolism and the __________ (7) has been extensively described. Other areas of biochemistry include the genetic code (DNA, RNA), protein synthesis, cell membrane transport, and signal transduction.

Task 3 Comprehension: Read the following passage and answer the questions below.

History of biochemistry

Originally, it was generally believed that life was not subject to the laws of science the way non-life was. It was thought that only living beings could produce the molecules of life (from other, previously existing biomolecules). Then, in 1828, Friedrich Woehler published a paper about the synthesis of urea, proving that organic compounds can be created artificially. The dawn of biochemistry may have been the discovery of the first enzyme, diastase (today called amylase), in 1833 by Anselme Payen. Eduard Buchner contributed the first demonstration of a complex biochemical process outside of a cell in 1896: alcoholic fermentation in cell extracts of yeast. Although the term “biochemistry” seems to have been first used in 1881, it is generally accepted that the formal coinage of biochemistry occurred in 1903 by Carl Neuber, a German chemist. Since then, biochemistry has advanced, especially since the mid-20th century, with the development of new techniques such as chromatography, X-ray diffraction, protein nuclear magnetic resonance spectroscopy(NMR spectroscopy), radioisotopic labelling, electron microscopy and molecular dynamics simulations. These techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle (citric acid cycle). Today, the findings of biochemistry are used in many areas, from genetics to molecular biology and from agriculture to medicine.

1 What was Woelher’s study about and what did it show?

2 In what way are diastase and amylase different?

3 What did Buchner use as his raw material in his 1896 demonstration?

4 Who is credited with making up the word ‘biochemistry’?

5 What is NMR spectroscopy?

6 What is another way to describe the Krebs cycle?

7 True or false: biochemistry is of no use to a farmer?

Task 4 Task Reconstruction: Read the following text about carbohydrates. There are 7 paragraphs. They have been mixed up. Put them in the correct order in the table below and note any clues that helped you.

Carbohydrates

A) Sugar polymers are characterised by having reducing or non-reducing ends. A reducing end of a carbohydrate is a carbon atom which can be in equilibrium with the open-chain aldehyde or keto form. If the joining of monomers takes place at such a carbon atom, the free hydroxy group of the pyranose or furanose form is exchanged with an OH-side chain of another sugar, yielding a full acetal. This prevents opening of the chain to the aldehyde or keto form and renders the modified residue non-reducing. Lactose contains a reducing end at its glucose moiety, whereas the galactose moiety form a full acetal with the C4-OH group of glucose. Saccharose does not have a reducing end because of full acetal formation between the aldehyde carbon of glucose (C1) and the keto carbon of fructose (C2).

B) The function of carbohydrates includes energy storage and providing structure. Sugars are carbohydrates, although there are carbohydrates that are not sugars. There are more carbohydrates on Earth than any other type of biomolecule. The simplest type of carbohydrate is a monosaccharide, which among other properties contains carbon, hydrogen, and oxygen, mostly in a ratio of 1:2:1 (generalized formula C_''n''H_2''n''O_''n'', where ''n'' is at least 3). Glucose, one of the most important carbohydrates, is an example of a monosaccharide. So is fructose, the sugar that gives fruits their sweet taste. Some carbohydrates (especially after condensation to oligo- and polysaccharides) contain less carbon relative to H and O, which still are present in 2:1 (H:O) ratio. Monosaccharides can be grouped into aldoses (having an aldehyde group at the end of the chain, e. g. glucose) and ketoses (having a keto group in their chain; e. g. fructose). Both aldoses and ketoses occur in an equilibrium between the open-chain forms and (starting with chain lengths of C4) cyclic forms. These are generated by bond formation between one of the hydroxy groups of the sugar chain with the carbon of the aldehyde or keto group in a semiacetal bond. This leads to saturated five-membered (in furanoses) or six-membered (in pyranoses) heterocyclic rings containing one O as heteroatom.

C) Many monosaccharides joined together make a polysaccharide. They can be joined together in one long linear chain, or they may be branched. Two of the most common polysaccharides are cellulose and glycogen, both consisting of repeating glucose monomers. Cellulose is made by plants and is an important structural component of their cell walls. Humans can neither manufacture nor digest it. Glycogen, on the other hand, is an animal carbohydrate; humans use it as a form of energy storage.

D) Two monosaccharides can be joined together using dehydration synthesis, in which a hydrogen atom is removed from the end of one molecule and a hydroxyl group (—OH) is removed from the other; the remaining residues are then attached at the sites from which the atoms were removed. The H—OH or H₂O is then released as a molecule of water, hence the term ''dehydration''. The new molecule, consisting of two monosaccharides, is called a ''disaccharide'' and is conjoined together by a glycosidic or ether bond. The reverse reaction can also occur, using a molecule of water to split up a disaccharide and break the glycosidic bond; this is termed ''hydrolysis''. The most well-known disaccharide is sucrose, ordinary sugar (in scientific contexts, called ''table sugar'' or ''cane sugar'' to differentiate it from other sugars). Sucrose consists of a glucose molecule and a fructose molecule joined together. Another important disaccharide is lactose, consisting of a glucose molecule and a galactose molecule. As most humans age, the production of lactase, the enzyme that hydrolyzes lactose back into glucose and galactose, typically decreases. This results in lactase deficiency, also called ''lactose intolerance''.

E) In vertebrates, vigorously contracting skeletal muscles (during weightlifting or sprinting, for example) do not receive enough oxygen to meet the energy demand, and so they shift to anaerobic metabolism, converting glucose to lactate (lactic acid). The liver regenerates the glucose, using a process called gluconeogenesis. This process is not quite the opposite of glycolysis, and actually requires three times the amount of energy gained from glycolysis (six molecules of ATP are used, compared to the two gained in glycolysis). Analogous to the above reactions, the glucose produced can then undergo glycolysis in tissues that need energy, be stored as glycogen (or starch in plants), or be converted to other monosaccharides or joined into di- or oligosaccharides.

F) Glucose is the major energy source in most life forms; a number of catabolic pathways converge on glucose. For instance, polysaccharides are broken down into their monomers (glycogen phosphorylase removes glucose residues from glycogen). Disaccharides like lactose or sucrose are cleaved into their two component monosaccharides. Glucose is mainly metabolized by a very important and ancient ten-step pathway called glycolysis, the net result of which is to break down one molecule of glucose into two molecules of pyruvate; this also produces a net two molecules of Adenosine triphosphate (ATP), the energy currency of cells, along with two reducing equivalents in the form of converting Nicotinamide adenine dinucleotide|NAD⁺ to NADH. This does not require oxygen; if no oxygen is available (or the cell cannot use oxygen), the Nicotinamide adenine dinucleotide(NAD) is restored by converting the pyruvate to lactate (e. g. in humans) or to ethanol plus carbon dioxide (e. g. in yeast). Other monosaccharides like galactose and fructose can be converted into intermediates of the glycolytic pathway. In aerobic cells with sufficient oxygen, like most human cells, the pyruvate is further metabolized. It is irreversibly converted to acetyl-CoA, giving off one carbon atom as the waste product carbon dioxide, generating another reducing equivalent as NADH. The two molecules acetyl-CoA (from one molecule of glucose) then enter the citric acid cycle, producing two more molecules of ATP, six more NADH molecules and two reduced (ubi)quinones (via FADH2|FADH₂ as enzyme-bound cofactor), and releasing the remaining carbon atoms as carbon dioxide. The produced NADH and quinol molecules then feed into the enzyme complexes of the respiratory chain, an electron transport system transferring the electrons ultimately to oxygen and conserving the released energy in the form of a proton gradient over a membrane (inner mitochondrial membrane in eukaryotes). Thereby, oxygen is reduced to water and the original electron acceptors NAD⁺ and quinone are regenerated. This is why humans breathe in oxygen and breathe out carbon dioxide. The energy released from transferring the electrons from high-energy states in NADH and quinol is conserved first as proton gradient and converted to ATP via ATP synthase. This generates an additional ''28'' molecules of ATP (24 from the 8 NADH + 4 from the 2 quinols), totaling to 32 molecules of ATP conserved per degraded glucose (two from glycolysis + two from the citrate cycle). It is clear that using oxygen to completely oxidize glucose provides an organism with far more energy than any oxygen-independent metabolic feature, and this is thought to be the reason why complex life appeared only after Earth's atmosphere accumulated large amounts of oxygen.

G) When a few (around three to six) monosaccharides are joined together, it is called an ''oligosaccharide'' (''oligo-'' meaning "few"). These molecules tend to be used as markers and signals, as well as having some other uses.

Para.	Letter	Clues
1^st
2^nd
3^rd
4^th
5^th
6^th
7^th

Proteins

Like carbohydrates, some proteins perform largely structural roles. For instance, movements of the proteins actin and myosin ultimately are responsible for the contraction of skeletal muscle. One property many proteins have is that they specifically bind to a certain molecule or class of molecules—they may be ''extremely'' selective in what they bind. Antibodies are an example of proteins that attach to one specific type of molecule. In fact, the enzyme-linked immunosorbent assay (ELISA), which uses antibodies, is currently one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins, however, are the enzymes. These amazing molecules recognize specific reactant molecules called ''substrates''; they then catalyze the reaction between them. By lowering the activation energy, the enzyme speeds up that reaction by a rate of 10¹¹ or more: a reaction that would normally take over 3,000 years to complete spontaneously might take less than a second with an enzyme. The enzyme itself is not used up in the process, and is free to catalyze the same reaction with a new set of substrates. Using various modifiers, the activity of the enzyme can be regulated, enabling control of the biochemistry of the cell as a whole.

Task 5 Pronouns: What do the highlighted pronouns in the paragraph above refer to.

In essence, proteins are chains of amino acids. An amino acid consists of a carbon atom bound to four groups. One is an amino group, —NH₂, and one is a carboxylic acid group, —COOH (although these exist as —NH₃⁺ and —COO⁻ under physiologic conditions). The third is a simple hydrogen atom. The fourth is commonly denoted "—R" and is different for each amino acid. There are twenty standard amino acids. Some of these have functions by themselves or in a modified form; for instance, glutamate functions as an important neurotransmitter.

Task 6 Visualization: Make a simple drawing of an amino acid showing the main parts.

Amino acids can be joined together via a peptide bond. In this dehydration synthesis, a water molecule is removed and the peptide bond connects the nitrogen of one amino acid's amino group to the carbon of the other's carboxylic acid group. The resulting molecule is called a ''dipeptide'', and short stretches of amino acids (usually, fewer than around thirty) are called ''peptides'' or polypeptides. Longer stretches merit the title ''proteins''. As an example, the imporant blood blood plasma protein albumin contains 585 amino acid residues.

Task 6 Restatement: In your own words explain what dehydration synthesis is.

The structure of proteins is traditionally described in a hierarchy of four levels. The primary structure of a protein simply consists of its linear sequence of amino acids; for instance,"alanine-glycine-tryptophan-serine-glutamate-asparagine-glycine-lysine-...". Secondary structure is concerned with local morphology. Some combinations of amino acids will tend to curl up in a coil called an α-helix; some of these can be seen in the hemoglobin schematic above. Tertiary structure is the entire three-dimensional shape of the protein. This shape is determined by the sequence of amino acids. In fact, a single change can change the entire structure. The β chain of hemoglobin contains 146 amino acid residues; substitution of the glutamate residue at position 6 with a valine residue changes the behavior of hemoglobin so much that it results in sickle-cell disease. Finally quaternary structure is concerned with the structure of a protein with multiple peptide subunits, like hemoglobin with its four subunits. Not all proteins have more than one subunit.

Task 7 Synonyms: Give synonyms for the words primary, secondary, tertiary, quaternary. What are the roots of these words.

Ingested proteins are usually broken up into single amino acids or dipeptides in the small intestine, and then absorbed. They can then be joined together to make new proteins. Intermediate products of glycolysis, the citric acid cycle, and the pentose phosphate pathway can be used to make all twenty amino acids, and most bacteria and plants possess all the necessary enzymes to synthesize them. Humans and other mammals, however, can only synthesize half of them. They cannot synthesize isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. These are the essential amino acids, since it is essential to ingest them. Mammals do possess the enzymes to synthesize alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine, the nonessential amino acids. While they can synthesize arginine and histidine, they cannot produce it in sufficient amounts for young, growing animals, and so these are often considered essential amino acids.

Task 8 Comprehension: Two of the following words do not belong in the group. Which are they and why do the not belong?

valine, threonine, lysine, asparagine, phenylalanine, leucine, glycine, tryptophan, methionine, isoleucine,

If the amino group is removed from an amino acid, it leaves behind a carbon skeleton called an α-keto acid. Enzymes called transaminases can easily transfer the amino group from one amino acid (making it an α-keto acid) to another α-keto acid (making it an amino acid). This is important in the biosynthesis of amino acids, as for many of the pathways, intermediates from other biochemical pathways are converted to the α-keto acid skeleton, and then an amino group is added, often via transamination. The amino acids may then be linked together to make a protein.

Task 9 Structure: What is the paragraph above about?

A similar process is used to break down proteins. It is first hydrolyzed into its component amino acids. Free ammonia (NH₃, existing as the ammonium ion NH₄⁺) in blood) is toxic to life forms. A suitable method for excreting it must therefore exist. Different strategies have evolved in different animals, depending on the animals' needs. Unicellular organisms, of course, simply release the ammonia into the environment. Similarly, osteichthyes (bony fish) can release the ammonia into the water where it is quickly diluted. In general, mammals convert the ammonia into urea, via the urea cycle.

Task 10 Structure: What is the topic sentence of the paragraph above.

Homework

Please read the following paragraphs about Lipids, Nucleic acid, and Relationship to other "molecular-scale" biological sciences. Make up a vocabulary matching exercise with three biochemical and three ordinary words from each paragraph. Also make up three comprehension questions from each section.

Lipids

The term lipid comprises a diverse range of molecules and to some extent is a catchall for relatively water-insoluble or nonpolar compounds of biological origin, including waxes, fatty acids, fatty-acid derived phospholipids, sphingolipids, glycolipids and terpenoids, such as retinoids and steroids. Some lipids are linear aliphatic molecules, while others have ring structures. Some are aromatic, while others are not. Some are flexible, while others are rigid.

Most lipids have some polar molecule|polar character in addition to being largely nonpolar. Generally, the bulk of their structure is nonpolar or hydrophobic ("water-fearing"), meaning that it does not interact well with polar solvents like water. Another part of their structure is polar or hydrophilic ("water-loving") and will tend to associate with polar solvents like water. This makes them amphiphilic molecules (having both hydrophobic and hydrophilic portions). In the case of cholesterol, the polar group is a mere -OH (hydroxyl or alcohol). In the case of phospholipids, the polar groups are considerably larger and more polar, as described below.

Nucleic acids

A nucleic acid is a complex, high-molecular-weight biochemistry|biochemical macromolecule composed of nucleotide chains that convey genetic information. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are found in all living cells and viruses.

Nucleic acid, so called because of its prevalence in cellular cell nuclei, is the generic name of family of biopolymers. The monomers are called nucleotides, and each consists of three components: a nitrogenous heterocyclic base (either a purine or a pyrimidine), a pentose sugar, and a phosphate group. Different nucleic acid types differ in the specific sugar found in their chain (e.g. DNA or deoxyribonucleic acid contains 2-deoxyriboses). Also, the nitrogenous bases possible in the two nucleic acids are different: adenine, cytosine, and guanine are possible in both RNA and DNA, while thymine is possible only in DNA and uracil is possible only in RNA.

Relationship to other "molecular-scale" biological sciences

Researchers in biochemistry use specific techniques native to biochemistry, but increasingly combine these with techniques and ideas from genetics, molecular biology and biophysics. There has never been a hard-line between these disciplines in terms of content and technique, but members of each discipline have in the past been very territorial; today the terms ''molecular biology'' and ''biochemistry'' are nearly interchangeable. The following figure is a schematic that depicts one possible view of the relationship between the fields:

l Biochemistry is the study of the chemical substances and vital processes occurring in living organisms.

l Genetics is the study of the effect of genetic differences on organisms. Often this can be inferred by the absence of a normal component (e.g. one gene). The study of "mutants" – organisms which lack one or more functional components with respect to the so-called "wild type" or normal phenotype. Genetic interactions (epistasis) can often confound simple interpretations of such "knock-out" studies.

l Molecular biology is the study of molecular underpinnings of the process of replication, transcription and translation of the genetic material. The central dogma of molecular biology where genetic material is transcribed into RNA and then translated into protein, despite being an oversimplified picture of molecular biology, still provides a good starting point for understanding the field. This picture, however, is undergoing revision in light of emerging novel roles for RNA.

l Chemical Biology seeks to develop new tools based on small molecules that allow minimal perturbation of biological systems while providing detailed information about their function. Further, chemical biology employs biological systems to create non-natural hybrids between biomolecules and synthetic devices (for example emptied viral capsids that can deliver gene therapy or drug molecules).