Chloroplast membrane

Chloroplasts contain several important membranes, vital for their function. Like mitochondria, chloroplasts have a double-membrane envelope, called the chloroplast envelope. Each membrane is a phospholipid bilayer, between 6 and 8 nm thick, and the two are separated by a gap of 10-20nm, called the intermembrane space. The outer membrane is permeable to most ions and metabolites, but the inner membrane is highly specialised with transport proteins.

The origin of chloroplasts is now largely accepted by the botany community as occurring via endosymbiosis on an ancestral basis with the engulfment of photosynthetic bacterium within the eukaryotic cell. Over millions of years the endosymbiotic cyanobacterium evolved structurally and functionally, retaining its own DNA and cellular mitosis capabilities but losing its ablility to live outside of the host cell.

[edit]Internal parts

Within the inner membrane, in the region called the stroma, there is a system of interconnecting flattened membrane compartments, called thethylakoids. These are the sites of light absorption and ATP synthesis, and contain many proteins, including those involved in the electron transport chain. Photosynthetic pigments such as chlorophyll α and B, and some others e.g. xanthophylls and carotenoids are also located within this space. These are responsible for the conversion of light energy to chemical energy as described below:

[edit]Functions of Thylakoids

The membranes of the chloroplasts contain photosystems I and II which harvest solar energy in order to excite electrons which travel down theelectron transport chain. This exergonic fall in potential energy along the way is used to pump H+ ions from the stroma into the thylakoid space. A concentration gradient is formed, which allows chemiosmosis to occur, where the protein ATP synthase harvests the potential energy of the Hydrogen ions and uses it to combine ADP and a phosphate group to form ATP.

Experiments have shown that the pH within the stroma is about 7.8, while that of the thylakoid space is about 5. This corresponds to a thousandfold difference in concentration of H- ions.

Chloroplast

The inside of a chloroplast

Chloroplasts are organelles found in plant cells and eukaryotic algae that conductphotosynthesis. Chloroplasts absorb light and use it in conjunction with water and carbon dioxide to produce sugars, the raw material for energy and biomass production in all green plants and the animals that depend on them, directly or indirectly, for food. Chloroplasts capture light energy to conserve free energy in the form of ATP and reduce NADP to NADPH through a complex set of processes called photosynthesis. The word chloroplast is derived from the Greek words chloros which means green andplast which means form or entity. Chloroplasts are members of a class of organelles known as plastids.

Evolutionary origin

Plant cells with visible chloroplasts.

Chloroplasts are one of the many different types of organelles in the cell. They are generally considered to have originated as endosymbiotic cyanobacteria (i.e. blue-green algae). This was first suggested by Mereschkowsky in 1905 ^[1] after an observation by Schimper in 1883 that chloroplasts closely resemble cyanobacteria. ^[2] All chloroplasts are thought to derive directly or indirectly from a single endosymbiotic event (in the Archaeplastida), except for Paulinellachromatophora, which has recently acquired a photosynthetic cyanobacterial endosymbiont which is not closely related to chloroplasts of other eukaryotes.^[3] In that they derive from an endosymbiotic event, chloroplasts are similar to mitochondria but chloroplasts are found only inplants and protista. The chloroplast is surrounded by a double-layered composite membrane with an intermembrane space; further, it has reticulations, or many infoldings, filling the inner spaces. The chloroplast has its own DNA which codes for redox proteins involved in electron transport in photosynthesis.

In green plants, chloroplasts are surrounded by two lipid-bilayer membranes. The inner membrane is now believed to correspond to the outer membrane of the ancestral cyanobacterium. Chloroplasts have their own genome, which is considerably reduced compared to that of free-living cyanobacteria, but the parts that are still present show clear similarities with the cyanobacterial genome. Plastids may contain 60-100 genes whereas cyanobacteria often contain more than 1500 genes.^[4] Many of the missing genes are encoded in the nuclear genome of the host. The transfer of nuclear information has been estimated in tobacco plants at one gene for every 16000 pollen grains.^[5]

In some algae (such as the heterokonts and other protists such as Euglenozoa and Cercozoa), chloroplasts seem to have evolved through a secondary event of endosymbiosis, in which a eukaryotic cell engulfed a second eukaryotic cell containing chloroplasts, forming chloroplasts with three or four membrane layers. In some cases, such secondary endosymbionts may have themselves been engulfed by still other eukaryotes, thus forming tertiary endosymbionts. In the alga Chlorella, there is only one chloroplast, which is bell shaped.

In some groups of mixotrophic protists such as the dinoflagellates, chloroplasts are separated from a captured alga or diatom and used temporarily. These klepto chloroplasts may only have a lifetime of a few days and are then replaced.^[6]

Structure

Chloroplasts are observable morphologically as flat discs usually 2 to 10 micrometer in diameter and 1 micrometer thick. In land plants they are generally 5 μm in diameter and 2.3 μm thick. The chloroplast is contained by an envelope that consists of an inner and an outer phospholipid membrane. Between these two layers is the intermembrane space. A typical parenchyma cell contains about 10 to 100 chloroplasts.

The material within the chloroplast is called the stroma, corresponding to the cytosol of the original bacterium, and contains one or more molecules of small circular DNA. It also contains ribosomes, although most of its proteins are encoded by genes contained in the host cell nucleus, with the protein products transported to the chloroplast.

Chloroplast ultrastructure:
1. outer membrane
2. intermembrane space
3. inner membrane (1+2+3: envelope)
4. stroma (aqueous fluid)
5. thylakoid lumen (inside of thylakoid)
6. thylakoid membrane
7. granum (stack of thylakoids)
8. thylakoid (lamella)
9. starch
10. ribosome
11. plastidial DNA
12. plastoglobule (drop of lipids)

Within the stroma are stacks of thylakoids, the sub-organelles which are the site of photosynthesis. The thylakoids are arranged in stacks called grana (singular: granum).^[7] A thylakoid has a flattened disk shape. Inside it is an empty area called the thylakoid space or lumen. Photosynthesis takes place on the thylakoid membrane; as in mitochondrial oxidative phosphorylation, it involves the coupling of cross-membrane fluxes withbiosynthesis via the dissipation of a proton electrochemical gradient.

In the electron microscope, thylakoid membranes appear as alternating light-and-dark bands, each 0.01 μm thick. Embedded in the thylakoid membrane is the antenna complex, which consists of the light-absorbing pigments, including chlorophyll and carotenoids, and proteins (which bind the chlorophyll). This complex both increases the surface area for light capture, and allows capture of photons with a wider range of wavelengths. The energy of the incident photons is absorbed by the pigments and funneled to the reaction centre of this complex through resonance energy transfer. Two chlorophyll molecules are then ionised, producing an excited electron which then passes onto the photochemical reaction centre.

Recent studies have shown that chloroplasts can be interconnected by tubular bridges called stromules, formed as extensions of their outer membranes.^[8][9] Chloroplasts appear to be able to exchange proteins via stromules,^[10] and thus function as a network.

Transplastomic plants

Recently, chloroplasts have caught attention by developers of genetically modified plants. In most flowering plants, chloroplasts are not inherited from the male parent, although in plants such as pines, chloroplasts are inherited from males.^[13] Where chloroplasts are inherited only from the female, transgenes in these plastids cannot be disseminated by pollen. This makes plastid transformation a valuable tool for the creation and cultivation of genetically modified plants that are biologically contained, thus posing significantly lower environmental risks. This biological containment strategy is therefore suitable for establishing the coexistence of conventional and organic agriculture. The reliability of this mechanism has not yet been studied for all relevant crop species. However, the research programme Co-Extra recently published results for tobacco plants, demonstrating that the containment of transplastomic plants is highly reliable with a tiny failure rate of 3 in 1,000,000.

Intermembrane space

Simplified structure of mitochondrion

Chloroplast

The intermembrane space is the region between the inner membrane and theouter membrane of a mitochondrion or a chloroplast. The main function of the intermembrane space is oxidative phosphorylation.

Channel proteins called porins in the outer membrane allow free movement of ionsand small molecules into the intermembrane space. This means that it is essentially continuous with the cytosol in terms of the solutes relevant for the functioning of these organelles. Enzymes destined for the mitochondrial matrix or the stroma can pass through the intermembrane space via transport throughtranslocators. These are known as translocase of the outer mitochondria membrane (TOM) and translocase of the inner mitochondrial membrane (TIM) in mitochondriaand translocase of the outer chloroplast membrane (TOC) and translocase of the inner chloroplast membrane (TIC) in chloroplasts. It tends to have a low pH because of the proton gradient which results when protons are pumped from themitochondrial matrix into the intermembrane space during electron transport. The structures responsible for this are coenzyme Q, NADH coenzyme Q oxidoreductasecomplex (complex I), succinate-coenzyme Q oxidoreductase complex (complex II), and coenzyme Q-cytochrome c oxidoreductase complex (complex III).

[edit]Intermembrane space of mitochondria

Main article: Intermembrane space of mitochondria

Because of channels in the outer membrane of the mitochondria, the content of the intermembrane space is similar to that of the content of the cytoplasm.

[edit]Intermembrane space of chloroplast

The intermembrane space of the chloroplast is extremely small, somewhere from 10-20 nm thick.

Mitochondrion

Electron micrograph of a mitochondrion from mammalian lung tissue showing its matrix and membranes.

In cell biology, a mitochondrion (plural mitochondria) is a membrane-enclosed organelle found in most eukaryotic cells.^[1] These organelles range from 1–10 micrometers (μm) in size. Mitochondria are sometimes described as "cellular power plants" because they generate most of the cell's supply ofadenosine triphosphate (ATP), used as a source of chemical energy. ^[2] In addition to supplying cellular energy, mitochondria are involved in a range of other processes, such as signaling, cellular differentiation, cell death, as well as the control of the cell cycle and cell growth.^[3] Mitochondria have been implicated in several human diseases, including mitochondrial disorders^[4] and cardiac dysfunction,^[5] and may play a role in the aging process. The word mitochondrion comes from the Greek μίτος or mitos, thread + χονδρίον orkhondrion, granule. Several characteristics make mitochondria unique. The number of mitochondria in a cell varies widely by organism and tissue type. Many cells have only a single mitochondrion, whereas others can contain several thousand mitochondria.^[6][7] The organelle is composed of compartments that carry out specialized functions. These compartments or regions include the outer membrane, the intermembrane space, the inner membrane, and the cristae and matrix. Mitochondrial proteins vary depending on the tissues and species. In human, 615 distinct types of proteins were identified from cardiac mitochondria;^[8] whereas in murinae (rats), 940 proteins encoded by distinct genes were reported.^[9] The mitochondrial proteome is thought to be dynamically regulated.^[10] Although most of a cell's DNA is contained in the cell nucleus, the mitochondrion has its own independent genome. Further, its DNA shows substantial similarity to bacterial genomes.

Chromosome

Diagram of a duplicated and condensed (metaphase) eukaryotic chromosome. (1)Chromatid - one of the two identical parts of the chromosome after S phase. (2) Centromere - the point where the two chromatids touch, and where the microtubules attach. (3) Short arm. (4) Long arm.

A chromosome is an organized structure of DNA and protein that is found in cells. A chromosome is a single piece of DNA that contains many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions. The word chromosome comes from the Greekχρῶμα (chroma, color) and σῶμα (soma, body) due to their property of being stained very strongly by some dyes. Chromosomes vary extensively between different organisms. The DNA molecule may be circular or linear, and can contain anything from 10,000 to 1,000,000,000^[1]nucleotides in length. Typically eukaryotic cells (cells with nuclei) have large linear chromosomes and prokaryotic cells (cells without defined nuclei) have smaller circular chromosomes, although there are many exceptions to this rule. Furthermore, cells may contain more than one type of chromosome; for example, mitochondria in most eukaryotes andchloroplasts in plants have their own small chromosomes. In eukaryotes, nuclear chromosomes are packaged by proteins into a condensed structure called chromatin. This allows the very long DNA molecules to fit into the cell nucleus. The structure of chromosomes and chromatin varies through the cell cycle. Chromosomes may exist as either duplicated or unduplicated—unduplicated chromosomes are single linear strands, whereas duplicated chromosomes (copied during synthesis phase) contain two copies joined by a centromere. Compaction of the duplicated chromosomes during mitosis and meiosis results in the classic four-arm structure (pictured to the right).

"Chromosome" is a rather loosely defined term. In prokaryotes, a small circular DNA molecule may be called either a plasmid or a small chromosome. These small circular genomes are also found in mitochondria and chloroplasts, reflecting their bacterial origins. The simplest chromosomes are found in viruses: these DNA or RNA molecules are short linear or circular chromosomes that often lack any structural proteins.

Techniques of molecular biology

Since the late 1950s and early 1960s, molecular biologists have learned to characterize, isolate, and manipulate the molecular components of cells and organisms. These components include DNA, the repository of genetic information; RNA, a close relative of DNA whose functions range from serving as a temporary working copy of DNA to actual structural and enzymatic functions as well as a functional and structural part of the translational apparatus; and proteins, the major structural and enzymatic type of molecule in cells.

For more extensive list on protein methods, see protein methods.

For more extensive list on nucleic acid methods, see nucleic acid methods.

[edit]Expression cloning

Main article: Expression cloning

One of the most basic techniques of molecular biology to study protein function is expression cloning. In this technique, DNA coding for a protein of interest is cloned (using PCR and/or restriction enzymes) into a plasmid (known as an expression vector). This plasmid may have special promoter elements to drive production of the protein of interest, and may also have antibiotic resistance markers to help follow the plasmid.

This plasmid can be inserted into either bacterial or animal cells. Introducing DNA into bacterial cells can be done by transformation (via uptake of naked DNA), conjugation (via cell-cell contact) or by transduction (via viral vector). Introducing DNA into eukaryotic cells, such as animal cells, by physical or chemical means is called transfection. Several different transfection techniques are available, such as calcium phosphate transfection,electroporation, microinjection and liposome transfection. DNA can also be introduced into eukaryotic cells using viruses or bacteria as carriers, the latter is sometimes called bactofection and in particular uses Agrobacterium tumefaciens. The plasmid may be integrated into the genome, resulting in a stable transfection, or may remain independent of the genome, called transient transfection.

In either case, DNA coding for a protein of interest is now inside a cell, and the protein can now be expressed. A variety of systems, such as inducible promoters and specific cell-signaling factors, are available to help express the protein of interest at high levels. Large quantities of a protein can then be extracted from the bacterial or eukaryotic cell. The protein can be tested for enzymatic activity under a variety of situations, the protein may be crystallized so its tertiary structure can be studied, or, in the pharmaceutical industry, the activity of new drugs against the protein can be studied.

[edit]Polymerase chain reaction (PCR)

Main article: Polymerase chain reaction

The polymerase chain reaction is an extremely versatile technique for copying DNA. In brief, PCR allows a single DNA sequence to be copied (millions of times), or altered in predetermined ways. For example, PCR can be used to introduce restriction enzyme sites, or to mutate (change) particular bases of DNA, the latter is a method referred to as "Quick change". PCR can also be used to determine whether a particular DNA fragment is found in a cDNA library. PCR has many variations, like reverse transcription PCR (RT-PCR) for amplification of RNA, and, more recently, real-time PCR (QPCR) which allow for quantitative measurement of DNA or RNA molecules.

[edit]Gel electrophoresis

Main article: Gel electrophoresis

Gel electrophoresis is one of the principal tools of molecular biology. The basic principle is that DNA, RNA, and proteins can all be separated by means of an electric field. In agarose gel electrophoresis, DNA and RNA can be separated on the basis of size by running the DNA through an agarose gel. Proteins can be separated on the basis of size by using an SDS-PAGE gel, or on the basis of size and their electric charge by using what is known as a 2D gel electrophoresis.

[edit]Southern blotting

Main article: Southern blot

Named after its inventor, biologist Edwin Southern, the Southern blot is a method for probing for the presence of a specific DNA sequence within a DNA sample. DNA samples before or after restriction enzyme digestion are separated by gel electrophoresis and then transferred to a membrane by blotting via capillary action. The membrane is then exposed to a labeled DNA probe that has a complement base sequence to the sequence on the DNA of interest. Most original protocols used radioactive labels, however non-radioactive alternatives are now available. Southern blotting is less commonly used in laboratory science due to the capacity of other techniques, such as PCR, to detect specific DNA sequences from DNA samples. These blots are still used for some applications, however, such as measuring transgene copy number intransgenic mice, or in the engineering of gene knockout embryonic stem cell lines.

[edit]Northern blotting

Main article: northern blot

The northern blot is used to study the expression patterns a specific type of RNA molecule as relative comparison among of a set of different samples of RNA. It is essentially a combination of denaturing RNA gel electrophoresis, and a blot. In this process RNA is separated based on size and is then transferred to a membrane that is then probed with a labeled complement of a sequence of interest. The results may be visualized through a variety of ways depending on the label used; however, most result in the revelation of bands representing the sizes of the RNA detected in sample. The intensity of these bands is related to the amount of the target RNA in the samples analyzed. The procedure is commonly used to study when and how much gene expression is occurring by measuring how much of that RNA is present in different samples. It is one of the most basic tools for determining at what time, and under what conditions, certain genes are expressed in living tissues.

[edit]Western blotting

Main article: western blot

Antibodies to most proteins can be created by injecting small amounts of the protein into an animal such as a mouse, rabbit, sheep, or donkey (polyclonal antibodies)or produced in cell culture (monoclonal antibodies). These antibodies can be used for a variety of analytical and preparative techniques.

In western blotting, proteins are first separated by size, in a thin gel sandwiched between two glass plates in a technique known as SDS-PAGE(sodium dodecyl sulfate polyacrylamide gel electrophoresis). The proteins in the gel are then transferred to a PVDF, nitrocellulose, nylon or other support membrane. This membrane can then be probed with solutions of antibodies. Antibodies that specifically bind to the protein of interest can then be visualized by a variety of techniques, including colored products, chemiluminescence, or autoradiography. Often, the antibodies are labeled with an enzymes. When a chemiluminescent substrate is exposed to the enzyme it allows detection. Using western blotting techniques allows not only detection but also quantitative analysis.

Analogous methods to western blotting can be used to directly stain specific proteins in live cells or tissue sections. However, theseimmunostaining methods, such as FISH, are used more often in cell biology research.

[edit]Blotting jokes

The terms "western" and "northern" are molecular biology jokes that play on the term southern blot. The first blots were with DNA, and since they were done by Ed Southern, they came to be known as Southerns. Patricia Thomas, inventor of the RNA blot, which became known as a "northern", actually didn't use the term. ^[2]. To carry the joke further, one can find references in the literature to "southwesterns" (protein-DNA interactions), "northwesterns" (protein-RNA interactions) and "farwesterns" (protein-protein interactions).

[edit]Arrays

Main article: DNA microarray

A DNA array is a collection of spots attached to a solid support such as a microscope slide where each spot contains one or more single-stranded DNA oligonucleotide fragment. Arrays make it possible to put down a large quantity of very small (100 micrometre diameter) spots on a single slide. Each spot has a DNA fragment molecule that is complementary to a single DNA sequence (similar to Southern blotting). A variation of this technique allows the gene expression of an organism at a particular stage in development to be qualified (expression profiling). In this technique the RNA in a tissue is isolated and converted to labeled cDNA. This cDNA is then hybridized to the fragments on the array and visualization of the hybridization can be done. Since multiple arrays can be made with the exact same position of fragments they are particularly useful for comparing the gene expression of two different tissues, such as a healthy and cancerous tissue. Also, one can measure what genes are expressed and how that expression changes with time or with other factors. For instance, the common baker's yeast,Saccharomyces cerevisiae, contains about 7000 genes; with a microarray, one can measure qualitatively how each gene is expressed, and how that expression changes, for example, with a change in temperature. There are many different ways to fabricate microarrays; the most common are silicon chips, microscope slides with spots of ~ 100 micrometre diameter, custom arrays, and arrays with larger spots on porous membranes (macroarrays). There can be anywhere from 100 spots to more than 10,000 on a given array.

Arrays can also be made with molecules other than DNA. For example, an antibody array can be used to determine what proteins or bacteriaare present in a blood sample.

[edit]Allele Specific Oligonucleotide

Allele specific oligonucleotide (ASO) is a technique that allows detection of single base mutations without the need for PCR or gel electrophoresis. Short (20-25 nucleotides in length), labeled probes are exposed to the non-fragmented target DNA. Hybridization occurs with high specificity due to the short length of the probes and even a single base change will hinder hybridization. The target DNA is then washed and the labeled probes that didn't hybridize are removed. The target DNA is then analyzed for the presence of the probe via radioactivity or fluorescence. In this experiment, as in most molecular biology techniques, a control must be used to ensure successful experimentation.

[edit]Abandoned technology

As new procedures and technology become available, the older technology is rapidly abandoned. A good example is methods for determining the size of DNA molecules. Prior to gel electrophoresis (agarose or polyacrylamide) DNA was sized with rate sedimentation in sucrose gradients, a slow and labor intensive technology requiring expensive instrumentation; prior to sucrose gradients, viscometry was used.

Aside from their historical interest, it is worth knowing about older technology as it may be useful to solve a particular problem.

Molecular biology

Molecular biology is the study of biology at a molecular level. The field overlaps with other areas of biology and chemistry, particularlygenetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis and learning how these interactions are regulated.

Writing in Nature, William Astbury described molecular biology as:

"[...]not so much a technique as an approach, an approach from the viewpoint of the so-called basic sciences with the leading idea of searching below the large-scale manifestations of classical biology for the corresponding molecular plan. It is concerned particularly with the forms of biological molecules and[...]is predominantly three-dimensional and structural—which does not mean, however, that it is merely a refinement of morphology. It must at the same time inquire into genesis and function." ^[1]

Central dogma of molecular biology

The central dogma of molecular biology was first enunciated by Francis Crick in 1958^[1]and re-stated in a Nature paper published in 1970:^[2]

The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that information cannot be transferred back from protein to either protein or nucleic acid.

In other words, 'once information gets into protein, it can't flow back to nucleic acid.'

The dogma is a framework for understanding the transfer of sequence information between sequential information-carrying biopolymers, in the most common or general case, in livingorganisms. There are 3 major classes of such biopolymers: DNA and RNA (both nucleic acids), and protein. There are 3×3 = 9 conceivable direct transfers of information that can occur between these. The dogma classes these into 3 groups of 3: 3 general transfers (believed to occur normally in most cells), 3 special transfers (known to occur, but only under specific conditions in case of some viruses or in a laboratory), and 3 unknown transfers (believed to never occur). The general transfers describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA information can be copied into mRNA, (transcription), and proteins can be synthesized using the information in mRNA as a template (translation).^[2]

DNA sequence

A DNA sequence or genetic sequence is a succession of letters representing the primary structure of a real or hypothetical DNA molecule or strand, with the capacity to carryinformation as described by the central dogma of molecular biology.

The possible letters are A, C, G, and T, representing the four nucleotide bases of a DNA strand — adenine, cytosine, guanine, thymine — covalently linked to a phosphodiesterbackbone. In the typical case, the sequences are printed abutting one another without gaps, as in the sequence AAAGTCTGAC, read left to right in the 5' to 3' direction. Short sequences of nucleotides are referred to as oligonucleotides and are used in a range of laboratory applications in molecular biology. With regard to biological function, a DNA sequence may be considered sense or antisense, and either coding or noncoding. DNA sequences can also contain "junk DNA."

Sequences can be derived from the biological raw material through a process called DNA sequencing.

In some special cases, letters besides A, T, C, and G are present in a sequence. These letters represent ambiguity. Of all the molecules sampled, there is more than one kind of nucleotide at that position. The rules of the International Union of Pure and Applied Chemistry (IUPAC) are as follows:

       A = adenine                   C = cytosine                    G = guanine                     T = thymine                   R = G A (purine)                Y = T C (pyrimidine)            K = G T (keto)            M = A C (amino)        S = G C (strong bonds)        W = A T (weak bonds)        B = G T C (all but A)        D = G A T (all but C)        H = A C T (all but G)        V = G C A (all but T)        N = A G C T (any)     

Phosphoryl Transfer

This reaction is characterized by the transfer of a phosphoryl group from ATP to an alcohol. The alcohol gives up the hydrogen while ADP and an organic phosphate are yielded.

Glycolysis

Glycolysis is the sequence of reactions that converts glucose into pyruvate with the concomitant production of a relatively small amount of ATP. Glycolysis can be carried out anerobically (in the absence of oxygen) and is thus an especially important pathway for organisms that can ferment sugars. For example, glycolysis is the pathway utilized by yeast to produce the alcohol found in beer. Glycolysis also serves as a source of raw materials for the synthesis of other compounds. For example, 3 phosphoglycerate can be converted into serine, while pyruvate can be aerobically degraded by the Krebs or TCA cycle to produce much larger amounts of ATP.