Cell Processes.pdf

Cell Processes

STAYING ALIVE IS NO EASY BUSINESS. To keep from dying, cells must constantly juggle a wide range of

tasks. They need to turn food into energy and produce the proteins and enzymes that choreograph crucial

life processes. But no matter how efficient a cell is, in the end, it will die. To make sure its work does not die

with it, every cell must be able to reproduce. This chapter reviews cellular respiration, protein synthesis, and

cellular reproduction, the three crucial cellular life processes.

Cell Respiration

Respiration is the process by which organisms burn food to produce energy. The starting material of cellular

respiration is the sugar glucose , which has energy stored in its chemical bonds. You can think of glucose as

a kind of cellular piece of coal: chock-full of energy, but useless when you want to power a stereo. Just as

burning coal produces heat and energy in the form of electricity, the chemical processes of respiration

convert the energy in glucose into usable form.

Adenosine triphosphate (ATP) is the usable form of energy produced by respiration. ATP is like

electricity: it contains the same energy as coal, but it’s easier to transport and is just what’s needed when the

cell needs some power to carry out a task.

ATP

ATP is a nucleic acid similar to RNA. It has a ribose sugar attached to the nitrogenous base adenine.

However, instead of the single phosphate group typical of RNA nucleotides, ATP has three phosphate

groups. Each of the ATP phosphate groups carries a negative charge. In order to hold the three negative

charges in such proximity, the bonds holding the phosphate groups have to be quite powerful. If one or two

of the bonds are broken and the additional phosphates are freed, the energy stored in the bonds is released

and can be used to fuel other chemical reactions. When the cell needs energy, it removes phosphates from

ATP by hydrolysis, creating energy and either adenosine diphosphate (ADP), which has two phosphates, or

adenosine monophosphate (AMP), which has one phosphate.

Respiration is the process of making ATP rather than breaking it down. To make ATP, the cell burns glucose

and adds new phosphate groups to AMP or ADP, creating new power molecules.

There are actually two general types of respiration, aerobic and anaerobic. Aerobic respiration occurs in the

presence of oxygen, while anaerobic respiration does not use oxygen. Both types of cell respiration begin

with the process of glycolysis, after which the two diverge. We’ll first discuss aerobic respiration and then

move to anaerobic.

Aerobic Cell Respiration

Aerobic respiration is more efficient and more complicated than anaerobic respiration. Aerobic respiration

uses oxygen and glucose to produce carbon dioxide, water, and ATP. More precisely, this process involves

six oxygen molecules for every sugar molecule:

6O 2 + C 6 H 12 O 6 6CO 2 + 6H 2 O + ATP energy

This general equation for aerobic respiration (which you should know for the test) is actually the product of

three separate stages: glycolysis, the Krebs cycle, and the electron transport chain. Typically, the SAT II

Biology only asks questions about the starting and ending products of each stage and the location where

each takes place. Understanding the internal details of stages will help you remember these key facts and

prepare you in case the testers throw in a more difficult question, but the details of all the complex reactions

will probably not be tested by the SAT II.

Glycolysis

Glycolysis is the first stage of aerobic (and anaerobic) respiration. It takes place in the cytoplasm of the cell.

In glycolysis (“glucose breaking”), ATP is used to split glucose molecules into a three-carbon compound

called pyruvate . This splitting produces energy that is stored in ATP and a molecule called NADH . The

chemical formula for glycolysis is:

C 6 H 12 O 6 + 2ATP + 2NAD +

2pyruvate + 4ATP + 2NADH

As the formula indicates, the cell must invest 2 ATP molecules in order to get glycolysis going. But by the

time glycolysis is complete, the cell has produced 4 new ATP, creating a net gain of 2 ATP. The 2 NADH

molecules travel to the mitochondria, where, in the next two stages of aerobic respiration, the energy stored

in them is converted to ATP.

The most important things to remember about glycolysis are:

 Glycolysis is part of both aerobic and anaerobic respiration.

 Glycolysis splits glucose, a six-carbon compound, into two pyruvate molecules, each of which has

three carbons.

 In glycolysis, a 2 ATP investment results in a 4 ATP payoff.

 Unlike the rest of aerobic respiration, which takes place in the mitochondria, glycolysis takes place

in the cytoplasm of the cell.

 Unlike the rest of aerobic respiration, glycolysis does not require oxygen.

The Krebs Cycle

After glycolysis, the pyruvate sugars are transported to the mitochondria. During this transport, the three-

carbon pyruvate is converted into the two-carbon molecule called acetate. The extra carbon from the

pyruvate is released as carbon dioxide, producing another NADH molecule that heads off to the electron

transport chain to help create more ATP. The acetate attaches to a coenzyme called coenzyme A to form the

compound acetyl-CoA . The acetyl-CoA then enters the Krebs cycle. The Krebs cycle is called a cycle

because one of the molecules it starts with, the four-carbon oxaloacetate, is regenerated by the end of the

cycle to start the cycle over again.

The Krebs cycle begins when acetyl-CoA and oxaloacetate interact to form the six-carbon compound citric

acid. (The Krebs cycle is also sometimes called the citric acid cycle .) This citric acid molecule then

undergoes a series of eight chemical reactions that strip carbons to produce a new oxaloacetate molecule.

The extra carbon atoms are expelled as CO 2 (the Krebs cycle is the source of the carbon dioxide you exhale).

In the process of breaking up citric acid, energy is produced. It is stored in ATP, NADH, and FADH 2 . The

NADH and FADH 2 proceed on to the electron transport chain.

The entire Krebs cycle is shown in the figure below. For the SAT II Biology, you don’t have to know the

intricacies of this figure, but you should be able to recognize that it shows the Krebs cycle.

It is also important to remember that each glucose molecule that enters glycolysis is split into two pyruvate

molecules, which are then converted into the acetyl-CoA that moves through the Krebs cycle. This means

that for every glucose molecule that enters glycolysis, the Krebs cycle runs twice. Therefore, for one glucose

molecule running through aerobic cell respiration, the equation for the Krebs cycle is:

2acetyl-CoA + 2oxaloacetate 4CO 2 + 6NADH + 2FADH 2 + 2ATP + 2oxaloacetate

For the SAT II Biology, the most important things to remember about the Krebs cycle are:

 The Krebs cycle results in 2 ATP molecules for each glucose molecule run through glycolysis.

 The Krebs cycle sends energy-laden NADH and FADH 2 molecules on to the next step in respiration,

the electron transport chain. It does not export carbon molecules for further processing.

 The Krebs cycle takes place in the mitochondrial matrix, the innermost compartment of the

mitochondria.

 Though the Krebs cycle does not directly require oxygen, it can only take place when oxygen is

present because it relies on by-products from the electron transport chain, which requires oxygen.

The Krebs cycle is therefore an aerobic process.

The Electron Transport Chain

A great deal of energy is stored in the NADH and FADH 2 molecules formed in glycolysis and the Krebs cycle.

This energy is converted to ATP in the final phase of respiration, the electron transport chain:

10NADH + 2FADH 2 34ATP

The electron transport chain consists of a set of three protein pumps embedded in the inner membrane of

the mitochondria. FADH 2 and NADH are used to power these pumps. Using the energy in NADH and

FADH 2 , these pumps move positive hydrogen ions (H + ) from the mitochondrial matrix to the

intermembrane space. This creates a concentration gradient over the membrane.

In a process called oxidative phosphorylation , H + ions flow back into the matrix through a membrane

protein called an ATP synthase. This channel is the opposite of the standard membrane pumps that burns

ATP to transport molecules against their concentration gradient: ATP synthase uses the natural movement

of ions along their concentration gradient to make ATP. All told, the flow of ions through this channel

produces 34 ATP molecules. The waste products from the powering of the electron transport chain protein

pumps combine with oxygen to produce water molecules. By accepting these waste products, oxygen frees

NAD + and FAD to play their roles in the Krebs cycle and the electron transport chain. Without oxygen, these

vital energy carrier molecules would not perform their roles and the processes of aerobic respiration could

not occur.

For the SAT II Biology, the most important things to remember about the electron transport chain and

oxidative phosphorylation are:

 Four ATP molecules are produced by glycolysis and the Krebs cycle combined. The electron

transport chain produces 34 ATP.

 The electron transport chain occurs across the inner membrane of the mitochondria.

 The electron transport chain requires oxygen.

Anaerobic Respiration

Aerobic respiration requires oxygen. However, some organisms live in places where oxygen is not always

present. Similarly, under extreme exertion, muscle cells may run out of oxygen. Anaerobic respiration is a

form of respiration that can function without oxygen.

In the absence of oxygen, organisms continue to carry out glycolysis, since glycolysis does not use oxygen in

its chemical process. But glycolysis does require NAD + . In aerobic respiration, the electron transport chain

turns NADH back to NAD + with the aid of oxygen, thereby averting any NAD + shortage and allowing

glycolysis to take place. In anaerobic respiration, cells must find another way to turn NADH back to NAD + .

This “other way” is called fermentation . Fermentation’s goal is not to produce additional energy, but

merely to replenish NAD + supplies so that glycolysis can continue churning out its slow but steady stream of

ATP. Because pyruvates are not needed in anaerobic respiration, fermentation uses them to help regenerate

NAD + . While employing the pyruvates in this way does allow glycolysis to continue, it also results in the loss

of the considerable energy contained in the pyruvate sugars.

There are two principle forms of fermentation, lactic acid fermentation and alcoholic fermentation .

For the SAT II Biology, remember that no matter what kind of fermentation occurs, anaerobic respiration

only produces 2 net ATP in glycolysis.

Lactic Acid Fermentation

In lactic acid fermentation, pyruvate is converted to a three-carbon compound called lactic acid:

pyruvate + NADH lactic acid + NAD +

In this reaction, the hydrogen from the NADH molecule is transferred to the pyruvate molecule.

Lactic acid fermentation is common in fungi and bacteria. Lactic acid fermentation also takes place in

human muscle cells when strenuous exercise causes temporary oxygen shortages. Since lactic acid is a toxic

substance, its buildup in the muscles produces fatigue and soreness.

Alcoholic Fermentation

Another route to NAD + produces alcohol (ethanol) as a by-product:

pyruvate + NADH ethyl alcohol + NAD + + CO 2

Alcoholic fermentation is the source of ethyl alcohol present in wines and liquors. It also accounts for the

bubbles in bread. When yeast in bread dough runs out of oxygen, it goes through alcoholic fermentation,

producing carbon dioxide. These carbon dioxide bubbles create spaces in the dough and cause it to rise.

Like lactic acid, the ethanol produced by alcoholic fermentation is toxic. When ethanol levels rise to about 12

percent, the yeast dies.

From DNA to Protein

DNA directs the cell’s activities by telling it what proteins to make and when. These proteins form structural

elements in the cell and regulate the production of other cell products. By controlling protein synthesis,

DNA is hugely important in directing life.

Protein synthesis is a two-step process. DNA resides in the nucleus, but proteins are made in the cytoplasm.

The cell copies the information held in DNA onto RNA molecules in a process called transcription. Proteins

are synthesized at the ribosomes from the codes in RNA in a process called translation.

Before getting into the way that the information on DNA can be transcribed and then translated into

protein, we have to spend some time studying the major players in the process: DNA and RNA.

DNA and the Genetic Code

The sequence of nucleotides in DNA makes up a code that controls the functions of the cell by telling it what

proteins to produce. Cells need to be able to produce 20 different amino acids in order to produce all the

proteins necessary to function. DNA, however, has only four nitrogen bases. How can these four bases code

for the 20 amino acids? If adenine, thymine, guanine, and cytosine each coded for one particular amino

acid, DNA would only be able to code for four amino acids. If two bases were used to specify an amino acid,

there would only be room to code for 16 ( ) different amino acids.

In order to be able to code for 20 amino acids, it is necessary to use three bases (which offer a total of 64

coding combinations) to code for each amino acid. These triplets of nucleotides that make up a single coding

group are called codons or genes . Two examples of codons are CAG, which codes for the amino acid

glutamine, and CGA, which codes for arginine.

Codons are always read in a non-overlapping sequence. This means that any one nucleotide can only be a

part of one codon. Given the code AUGCA, AUG could be a codon for the amino acid methionine, with CA

starting a new codon. Alternatively, GCA could be a codon specifying alanine, while the initial AU was the

last two letters of a previous codon. But AUG and GCA cannot both be codons at the same time.

Degeneracy of the Genetic Code

There are 64 codons but only 20 amino acids. What happens to the other 44 coding possibilities? It happens

that some of the different codons call for the same amino acid. The genetic code is said to be degenerate

because of its redundancy.

Experiments have shown that there are also three stop codons, which signal when a protein is fully

formed, and one start codon, which signals the beginning of an amino acid sequence.

Mutations of the Genetic Code

Since the sequence of nucleotides in DNA determines the order of amino acids in proteins, a change or error

in the DNA sequence can affect a protein’s function. These errors or changes in the DNA sequence are called

mutations.

There are two basic types of mutations: substitution mutations and frameshift mutations.

Substitution Mutation

A substitution mutation occurs when a single nucleotide is replaced by a different nucleotide. The effects of

substitution mutations can vary. Certain mutations might have no effect at all: these are called silent

mutations. For instance, because the genetic code is degenerate, if the particular codon GAA becomes GAG,

it will still code for the amino acid glutamate and the function of the cell will not change. Other substitution

mutations can drastically affect cellular and organismal function. Sickle-cell anemia, which cripples human

red blood cells, is caused by a substitution mutation. A person will suffer from sickle-cell anemia if he has

the amino acid valine in his hemoglobin rather than glutamic acid. The codon for valine is GUA or GUG,

while the codon for glutamic acid is GAA or GAG. A simple substitution of A for U results in the disease.

Frameshift Mutation

A frameshift mutation occurs when a nucleotide is wrongly inserted or deleted from a codon. Both types of

frameshifts usually have debilitating or lethal effects. An insertion or deletion will affect every codon in a

particular genetic sequence by throwing the entire three-by-three codon structure out of whack. For

example, if the A in the GAU were to be deleted, the code:

GAU GAC UCC GCU AGG

GUG ACU CCG CUA GG

and code for an entirely different set of amino acids in translation. The results of such mutations on an

organism are usually catastrophic.

The only sort of frameshift mutation that might not have dire effects is one in which an entire codon is

inserted or deleted. This will result in the gain or loss of one amino acid but will not affect surrounding

codons.

Chromosomes

Even the tiniest cells contain meters upon meters of DNA. With the aid of special proteins called histones,

this DNA is coiled into an entangled fibrous mass called chromatin. When it comes time for the cell to

replicate (a process covered later in this chapter), these masses gather into a number of discrete compact

structures called chromosomes.

In eukaryotes, the chromosomes are located in the nucleus of the cell. Prokaryotes don’t have a nucleus:

their DNA is located in a single chromosome that is joined together in a ring. This ring chromosome is found

in the cytoplasm. In this chapter, when we talk about chromosomes, we will be referring to eukaryotic

chromosomes.

Different eukaryotes have varying numbers of chromosomes. Humans, for example, have 46 chromosomes

arranged in 23 pairs. (Dogs have 78 chromosomes in 39 pairs. A larger number of chromosomes is not a

sign of greater biological sophistication.) The total number of distinct chromosomes in a cell is the cell’s

diploid number .

The cells in a human body that are not passed down to offspring, called somatic cells, contain

chromosomes in two closely related setsone set of 23 each from a person’s mother and fathermaking up

a total of 46 chromosomes. These sets pair up, and the pairs are known as homologous chromosomes .

Each homologous pair consists of one maternal and one paternal chromosome. The haploid number of a

cell refers to half of the total number of chromosomes in a cell (half the diploid number), or the number of

homologous pairs in somatic cells.

In humans and other higher animals, only the sex cells that are passed on to offspring have the haploid

number of chromosomes. These sex cells are also called gametes .

RNA

Ribonucleic acid (RNA) helps DNA turn stored genetic messages into proteins. As discussed in the

Biochemistry chapter, RNA monomers (nucleotides) are similar to those of DNA, but with three crucial

differences:

 DNA’s five-carbon sugar is deoxyribose. RNA nucleotides contain a slightly different sugar, called

ribose.

 RNA uses the nitrogenous base uracil in place of DNA’s thymine.

 The RNA molecule takes the form of a single helixhalf a spiral ladderas compared with the

double helix structure of DNA.

Two different types of RNA play important roles in protein synthesis. During transcription, DNA is copied

to make messenger RNA (mRNA) , which then leaves the nucleus to bring its still encoded information to

the ribosomes in the cytoplasm. In order to use the information contained in the transcribed mRNA to make

a protein, a second type of RNA is used. Transfer RNA (tRNA) moves amino acids to the site of protein

synthesis at the ribosome according to the code specified by the mRNA strand. There are many different

would become:

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