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5.6: Chapter Resources - Biology

5.6: Chapter Resources - Biology


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Summary

Biodiversity exists at multiple levels of organization, and is measured in different ways depending on the goals of those taking the measurements. Examples of restoration include reintroduction of keystone species and removal of dams on rivers.

Review Questions

  1. Bacteria that feed upon decaying organic matter in the soil would best be described as which one of the following?
    1. Eukaryotic
    2. Autotrophic
    3. Fungi
    4. Cyanobacteria
    5. Heterotrophic
  2. As Darwin recognized, populations evolve through natural selection when which of the following condition(s) are met?
    1. Variation of traits among individuals
    2. Competition for limited resources
    3. More offspring are produced than can survive
    4. All of the above
  3. You are the world’s foremost expert on lizards. You have traveled the world extensively and have found that a particular species of lizard is found only in one desert near of the Chilean Andes. Which of following terms, with regard to its distribution, can be definitively applied to this species?
    1. Endangered
    2. Prokaryotic
    3. Endemic
    4. Disbursed
    5. Clustered
  4. Which one of the following is not a major cause of biodiversity loss?
    1. Habitat loss
    2. Climate change
    3. Invasive Species
    4. Zoonotic diseases
    5. Overharvesting
  5. Which one of the following statements is false?
    1. There have been five mass extinctions preserved in the fossil record
    2. Some bacteria are autotrophs
    3. Current rates of extinction are higher than background extinction rates
    4. Speciation is the process of creating new species
    5. All living things can be classified into one of four taxonomic domains
  6. During the middle of the 19th century, which scientist independently derived and proposed a theory of evolution that was similar to Darwin’s?
    1. Gregor Mendel
    2. Alfred Wallace
    3. Isaac Newton
    4. Rachel Carson
    5. Niels Bohr
  7. The study of the distribution of the world’s species both in the past and in the present is known by what term?
    1. Geology
    2. Biogeography
    3. Biodiversity
    4. Biogeomorphology
    5. Ecological Succession
  8. Which one of the following would be described as anthropogenic?
    1. Water backing up behind a beaver dam
    2. The dinosaurs going extinct
    3. Logging a forest
    4. A mudslide burying a stream
    5. A volcanic eruption
  9. By definition, what are you most likely to find in a biodiversity hotspot?
    1. A large abundance of endangered species
    2. A large number of endemic species
    3. Mostly eukaryotic species
    4. Extremophiles
    5. Heat-loving microbes
  10. You are working as a biologist for a team surveying biodiversity in the Amazon rainforest. You find a non-motile organism that grows in the soil, has eukaryotic cells, and is heterotrophic. Which one of the following could potentially describe this species?
    1. Fungus
    2. Animal
    3. Bacteria
    4. Plant
    5. Archaea

See Appendix for answers


6.5 Enzymes

By the end of this section, you will be able to do the following:

  • Describe the role of enzymes in metabolic pathways
  • Explain how enzymes function as molecular catalysts
  • Discuss enzyme regulation by various factors

A substance that helps a chemical reaction to occur is a catalyst, and the special molecules that catalyze biochemical reactions are enzymes. Almost all enzymes are proteins, comprised of amino acid chains, and they perform the critical task of lowering the activation energies of chemical reactions inside the cell. Enzymes do this by binding to the reactant molecules, and holding them in such a way as to make the chemical bond-breaking and bond-forming processes take place more readily. It is important to remember that enzymes do not change the reaction's ∆G. In other words, they do not change whether a reaction is exergonic (spontaneous) or endergonic. This is because they do not change the reactants' or products' free energy. They only reduce the activation energy required to reach the transition state (Figure 6.15).

Enzyme Active Site and Substrate Specificity

The chemical reactants to which an enzyme binds are the enzyme’s substrates . There may be one or more substrates, depending on the particular chemical reaction. In some reactions, a single-reactant substrate breaks down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction, both become modified, and leave the reaction as two products. The location within the enzyme where the substrate binds is the enzyme’s active site . This is where the “action” happens. Since enzymes are proteins, there is a unique combination of amino acid residues (also side chains, or R groups) within the active site. Different properties characterize each residue. These can be large or small, weakly acidic or basic, hydrophilic or hydrophobic, positively or negatively charged, or neutral. The unique combination of amino acid residues, their positions, sequences, structures, and properties, creates a very specific chemical environment within the active site. This specific environment is suited to bind, albeit briefly, to a specific chemical substrate (or substrates). Due to this jigsaw puzzle-like match between an enzyme and its substrates (which adapts to find the best fit between the transition state and the active site), enzymes are known for their specificity. The “best fit” results from the shape and the amino acid functional group’s attraction to the substrate. There is a specifically matched enzyme for each substrate and, thus, for each chemical reaction however, there is flexibility as well.

The fact that active sites are so perfectly suited to provide specific environmental conditions also means that they are subject to local enviromental influences. It is true that increasing the environmental temperature generally increases reaction rates, enzyme-catalyzed or otherwise. However, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site in such a way that they are less well suited to bind substrates. High temperatures will eventually cause enzymes, like other biological molecules, to denature , a process that changes the substance's natural properties. Likewise, the local environment's pH can also affect enzyme function. Active site amino acid residues have their own acidic or basic properties that are optimal for catalysis. These residues are sensitive to changes in pH that can impair the way substrate molecules bind. Enzymes are suited to function best within a certain pH range, and, as with temperature, extreme environmental pH values (acidic or basic) can cause enzymes to denature.

Induced Fit and Enzyme Function

For many years, scientists thought that enzyme-substrate binding took place in a simple “lock-and-key” fashion. This model asserted that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit (Figure 6.16). This model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme’s structure that confirms an ideal binding arrangement between the enzyme and the substrate's transition state. This ideal binding maximizes the enzyme’s ability to catalyze its reaction.

Link to Learning

View an induced fit animation at this website.

When an enzyme binds its substrate, it forms an enzyme-substrate complex. This complex lowers the reaction's activation energy and promotes its rapid progression in one of many ways. On a basic level, enzymes promote chemical reactions that involve more than one substrate by bringing the substrates together in an optimal orientation. The appropriate region (atoms and bonds) of one molecule is juxtaposed to the other molecule's appropriate region with which it must react. Another way in which enzymes promote substrate reaction is by creating an optimal environment within the active site for the reaction to occur. Certain chemical reactions might proceed best in a slightly acidic or non-polar environment. The chemical properties that emerge from the particular arrangement of amino acid residues within an active site create the perfect environment for an enzyme’s specific substrates to react.

You have learned that the activation energy required for many reactions includes the energy involved in manipulating or slightly contorting chemical bonds so that they can easily break and allow others to reform. Enzymatic action can aid this process. The enzyme-substrate complex can lower the activation energy by contorting substrate molecules in such a way as to facilitate bond-breaking, helping to reach the transition state. Finally, enzymes can also lower activation energies by taking part in the chemical reaction itself. The amino acid residues can provide certain ions or chemical groups that actually form covalent bonds with substrate molecules as a necessary step of the reaction process. In these cases, it is important to remember that the enzyme will always return to its original state at the reaction's completion. One of enzymes' hallmark properties is that they remain ultimately unchanged by the reactions they catalyze. After an enzyme catalyzes a reaction, it releases its product(s).

Metabolism Control Through Enzyme Regulation

It would seem ideal to have a scenario in which all the encoded enzymes in an organism’s genome existed in abundant supply and functioned optimally under all cellular conditions, in all cells, at all times. In reality, this is far from the case. A variety of mechanisms ensure that this does not happen. Cellular needs and conditions vary from cell to cell, and change within individual cells over time. The required enzymes and energetic demands of stomach cells are different from those of fat storage cells, skin cells, blood cells, and nerve cells. Furthermore, a digestive cell works much harder to process and break down nutrients during the time that closely follows a meal compared with many hours after a meal. As these cellular demands and conditions vary, so do the amounts and functionality of different enzymes.

Since the rates of biochemical reactions are controlled by activation energy, and enzymes lower and determine activation energies for chemical reactions, the relative amounts and functioning of the variety of enzymes within a cell ultimately determine which reactions will proceed and at which rates. This determination is tightly controlled. In certain cellular environments, environmental factors like pH and temperature partly control enzyme activity. There are other mechanisms through which cells control enzyme activity and determine the rates at which various biochemical reactions will occur.

Molecular Regulation of Enzymes

Enzymes can be regulated in ways that either promote or reduce their activity. There are many different kinds of molecules that inhibit or promote enzyme function, and various mechanisms exist for doing so. For example, in some cases of enzyme inhibition, an inhibitor molecule is similar enough to a substrate that it can bind to the active site and simply block the substrate from binding. When this happens, the enzyme is inhibited through competitive inhibition , because an inhibitor molecule competes with the substrate for active site binding (Figure 6.17). On the other hand, in noncompetitive inhibition , an inhibitor molecule binds to the enzyme in a location other than the active site, called an allosteric site, but still manages to prevent substrate binding to the active site. Some inhibitor molecules bind to enzymes in a location where their binding induces a conformational change that reduces the enzyme activity as it no longer effectively catalyzes the conversion of the substrate to product.

Some inhibitor molecules bind to enzymes in a location where their binding induces a conformational change that reduces the enzyme's affinity for its substrate. This type of inhibition is an allosteric inhibition (Figure 6.18). More than one polypeptide comprise most allosterically regulated enzymes, meaning that they have more than one protein subunit. When an allosteric inhibitor binds to an enzyme, all active sites on the protein subunits change slightly such that they bind their substrates with less efficiency. There are allosteric activators as well as inhibitors. Allosteric activators bind to locations on an enzyme away from the active site, inducing a conformational change that increases the affinity of the enzyme’s active site(s) for its substrate(s).

Everyday Connection

Drug Discovery by Looking for Inhibitors of Key Enzymes in Specific Pathways

Enzymes are key components of metabolic pathways. Understanding how enzymes work and how they can be regulated is a key principle behind developing many pharmaceutical drugs (Figure 6.19) on the market today. Biologists working in this field collaborate with other scientists, usually chemists, to design drugs.

Consider statins for example—which is a class of drugs that reduces cholesterol levels. These compounds are essentially inhibitors of the enzyme HMG-CoA reductase. HMG-CoA reductase is the enzyme that synthesizes cholesterol from lipids in the body. By inhibiting this enzyme, the drug reduces cholesterol levels synthesized in the body. Similarly, acetaminophen, popularly marketed under the brand name Tylenol, is an inhibitor of the enzyme cyclooxygenase. While it is effective in providing relief from fever and inflammation (pain), scientists still do not completely understand its mechanism of action.

How are drugs developed? One of the first challenges in drug development is identifying the specific molecule that the drug is intended to target. In the case of statins, HMG-CoA reductase is the drug target. Researchers identify targets through painstaking research in the laboratory. Identifying the target alone is not sufficient. Scientists also need to know how the target acts inside the cell and which reactions go awry in the case of disease. Once researchers identify the target and the pathway, then the actual drug design process begins. During this stage, chemists and biologists work together to design and synthesize molecules that can either block or activate a particular reaction. However, this is only the beginning: both if and when a drug prototype is successful in performing its function, then it must undergo many tests from in vitro experiments to clinical trials before it can obtain FDA approval to be on the market.

Many enzymes don’t work optimally, or even at all, unless bound to other specific non-protein helper molecules, either temporarily through ionic or hydrogen bonds or permanently through stronger covalent bonds. Two types of helper molecules are cofactors and coenzymes . Binding to these molecules promotes optimal conformation and function for their respective enzymes. Cofactors are inorganic ions such as iron (Fe++) and magnesium (Mg++). One example of an enzyme that requires a metal ion as a cofactor is the enzyme that builds DNA molecules, DNA polymerase, which requires a bound zinc ion (Zn++) to function. Coenzymes are organic helper molecules, with a basic atomic structure comprised of carbon and hydrogen, which are required for enzyme action. The most common sources of coenzymes are dietary vitamins (Figure 6.20). Some vitamins are precursors to coenzymes and others act directly as coenzymes. Vitamin C is a coenzyme for multiple enzymes that take part in building the important connective tissue component, collagen. An important step in breaking down glucose to yield energy is catalysis by a multi-enzyme complex scientists call pyruvate dehydrogenase. Pyruvate dehydrogenase is a complex of several enzymes that actually requires one cofactor (a magnesium ion) and five different organic coenzymes to catalyze its specific chemical reaction. Therefore, enzyme function is, in part, regulated by an abundance of various cofactors and coenzymes, which the diets of most organisms supply.

Enzyme Compartmentalization

In eukaryotic cells, molecules such as enzymes are usually compartmentalized into different organelles. This allows for yet another level of regulation of enzyme activity. Enzymes required only for certain cellular processes are sometimes housed separately along with their substrates, allowing for more efficient chemical reactions. Examples of this sort of enzyme regulation based on location and proximity include the enzymes involved in the latter stages of cellular respiration, which take place exclusively in the mitochondria, and the enzymes involved in digesting cellular debris and foreign materials, located within lysosomes.

Feedback Inhibition in Metabolic Pathways

Molecules can regulate enzyme function in many ways. However, a major question remains: What are these molecules and from where do they come? Some are cofactors and coenzymes, ions, and organic molecules, as you have learned. What other molecules in the cell provide enzymatic regulation, such as allosteric modulation, and competitive and noncompetitive inhibition? The answer is that a wide variety of molecules can perform these roles. Some include pharmaceutical and non-pharmaceutical drugs, toxins, and poisons from the environment. Perhaps the most relevant sources of enzyme regulatory molecules, with respect to cellular metabolism, are cellular metabolic reaction products themselves. In a most efficient and elegant way, cells have evolved to use their own reactions' products for feedback inhibition of enzyme activity. Feedback inhibition involves using a reaction product to regulate its own further production (Figure 6.21). The cell responds to the abundance of specific products by slowing down production during anabolic or catabolic reactions. Such reaction products may inhibit the enzymes that catalyzed their production through the mechanisms that we described above.

Producing both amino acids and nucleotides is controlled through feedback inhibition. Additionally, ATP is an allosteric regulator of some of the enzymes involved in sugar's catabolic breakdown, the process that produces ATP. In this way, when ATP is abundant, the cell can prevent its further production. Remember that ATP is an unstable molecule that can spontaneously dissociate into ADP and inorganic phosphate. If too much ATP were present in a cell, much of it would go to waste. Alternatively, ADP serves as a positive allosteric regulator (an allosteric activator) for some of the same enzymes that ATP inhibits. Thus, when relative ADP levels are high compared to ATP, the cell is triggered to produce more ATP through sugar catabolism.


An Interactive Introduction to Organismal and Molecular Biology

Publisher: Michigan State University

This "textbook" is interactive, meaning that although each chapter has text, they also have interactive HTML5 content, such as quizzes, simulations, interactive videos, and images with clickable hotspots. Students receive instant feedback when they complete the interactive content, and therefore, can learn and check their understanding all in one place. The first unit introduces students to the nature of science, including scientific controversies, and information literacy, including how to analyze literature and identify stakeholders. Unit 2 is organismal biology, including carbon cycling and population growth, and unit 3 is molecular biology with a focus on gene expression.


5.6: Chapter Resources - Biology

Purpose: To explore how scientific knowledge changes in the context of abrupt climate change.

To understand that El Nino is caused by changes in the atmospheric and ocean content.

Chapter 6
Humans in the Biosphere

Hot Links Take it to the Net
Chapter Self-Test Teaching Links


What are Web Codes?
Web Codes for Chapter 6:
Science News: Natural Resources and Pollution
SciLinks: Sustainable Agriculture
SciLinks: Biodiversity
SciLinks: Global Warming
Self-Test

Does the fish above look hungry? It's a grass carp, and it may be the solution to the Hydrilla plants that are clogging Lake Austin in Texas. Hydrilla is an invasive foreign species that is growing out of control in many waterways and lakes, and the grass carp is part of a plan to control it.For more information, check out these links:

Renewable Resources
A web site dedicated to renewable resources and their use - from the US Department of Energy


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Solved Questions For You:

Question 1. A baby is not able to tell her/his caretakers that she/he is sick. What would help us to find out?

(a) That the baby is sick?
(b) What is the sickness?

Question 2. Under which of the following conditions is a person most likely to fall sick?

(a) When she is recovering from malaria.
(b) When she has recovered from malaria and is taking care of someone suffering from chicken-pox.
(c) When she is on a four-day fast after recovering from malaria and is taking care of someone suffering from chicken-pox. Why?

Answer: A person is more likely to fall sick when she is on a four-day fast after recovering from malaria and is taking care of someone suffering from chickenpox. This is because since she has suffered from malaria and is in the recovery phase, it means that she is still not completely diseases-free. Fasting affects the immune system as the body is deprived of essential nutrients required to maintain a healthy body. Chickenpox is a contagious disease, this also makes her susceptible to contracting the disease while taking care of a person suffering from chickenpox.

Question 3. A doctor/nurse/health-worker is exposed to more sick people than others in the community. Find out how she/he avoids getting sick herself/himself.

Answer: Medical personnel are constantly in contact with the sick and diseased people coming in the hospitals for the treatment. They follow various measures in order to prevent themselves from getting infected:


2 Biology

First-year biology. Views detailed slides with a microscope and explores types of adipose tissue. It would require some more activities, such as review type questions to make it into a standalone lab. Could use it as a supplement to an introductory lab on tissue types.

Introduction to tissues. See five tissue types under the microscope, such as epithelial, muscle, and nervous tissue. Good resolution for the images, but a not enough for a lab: good supplemental material. Requires a free Open University account.

Introduction to cell biology. Decent introduction to lab equipment for cell and molecular biology, such as micropipettes, cytometers, thermocyclers, incubators, etc. The introduction is a bit silly, but push through: it gets better.

First-year biology. This is a fun little simulation that could help teach some basic genetic concepts (homozygosity, heterozygosity, dominance, etc.) using rabbit coat colour and ear type. Good for an introduction to genetics.

First-year biology. Learn the basics of photons, monochromatic light, and the red, green, and blue light photoreception by cones of the retina of the eye. Could be used as part of a first-year lab on sensory reception.

This involves investigation into the genetic basis for different bacterial strains. Uses several large but detailed files. Requires a free BioQUEST account.

Second-year genetics. Walks students through the steps of comparing the genes being expressed in different cell types. The sounds that accompany the animation are silly, but could be turned off. Can isolate mRNA. This is not an experiment we could do in our labs easily, so it would be a good introduction to a microarray. Requires Flash.

First-year biology or second-year genetics. Good introduction to use of spectrophotometer, used in this case to measure absorbance of DNA at 260 and 280 nm. Requires a free Open University account.

Second-year genetics. Fun little simulation of the lac operon. Good visual aid for explaining the operon.

Great for understanding genetic drift mathematically.

Walk-through of how to extract DNA from any living thing at home.

From the site: “The goal of this simulation is to understand three factors (the initial amount of glucose, pH, and temperature) that affect the rate that the enzyme lactase converts lactose into glucose and galactose.” Requires Flash.

Botany. This is a nice overview of leaf structure in different environments. Has good images and activities with a little quiz. Could be used as part of a plant or photosynthesis lab. Requires a free Open University account.

Good overview of microscope parts and basic use. Would be a pretty short lab activity (about 30 minutes) involving adjusting focus, lighting, etc., to see lettuce and onion cells. Contains a video, a quiz, and a virtual practice lab exercise.

This is a great online module that asks students to gather data by measuring limb length from photos and interpret this to answer evolutionary questions about speciation and convergent evolution in anole lizards.

Fun simulation game of natural selection based on rabbits and their coat colours, teeth, and tail lengths and selective pressure from wolves and food finding.

This simulation allows you to watch natural selection in action. You act as a predator eating light and dark moths, and at the end of the activity, you see how many light and how many dark moths survived, thanks to their colouring.

From BioInteractive: “This interactive simulation allows students to explore two classic mathematical models that describe how populations change over time: the exponential and logistic growth models.”

First-year biology. Simulates John Endler’s classic 1980 experiment with guppies and the number of spots on males and how it changes over time as you adjust preference of females and number of predators. Could be a good resource to complement an introductory lab on natural and sexual selection.

Citizen science project to map every tree in Britain. Fun exercise with a map and “adding” tree species (comparing tree species) to determine economic and ecosystem benefits such as carbon sequestration. Very much focused on trees in the UK, but still interesting to play around with. Fun complement to an introduction to biosphere or ecosystem ecology lab.

First-year anatomy and histology. Could also be used for other labs, such as an introductory lab to tissue types, introduction to organs (skin), and pre-dissection activities, such as what the different body cavities and planes are.

Population, community, behavioural, conservation, and biodiversity ecology modelling labs. Looks awesome for ecology. Data is biologically realistic and is displayed numerically and graphically.

Full of good images. Would be a good tool to supplement a pig dissection lab. There is a lot of clicking the mouse to see each section, but would still be quite useful.

A series of interactive tutorials that explore various aspects of virtual scanning electron microscopy. Toggle focus, contrast, brightness, and magnification when looking at a variety of samples.


5.6: Chapter Resources - Biology

Educational Resources for Schools

  1. ExpandBusiness and Economics
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  • ISBN: 9781108859028
  • Format: Print/online bundle
  • Subject(s): Biology
  • Qualification: Cambridge AS and A Level
  • Author(s): Mary Jones, Richard Fosbery, Dennis Taylor, Jennifer Gregory
  • Available from: April 2020

For first examination from 2022, these resources meet the real needs of the biology classroom.

Extensive research through lesson observations, teacher interviews and work with our online research community (the Cambridge Panel) means that this coursebook with digital access meets the real teaching needs of the biology classroom. Multi-part exam-style questions ensure students feel confident approaching assessment. New features provide reflection opportunities and self-evaluation checklists develop responsible learners. The coursebook provides a range of enquiry questions such as practical activities, group work and debate questions that develop 21st century skills. This resource is written to support English as a second language learners with key command terms, key words, accessible language throughout and glossary definitions in context throughout the text. The coursebook is part of a flexible suite of resources revised for examination from 2022. The series provides activities to develop and enhance students’ investigative skills, with a step-by-step approach tailored to syllabus objectives. The resources offer a large variety of active lesson ideas and practical support, which helps with differentiation and reflection.

Features (such as ‘Before You Start’), summaries and reflection boxes provide students with metacognitive and content-based reflection opportunities.

Science in Context features with open-ended discussion questions enable students to practise their English skills, interpret ideas in a real-world context, and debate concepts with other learners.

Multi-part exam-style questions at the end of each chapter help prepare students for examinations and cover the range of paper styles.

Provides a range of enquiry questions – such as practical activities, group work and debate questions, that help students develop 21st century skills.

Combined print and digital resource enables you to use the content in a format that suits you.

Includes answers to in-chapter and exam-style questions so students have everything they need to revise when they want

Practical activity features build student understanding so that they can put theory into a practical context.


5.6: Chapter Resources - Biology

Population.com
A web site with population statistics of countries worldwide, which includes age-specific population data

Chapter 5
Populations

In this chapter, you will read about patterns of population growth and the major factors that affect the growth of populations. You will also find out how biological and social factors affect the growth of human populations. The links below lead to additional resources to help you with this chapter. These include Hot Links to Web sites related to the topics in this chapter, the Take It to the Net activities referred to in your textbook, a Self-Test you can use to test your knowledge of this chapter, and Teaching Links that instructors may find useful for their students.

Hot Links Take it to the Net
Chapter Self-Test Teaching Links

Section 5-1: How Populations Grow
Three important characteristics of a population are its geographic distribution, density, and growth rate.
Three factors affect population size: the number of births, the number of deaths, and the number of individuals that enter or leave the population.
Under ideal conditions and with unlimited resources, a population will continue to grow in a pattern called exponential growth. As resources are used up and population growth slows or stops, the population exhibits logistic growth.

Section 5-2: Limits to Growth
Density-dependent limiting factors include competition, predation, parasitism, and disease.
Unusual weather, natural disasters, seasonal cycles, and certain human activities—such as damming rivers and clear-cutting forests—are all examples of density-independent limiting factors.

Section 5-3: Human Population Growth
Like the populations of many other living organisms, the size of the human population tends to increase with time.
The characteristics of populations, and the social and economic factors that affect them, explain why some countries have high population growth rates while populations of other countries grow slowly or not at all.


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What are Web Codes?