PCAT Biology Under the Microscope

In this part you will learn about...

  • Cellular and Molecular Biology
  • Genetics
  • Evolution
  • Nutrition and metabolism
  • Energy transformations within cells
In recent years, the science of biology has become ever more important to the pharmacy profession. Unfortunately, it seems pharmacists are running out of ideas for distinct, inorganic chemical elements to make into medicines and are progressing more towards biological medicines (called biopharmaceutics). Therefore, a comprehensive knowledge of the biological science has become an ever-growing perquisite for a pharmacy student.
This chapter is concerned with the very small things and takes a look at the structure and functions of cells and how this relates to key subject matter such as genetics, cell division, nutrition, metabolism and how they all fit together.

Cell theory - The Important Bits

Taking it from the smallest parts to the tiny building blocks that make every organism known to exist... Atoms combine together to make molecules; these molecules combine together to form structures (called cellular organelles). In turn these organelles group together to make cells, which make up all of us (scientist recon you have between 10-50 trillion cells in you body). This bottom up view is a useful way to understand the immense complexity of biology.

Cell theory is one of the fundamental principles of biology. This theory describes that all living organisms on earth consists of one or more cells. These cells are the structural, functional, and organizational unit of all living species and they carry genetic information from generation to generation. Don't be put of that it is only called a "theory” it is more like a robust fact and has been known for as far back as the 17th century. In a nutshell cell theory has three main stipulations:

  • All living organisms are composed of one (unicellular) or more cells (multicellular).
  • The cell is the basic unit of structure, function, and organization in all organisms.
  • All cells come from preexisting, living cells.

Introducing very small things that make up us all

Think of a cell as a machine consisting of different mechanical parts. The machine itself is packed into a semi permeable bag called the membrane, with a rigid outer cell wall. The parts inside are membrane-bound organelles such as mitochondria, chloroplasts and the Golgi apparatus.

Each organelle has its own function, much like cogs in a machine, each part has its own part to play, which effects the overall function of the cell, the most important parts include:

  • Mitochondriaare the power stations generating the power for all the different functions within the cell, from cellular division to protein formation.
  • Plasmidscontain many important genes which the cell uses to replicate itself these are stored as separate circular DNA structures.
  • Centriolesare a cylindrically shaped cell structures found in most eukaryotic cells, though it is absent in higher plants and most fungi. The walls of each centriole are usually composed of nine triplets of microtubules (protein of the cytoskeleton).
  • Nucleuseslike plasmids but bigger, contain the cells genes, encoded as DeoxyriboNucleic Acid (DNA) which is a helical molecule encoding the genetic instructions used in the development and functioning of all known living organisms and many viruses.
  • Endoplasmic reticulum is the structure that holds everything together; it can be seen as the framework, the skeleton that serves to transport vital nutrients and building blocks to the various organelles. The rough endoplasmic reticulum contains ribosomes attached to the cytosolic side of their membrane and aids in phospholipid synthesis and assembly of polypeptides. The smooth endoplasmic reticulum has no ribosomes and is necessary for steroid synthesis, metabolism and detoxification, lipid synthesis
  • Ribosomes found inside the rough endoplasmic reticulum are complex protein factories, found within all living cells; they serve as the primary site of biological protein synthesis (translation).
  • Golgi apparatus - under a microscope look like a stack of droopy sacs surrounded by membrane. The purpose of the Golgi apparatus is to receive protein-filled vesicles from the rough ER and the use enzymes to modify these proteins (e.g. add a sugar chain, making glycoprotein).
  • Lysosomes- play an important role in intracellular digestion - and are more numerous in cells performing phagocytosis (which is when a cell swallows up another cell).

During the PCAT exam, the examiners require every student (including you!) to know the variety of parts that make up a common cell, how these interact and ultimately replicate themselves through meiosis and mitosis. All large complex organisms are eukaryotes, including animals, plants and fungi. Questions presented in the exam are usually based around cellular organelles and genetics so make sure you learn these well.

Prokaryote Vs Eukaryote

Cells are the principal unit of life. Depending on the structural differences, they can be classes in to two main broad groups either Eukaryote or Prokaryote. The differences are best explained digramatically, check out Figure 8-1 below for the key differences:

 Eukaryote Vs Prokaryote

Figure 8-1: Eukaryotes and prokaryotes side by side.

The main differences between prokaryotes and eukaryotes, are as follows:

1. Prokaryote: These cells don't have a nucleus or any other organelles, membrane bound structures within a cell. Bacteria and Archaea are examples of prokaryotes.

2. Eukaryote: These are organisms whose cells consists of complex structures (e.g. nucleus, mitochondria, golgi complex, etc.) enclosed within membranes. All large complex organisms are eukaryotes, including animals, plants, and fungi.

The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear envelop, within which the genetic material is carried (more on this later).

A good way to remember what a eukaryote is to remember (you)karyote - i.e. the cells that make up you!

Eukaryotes

The majority of animals which are visible to the naked human eye are Eukaryotes, including you and me, i.e. humans (hopefully ;)). Some differential characteristics of Eukaryotic include:

  • DNAis organized within the cell nucleus into complex chromosomes unlike prokaryotes which have DNA free roaming in the cell.
  • Mitochondriaare organelles which are vital from metabolism and provide energy the cell needs to perform specific tasks.
  • Membrane-bound organelles such as Golgi apparatus provide useful functions within the cell.

Prokaryotes

The easiest way to remember what a prokaryote is; is to remember that they lack a cell nucleus and membrane-bound organelles. In addition they are almost always a single cell organism (unicellular) although they sometimes aggregated into large clumps.


Question

An organelle is a membrane-bound structure within a cell. Just like different organs of our body, each organelle within a cell has specific function or role. Which of the following statement about organelles is incorrect?

(A)   Prokaryotic cells are absent of organelles.

(B)   Most eukaryotic cells contain organelles.

(C)   Nucleus and plastids are major organelles that are found in all eukaryotic cells.

(D)   Lysosomes, ribosomes, cytoplasm, nucleolus, cell membrane, and mitochondria are essential organelles that are present in most eukaryotic cells.

Answer: C

Explanation

Nucleus and plastids are major organelles of eukaryotic cells, but they are not present in all eukaryotes. A nucleus is present in almost all eukaryotes, but plastids are mainly present in plant species.

Green with envy - The difference between plants and us

In addition to the organelles mentioned above, plant cells differentiate from other cells in that they can also contain:

  • Cell walls can be found in most plants and fungi. The cell wall serves as a fairly rigid cellulose layer outside the cell membrane, providing the cell with structural support, protection, and a filtering mechanism.
  • Vacuolesare membrane-bound organelles that are filled with inorganic and organic liquid. Vacuoles maintain the cell's rigidity and control movement of molecules between the cytosol (intracellular fluid that is composed of a complex mixture of substances) and cell sap (liquid present in large central vacuole).
  • Plasmodesmata, linking pores in the cell wall that allow each plant cell to communicate with other adjacent cells. Functionally, plasmodesmata are analogous to the gap junction, a specialized intracellular linking between animal cells. However, plasmodesmata and gap junction are distinctly different in their structure.
  • Chloroplasts(plastids) give plants their distinct green color as they contain chlorophyll, and allow them to perform photosynthesis, which creates sugar from carbon dioxide and water.

Photosynthesis comes from the Greek, "photo” meaning light and "synthesis” meaning coming together of water, light, and carbon dioxide to make the sugars they need to grow.

The theory of endosymbiosis

The theory of endosymbiosis explains that the mitochondria and chloroplasts, two double membrane organelles found in most eukaryotic cells, are descended from primitive bacterial cells. Because, they contain ribosomes similar in size and makeup to those found in prokaryotes.

According to the theory, endosymbiosis occurs when one organism starts living in another organism due to evolution and become dependent on each other for survival, this is called symbiotic relationship. The endosymbiotic theory postulates that early eukaryotic cells took in primitive prokaryotic cells by millions of years of evolution and modified themselves to incorporate their structures and functions, resulting in mitochondria, chloroplasts and other key organelles. The symbiosis has developed as such that now plant and animal cells are now fully dependent on mitochondria and chloroplasts to provide them with the energy they need.

Replication from the Nucleation

An organism that only has one cell (unicellular) is pretty happy plodding along however, it is somewhat limited. Because the organism only has one cell, and it can only really do one thing at a time. For organisms to be more successful, they developed into groups of cells together, so they could multitask as multicellular organism. The only way single cell organisms can become multicellular is by replicating themselves using the common blue print DNA.

In this section, the concepts of replication, including what goes on in a cell's nucleus, how nucleotides form DNA, and how cells make copies of themselves (no photocopier necessary) are described below.

Narrowing in on the nucleus

In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. It is usually elongated or rounded and often found in the center of the cell. It contains most of the cell's genetic information, organized as multiple long linear DNA molecules in complex strands with a large variety of proteins, to form chromosomes, an organized structure of DNA and protein present in most eukaryotic cell's nucleus (more on this later).

Components of nucleus

1. Nuclear envelope: The nucleus is surrounded by two-lipid bilayer membrane called nuclear envelope (also known as nuclear membrane). In light microscope, nuclear envelope is detected as a tinny line surrounding the nucleus. The nuclear envelope allows the nucleus to control its contents, and separate them from the rest of the cytoplasm where necessary. This is important for controlling processes on either side of the nuclear membrane.

2. Chromatin: In the interphase or resting phase of cell division (more on this later), the chromosomal material stays less tightly packed in nucleus and it is then designated as chromatin.

3. Nucleolus: A round or spherical type structure present within the nucleus, which is rich in rRNA (ribosomal RNA) and protein.  

4. Nuclear Matrix: The component fills the space between the chromatin and the nucleoli (plural of nucleolus) in the nucleus.

5. Nuclear lamina: composed mostly of lamin proteins, is the part of the nucleuses which provides the mechanical support much like a scaffold on a builing.

The function of the nucleus is to maintain the integrity of the genes, subunits of DNA, and to control the activities of the cell by regulating gene expression, a process by which functional genes are transcribed and translated (more on this later) -- the nucleus is, therefore, the control center of the cell. 

In molecular biology and genetics, the genome is the entirety of an organism's hereditary information, which comprises the entire "blueprint”.

CATG: The building blocks of DNA

DNA is a double helix, a structure similar to that of spiral staircase, consisting of two strands of polynucleotide chain (polymer chain consisting of nucleotide monomers) twisted spirally. Each nucleotide is a hybrid molecule contains a nitrogenous base, a five - carbon sugar (deoxyribose), and a phosphate group (PO4). Each single DNA strand contains same deoxyribose sugar and phosphate group, but differs with other strands only in nitrogenous base. Consequently, four different nucleotides are found in DNA.

Adenine (A), cytosine (C), thymine (T), and guanine (G) are four different nitrogenous bases that used to make four different nucleotides in DNA. Chemically, depending on structural similarities, these nitrogenous bases can be classified into two other classes.

1. Purine base: Consists of double-ringed structures with larger molecules. Adenine (A) and guanine (G) are larger molecules with double ring and for that, they are considered in purine base. 

2. Pyrimidine base: Consists of single-ringed structures with smaller molecules. Cytosine (C) and thymine (T) bases are considered as pyrimidine base for their single-ringed and smaller molecular structures.

In 1953, Watson and Crick first introduced their famous model of DNA structure and proposed that DNA has two strands twisted together spirally - the double helix. They discovered that in a DNA molecule, the number of A = T and C = G, and accordingly, they established the double helix model of DNA structure what we see today.

A bit of a silly way to remember the different bases is G-CAT. Think of a CAT which is a "G” (gangster). The cat who is a G, otherwise known as GCAT. This is a picture of the For Dummies pet (Figure 8-2), he's called Neville by the way, respect.

Ssssup dog

Figure 8-2: Gangster cat, bases within DNA.

Each single strand of DNA has a backbone containing sugar and phosphate sequence. A sugar molecule (3 - carbon) of one nucleotide is covalently bonded (a bond that is formed by sharing of one or more pairs of electrons between atoms) to the sugar molecule (5 - carbon) of next nucleotide via phosphate group. The hydrogen bonds between phosphates are the reason for twisted structure of the DNA strand.

The double helix of DNA has two strands that are always hydrogen-bonded together through their purine and pyrimidine bases. This suggests that a purine base must bond with a pyrimidine base. An adenine (a) base of one strand will always pairs with a thymine (T) base of another strand and this same rule will be followed for guanine (G) and cytosine (C). The base pair between A and T is bonded via two hydrogen bonds, and the G - C base pair are connected via three hydrogen bonds. For that, the G-C hydrogen bonding is stronger (by about 30%) than A-T. So the GCAT analogy holds true when trying to remember both the different bases and who they bond to i.e. G with C and A with T, that could probably form into a rap, but I wont.

It just keeps going: The cell cycle and division

The cell cycle, or cell-division cycle, is a series of events that takes place in a cell leading to its division and duplication (replication). The cell-division cycle is a vital process by which a single-celled fertilized egg develops into a mature organism, as well as the process by which hair, skin, blood cells, and some internal organs are renewed.

In cells without a nucleus (prokaryotic), the cell cycle occurs via a process termed binary fission. During this process, the parent cell is divided into two equal size daughter cells comprising equally partitioned heredity material i.e. it splits in two.  

In cells with a nucleus (eukaryotes), the cell cycle can be divided into two periods:

  • Interphase--during which the cell grows, accumulating nutrients needed for mitosis and duplicating its DNA.
  • Mitotic (M) phase, during which the cell splits itself into two distinct cells, often called "daughter cells".  

These two stages, can be further subdivided into four distinct phases listed below (Figure 8-3):

  • G1 phase,
  • S phase (synthesis)
  • G2 phase
  • M phase (mitosis)

 Cell cycle

Figure 8-3:  A bad picture of the distinct phases of the cell cycle.

G1, S, and G2 phases are the first three phases of the cell cycle and collectively known as interphase.

The G1 phase stands for the first gap phase of the cell cycle. In this phase, the parent cell size increases and replicating organelles and cytoplasm are added. 

The S phase is the phase of DNA synthesis. During this phase, all chromosomes are replicated.

The G2 phase is the second gap phase of cell cycle. In this phase, the cell size will continue to grow. This phase also ensures that the cell is ready to enter the next phase (M) of cell division.

M phase is itself composed of two tightly coupled processes:

  • Mitosis: it is the phase in which the cell's chromosomes are divided between the two sister cells, and
  • Cytokinesis: the last stage in which the cell's cytoplasm divides in half forming distinct cells and new cell is completely divided.

Activation of each phase is dependent on the proper progression and completion of the previous one. Cells that temporarily or reversibly stopped dividing are said to have entered a state of quiescence called G0 phase.

After cell division, each of the daughter cells begins the interphase of a new cycle. Although the various stages of interphase are not usually morphologically distinguishable, each phase of the cell cycle has a distinct set of specialized biochemical processes that prepare the cell for initiation of cell division.


Question

The G1 phase is the first gap phase of cell division. Cytoplasm and replicating organelles are added during this phase. The G1 phase is also a part of which of the following options?

(A)   Mitotic phase

(B)   G0 phase

(C)   Cytokinesis

(D)   Interphase

Answer: D

Explanation

The G1 phase is a part of Interphase. Because interphase comprises first three phases of cell cycle and G1 is the first phase among all phases of cell cycle.

Genetics - How We Replicate at the Subcellular Level

The main reason any organism is on the planet is to replicate itself and carry on a version of its own building blueprint - DNA to its kids (progeny). Organisms with the help of cellular mechanism have become extremely efficient at this.

It is not always in the best interest for the progeny of the organism to have the same DNA. This would be deemed a clone and would be genetically identical to the parent. It is of benefit for the progeny to be a bit different from the parent as these differences may provide an advantage for survival.

For instance, a mother's DNA may code for her to be too short in height so she is unable to reach the fruit in an apple tree. However, a father's DNA may enable him to grow to the correct height to pick the yummy fruit. The question then remains how tall the progeny will be. Welcome to the wonderful world of hereditary genetics...

In this section, the classical genetics, Mendel laws, evolutionary science - origin of evolution, evidence, process, and types of evolution - relationship between DNA and RNA, chromosomes, gene expression, and protein synthesis are explained below.  

Heredity, Mendelian and classical genetics

The study of genetics all started way before Watson and Crick discovered DNA in 1953. To find where it all started you need to go further back, much further back to the 1800's. It all started with a simple Czech monk called Mendel who loved pea plants.

Mendel demonstrated that the inheritance of certain traits in pea plants follows particular patterns, now referred to as the laws of Mendelian inheritance. It all sounds very complicated but in fact it is very simple. Heredity is the passing of traits to offspring (from its parent or ancestors). This is the process by which an offspring cell or organism acquires or becomes predisposed to the characteristics of its parent cell or organism. Through heredity, variations exhibited by individuals can accumulate and cause some species to evolve.

In humans, eye color is an example of an inherited characteristic: an individual might inherit the "brown-eye trait" from one of the parents via DNA. Genes control inherited traits and the complete set of genes within an organism's genome is called its genotype.

The complete set of observable traits of the structure and behavior of an organism is called its phenotype. These traits arise from the interaction of its genotype with the environment. As a result, many aspects of an organism's phenotype are not inherited. An organism's phenotype examples may include particular traits such as eye color, hair color, size, voice, blood group, certain behavior, etc.

Before a cell divides, the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence. A portion of a DNA molecule that specifies a single functional unit is called a gene; different genes have different sequences of bases. Within cells, the long strands of DNA form condensed structures called chromosomes. The specific location of a DNA sequence within a chromosome is known as a locus. If the DNA sequence at a particular locus varies between individuals, the different forms of this sequence are called alleles. DNA sequences can change through mutations, producing new alleles. If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism.

The PCAT examiners love to ask about the differences between genetic terminologies. Make sure you understand the difference between genome and gene, phenotype and genotype...

Evolutionary Science

In biology, Evolution simply refers to the changes or modifications in the genetic characteristics of biological inhabitants over succeeding generations. Thus, evolutionary science is the study by which scientists understand how evolution occurs. In addition, biologists use the principal theory of evolution to research and understand the evolutionary processes in every biological life. 

Mutation, natural selection, gene flow, and genetic drift are the principal processes for evolving life on earth.

Mutation

In cell biology, mutation is the changes in genetic information of a biological organism. In other words, it is the changes of the nucleotide sequence of a genome, the total genetic information in chromosomes of an organism. In fact, mutation is the result of damages to DNA or RNA sequence that are not repairable, abnormal replication processes, and inclusion or removal of segments of DNA.

With mutation processes, new alleles, the alternative forms of the same gene, are formed. These new genetic coding for proteins is sometimes harmful, neutral, or beneficial as compared to the original protein. However, to avoid damaging effects on gene from a mutation, most of the organisms have mechanisms like DNA repair to stop harmful mutation. New alleles produced by mutation that code for harmful proteins could prevent the normal functions of the gene. On the other hand, alleles that are produced by natural mutation and code for beneficial proteins could provide advantageous effects on gene. Ultimately, these new beneficial alleles are designated for by natural selection and are delivered to the successive generation.

Natural Selection

In biological evolution, natural selection is the gradual but anticipated or awaited process by which genetical traits turn into more or less common in a biological population. Charles Darwin, the father of theoretical evolution, popularized the term "natural selection" and explained how evolution occurs by natural selection process.

Environment plays a big part in the natural selection process of an individual. Throughout the lifespan of every individual, genomes of individual's interact with environment to create favorable variations in traits. These variations in traits pass from one generation to the next via natural selection process. However, not all variations are passed to next generation. The environment determines which variants in traits will pass.

Hence, the natural selection is the process through which only the population best adapted to their environment likely to exist and pass variations of the trait in increasing numbers to next generations while individuals less adapted to their environment tend to be excluded.

Gene Flow

In genetics, Gene Flow is the alleles' or gene's migration, transfer, or shifting from one population to another. This process is usually occurred when an individual leaves a population and moves to another population of the same species. Gene flow is also termed as Gene Migration.

Gene flow is an essential process of genetic variation. Migration of alleles or genes to a new population can add genetic variants in their established gene pool.

Genetic Drift

In genetics, Genetic drift is the random changes in the frequency of an allele variant (gene) within a population from generation to generation. It is usually takes place when the frequency of allele variants increases or decreases due to random sampling.

Genetic drift has relatively minor effects over large population, whereas it has significant effect over smaller populations. Thus, it may cause allele variants to hide completely from a population or to become prevalent in a population ignoring generic variation.

It may be difficult for you to remember the definitions of these four major processes of evolution. So we have condensed it down into bullet points for you:

  • Mutation - responsible for evolution due to damages or errors in cell processes
  • Natural Selection - natural, gradual and non-random process of evolution
  • Gene Flow - transfer of alleles from one population to another
  • Genetic Drift - a random process of evolution and changes in the frequency of gene variants occurs due to chance.

The Hardy-Weinberg Equation

The allelic frequencies within a population - where the population size is infinite, zero occurrence of gene flow, zero mutation rate between generations, zero occurrence of artificial selection, and mating is totally random - can be determined using the Hardy-Weinberg equation. However, according to evolutionary perspectives, this equation is very unrealistic based on the situations mentioned above.

Equation 1:

p + q = 1

Here,

p = the frequency of a dominant allele

q = the frequency of a recessive allele

Equation 2:

p2 + 2pq + q2 = 1

Here,

p2 = the frequency of homozygous dominant individuals

q2 = the frequency of homozygous recessive individuals

2pq = heterozygotes

A rolling stone gathers no moss, evolution in a nutshell

The evolution of life on Earth involved a limitless series of progressive steps. In this next section, the major events in the evolutionary history of life will be discussed.

Although, in today's world, science have advanced far beyond our ancestors thoughts, but humans still can't uncover the exact explanation about the origin of life on Earth. However, the big bang theory by Dr. Stephen Hawking provides some thoughts about how the universe built, life formed on Earth, and evolution started.   

Based on the oldest fossil sample findings, Prokaryotes, were the first life form on Earth, which started, roughly 4 billion years ago. After the Prokaryote's invasion on Earth, they remained nearly unchanged in there cellular organization for the next few billion years. According to researches, the eukaryotic cells or the membrane bound complex cells appeared between 1.6 and 2.7 billion years ago.

After the arrival of unicellular eukaryotic cells, multicellular organisms appeared on Earth about 610 million years ago. These multicellular organisms were believed to have first appeared in the oceans. In biological evolution, genetic diversity evolved over nearly 10 million years after the appearance of first multicellular species. According to fossil records, species of plants and fungi inhabited the Earth's soil around five hundred million years ago. Most of the modern species of plants and animals appeared between 10 -350 million years ago and present day humans (Homo sapience) estimated to appear approximately 250,000 years ago.

Evidence for Evolution

When Darwin first published the theory of evolution, in his seminal book "The Origins of Species” in the nineteenth century, many people of that time thought that it was total nonsense, lacking proper evidence and rigorous scientific analysis. However, as of today, there is a wide range of significant evidence that support Darwin's theory and is almost considered "Darwin fact”.

Scientific evidence to support evolutionary theories comes from various aspects of biological science and includes paleontology, comparative anatomy, embryology, biogeography, molecular biology, artificial selection, etc.   

  • Paleontology, or the study of fossils, provides evidence that today's diverse forms of life have been created the by small changes in organisms over extended phases of time. Fossils of ancestor organisms allow paleontologists to postulate a family tree and reveal structural and other biological relationship between existing and extinct species.
  • Comparative Anatomy - in evolutionary evidence, comparative anatomy, is the study that compares similarities and dissimilarities between organisms of different forms. Biologists study comparative anatomy to find out common ancestral species of organisms.
  • Embryology  - in many cases, when biologists compared two or more species of dissimilar anatomical structures, they found similar anatomical structures in their embryos, as evidence for a shared ancestor, though the adult forms are distinctly different. Biologists study embryology to determine the common ancestral species of two or more organisms researching their embryonic similarities. 
  • Biogeography - is the discipline in which biologists study geographical distribution of organisms over the Earth. Studying the similarities and dissimilarities between diverse species living in different parts of the world, biologists can help decode evolutionary relationships between different species and their common ancestors.
  • Artificial selection - is one of the best evidences to understand evolution of life on earth. In genetics, artificial selection is characterized as controlled breeding where specific alleles are intentionally selected for based on nonrandom mating. Breeding of domestic plant or animal are excellent examples of artificial selection.
  • Types of Evolution - depending on time, the biological evolution can proceed in a variety of patterns or directions. Based on the effects of predation and environment pressure, biologists have patterned three different types of evolution: parallel, convergent, and divergent evolution.
  • Parallel Evolution - Biologists explained parallel evolution as an evolution in which similar adaptive mechanism occurs between different species due to the nature of environmental condition. More understandably, when two unrelated organisms share alike environment, adaption of new characteristic by one organism will effect on the evolutionary mechanism of another organism. Consequently, in order to keep existence in the same environment, another organism must adapt similar characteristic.
  • Convergent Evolution - occurs when two populations share same selective pressure or environmental circumstances. This is because the sharing of same selective pressure in species requires adaption of similar structural alterations in order to survive and function properly. As a result, convergent evolution allows adapting similar analogous structures even though the species vary in descent.
  • Divergent Evolution - due to different environmental conditions when two groups from a specific population over time evolve into distinct species divergent evolution occurs. In fact, the study of divergent evolution explains how present diversity of organisms comes from the first living cells on earth.

DNA and RNA: An intertwined relationship

DNA is well suited for biological information storage, since the DNA backbone is resistant to cleavage and the double-stranded structure provides the molecule with a built-in duplicate of the encoded information.

RNA or ribonucleic acid is present in the nucleus and cytoplasm of the cell and it functions as a template for synthesis of proteins by the cell.

DNA and RNA have a basic similarity in their structure. They both have linear sequence of nucleotides. However, unlike DNA, RNA is single stranded linear sequence of nucleotides and the sugar molecule present in RNA is ribose whereas DNA contains deoxyribose sugar.  Like DNA, the nucleotides in RNA are also consists of four different nitrogenous bases, but RNA nucleotides contain uracil (U) instead of thymine (T). So, RNA is consists of Adenine (A), cytosine (C), uracil (U), and guanine (G).

DNA and RNA molecules are interrelated with one another within the cell via transcription process. In cell biology, transcription is a process of transferring cell's genetic material between DNA and RNA. During this process, mRNA (messenger RNA) functions as an intermediary for carrying the genetic information encoded in DNA from the nucleus to the protein synthesizing machinery in the cytoplasm. Transcription process generates a complementary RNA copy of a sequence of DNA.

Crisk structure 

Figure 8-4: The structure of DNA

Nearly 60 years ago two English scientists, Francis Crick and James Watson's worked out the structure of DNA - the twisted ladder of the double helix - can legitimately be regarded as a turning point: our understanding of life was changed forever that day, and the modern era of biology began.

The elegant spiral, first drawn by Crick's wife Odile, depicts life's most famous molecule. Since its elucidation in 1953, biology has evolved into a global industry, with our ever-increasing command over DNA at its core. We have seen the emergence of genetic modification and now synthetic biology - for both scientific and commercial gain - each with its own mire of ongoing legal wrangles. And now we are entering the post-DNA era. In the past couple of years, the nature of DNA itself has been modified, its alphabet mutated and its function reinvented for non-biological uses.

Chromosome

In cell biology, a chromosome is a highly condensed form of chromatin that is visible through light microscope during mitosis. Chromosomes are the crucial unit of genetics. During cell division, chromosomes must replicate, divide, and transfer fruitfully to their daughter cells to confirm the genetic diversity and existence of their progeny (production of new products from one or more parent products, more specifically collective offspring). 

In normal cells (human), there are 46 chromosomes present in 23 homologous pairs of chromosomes. One member of each of these chromosome pairs is derived from the maternal parent and another one is from the paternal parent. Among these 23 pairs, 22 are called autosomes, whereas the remaining one pair that determines gender is the sex chromosomes.

The chromosomes are consists of DNA and basic protein (histone). In eukaryotic cells, more than 99% of the cellular DNA is localized in the chromosomes. Each chromosome bears a linear sequence of points (in a specific DNA molecule), called genes.  

Gene expression

In biology, gene expression is the principle process in which the genotype of an organism gives rise to its phenotype. Using gene expression, the genetic information saved in DNA is interpreted. In fact, gene expression is the process that regulates which genes to be transcribed and translated. As every cell consists of many genes, it not essential for each cell to express all genes it contains. For that, every cell is selective about which genes it will express. Indeed, cells only express genes that are essential for making proteins at a given time.

When a less specialized cell type turns into a more specialized cell type, this process is called cellular differentiation. The process of differentiation occurs early in development period (childhood) and is thought to be irreversible. In adults, cells that have yet to differentiate are referred to as stem cells. In genetics, due to the cellular differentiation process, gene expression is regulated on a permanent level. Because cell's requires expressing genes related to a specific function, as nearly 99% of the cells are specialized within the body. Despite the fact, almost all cells have the same genes, but every specialized cell is able to express only a small subset of those genes. 

For example, the brain cells are unable to express the genes of insulin production though their cells have the gene to produce the insulin protein. As the production of insulin protein is unnecessary for the functioning of a brain cell, it is really useless to produce such type of protein. So a brain cell doesn't produce unnecessary protein due to regulation of gene expression.

Creation of proteins

A gene represents a specific segment of the DNA molecule. Usually, the DNA molecule is located on a chromosome and has information to code for the synthesis of a particular protein.

Protein synthesis is carried out in the "working space” of the cell called the  cytoplasm. For the creation of a particular protein, genetic codes from the gene of a specific DNA must be carried to the cytoplasm or to the ribosomes. However, there is a big problem in transferring the DNA of a chromosome to the cytoplasm and ribosomes. Except mitochondria and chloroplast, DNA is restricted in nucleus, and ribosomes also can't enter into the nucleus. To solve this problem, the genetic information in DNA needs to be converted into RNA (ribonucleic acid) message, so a complementary RNA copy of the DNA sequence is generated. This RNA copy of the DNA sequence then travel to the cytoplasm and translated by the ribosomes to create a protein (See figure 8-5).

Transcription 

Figure 8-5: Transcription between DNA and RNA.

Protein synthesis or creation of protein is done in a two-step process:

1.    Transcription: The transfer of genetic material between DNA and RNA

2.    Translation: The conversion of RNA to a particular protein

Looking to the future of genetics

Genetic research is progressing increasingly, often rapidly, on diverse aspects though there are not many success stories over the past decades. Biological scientists have previously explained some of the once unexplained concepts of genetics and have grown the ability to interpret the genetic codes. Scientists believe, in the near future, these small successes over different areas of genetics will help them to unfold mysteries related to genetic disorders.

Many disorders from inherited traits, which are still mystery to biological scientists, may be prevented via genetic research. This research may bring light to various disorders of single organs including the skin, teeth, eye, and cochlea (the hearing organ of the ear). Finding the specific genes in the DNA sequence that are responsible for various inherited disorders and altering the gene expression, it may be possible to stop the genetic defects from affecting our existing generations as well as future generations.

Nutrition and Metabolism

In biology, nutrition and metabolism are interrelated with one another like fuel and the engine of a car. They are interdependent meaning the absence of one of them can stop the total functioning of the other. A healthy source of nutrition means healthy metabolism in the body and healthy metabolic rate eventually helps to keep healthy and fit.

Like the fuel of a car, nutrition is the raw material of the body. In other words, nutrition is the raw source of energy in the body and when it ingested, it breaks down and provides energy. On the other hand, metabolism is like the engine of a car, it carries out all the processes of breakdown, repair, and growth in the body.

In this section, the major nutritional sources (carbohydrates, lipids, nucleic acids, proteins, minerals and vitamins) of energy in the body are discussed below. 

Carbohydrates

Organic compounds that contain only carbon (C), hydrogen (H), and oxygen (O) in their molecular structure are called as carbohydrates.

Carbohydrates perform a number of important roles in living organisms. Polysaccharides serve for the storage of energy (e.g., starch and glycogen), and as structural components (e.g., cellulose in plants and chitin in arthropods). As food, the term carbohydrate often means any food that is particularly rich in the complex carbohydrate starch (such as cereals, bread, and pasta) or simple carbohydrates, such as sugar, however no carbohydrate is an essential nutrient in humans (i.e. it can be created within cells and does not need to be a part of the diet) as we can obtain out energy from other sources such as proteins and fats. Humans can actually synthesize some glucose (in a set of processes known as gluconeogenesis) from specific amino acids, from the glycerol backbone in triglycerides and in some cases from fatty acids.

Nutritionists often refer to carbohydrates as either complex or simple. There is a lot of debate around the different classifications however, if they are sugars (monosaccharides and disaccharides) and complex if they are polysaccharides (or oligosaccharides)

Lipids

Lipids are basically fats, like the corn oil you can find in your kitchen cupboard. More specifically lipids are a group of naturally occurring molecules that include fats, waxes, sterols and fat-soluble vitamins such as vitamins A, D, E, and K (more on those later). The majority of lipids are water repellent termed hydrophobic this means they do not mix with water and actively avoid it. Some lipids are amphiphillicmeaning that one end of the molecule hates water and the other is hydrophilic meaning it love water.

  • Hydrophilic - these are molecules which "love” water and don't mind mixing with it.
  • Hydrophobic - these molecules heat water and actively repel it.
  • Lipophilic - refers to the ability of a chemical compound to dissolve in fats, oils, lipids, and non-polar solvents.
  • Lyophobic - means the opposite of lipophilic, i.e. an inability of a chemical compound to dissolve in fats, oils, lipids, and non-polar solvents.
  • Amphiphillic - these molecules are ambiguous and usually have -phobicheads and -phillic tails.

Liposome

Figure 8-6: The different lipid structural configurations.

When amphillic molecules group together, they form layers (which can be seen in Figure 8-6), dividing water from everything else such as cell membranes whose purpose is to keep hyperosmotic water out and stop the cell from bursting. The image above explains the three main macrostructures of lipids. They all form structures as they repel water, they curl in on themselves with their hydrophilic heads on the outside and interacting with water and their lipophilic tails on the inside.

  • Liposome - is an artificially-prepared vesicle composed of a lipid bilayer. The liposome can be used as a vehicle for administration of nutrients and are some times even used in the creation of pharmaceutical drugs.
  • Micelle - is a lipid structure in aqueous solution, which combine, leading to hydrophilic "head" regions in contact with surrounding solvent, sequestering the hydrophobic single-tail regions in the micelle centre.
  • Lipid bilayer - comprises of a thin polar membrane made of two layers of lipid molecules. These layers are flat sheets that form a continuous membrane barrier around cells. The cell membrane of almost all living organisms and many viruses are made of a lipid bilayer, as are the membranes surrounding the cell nucleus and other sub-cellular structures.

Nucleic acids

The most famous nucleic acids are DNA and RNA (see figure 8-7), which was discussed earlier. Without them we would not have genetic code and therefore we wouldn't have life! DNA molecules are probably the largest nucleic acid molecules known. In fact one strand of DNA is 2.0 × 1013meters which is the equivalent of nearly 70 trips from the earth to the sun and back and that is just what is in one cell.

RNA and DNA

Figure 8-7: The difference between RNA and DNA

Proteins

Proteins as you know them is the meat that you may eat. They are large biological molecules consisting of one or more chains of amino acids. Proteins perform a vast array of functions within living organisms, including catalyzing metabolic reactions, replicating DNA, responding to stimuli, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in folding of the protein into a specific three-dimensional structure that determines its activity.

Protein structure

Figure 8-8: The different protein structures.

Proteins can be classified on the basis of their structure. Primary proteins can just be a simple combination of amino acids strung together. Secondary structure, is when these smaller amino acid sequence join together making a characteristic structure like an alpha helix or beta sheets. The territory structure is even more complicated and the proteins form to make a three dimensional structure. The last protein structure, is the quaternary structure, this is when these three-dimensional structures become multiple subunits and larger macromolecules.

Minerals

Minerals are the inorganic things you dig out of the ground, not very exciting but they perform vital functions in the body, most important of which include:

  • Calcium (Ca) naturally occurs in milk, cereals and cheese. Required for formation of teeth and Bones, blood clotting, function of nerves and muscles. If you lack this in your diet, often called a deficiency, it can result in weak teeth and bones; retarded body growth.
  • Potassium (K) found in meat, milk, cereals, fruits and vegetables. Potassium is required for acid-base balance, water regulation and function of nerves. If you become deficient in your dietary intake you risk low blood pressure, weak muscles and there is even a risk of paralysis.
  • Iron (Fe) found in red meats, eggs, cereals and green vegetables. Iron is a vital component of hemoglobin, which enables the transport of oxygen around your body. If you do not have a sufficient amount of iron in your diet you can risk certain anemia's, weakness and weak immunity.
  • Zinc (Zn) can be found in cereals, milk, eggs, meat and seafoods. Zinc is a cofactor of digestive and many other enzymes. A diet lacking in this mineral can cause retarded growth, anemia, rough skin, weak immunity and fertility.
  • Selenium (SE) like other minerals can be found in meat, cereals, seafood. Selenium is thought to work as a cofactor of many enzymes. Lack of this mineral can result in muscular pain and weakness of cardiac muscles.

One thing to learn from the broad spectrum of minerals is that a healthy, varied diet is extremely important to maintain a healthy well being and stave of certain deficiency diseases.

Vitamins: Essential and non-essential

The word vitamin comes from the word "vita” which in many Latin languages means life and quite rightly so many vitamins are required just so that we can stay alive. The most important ones include:

  • Vitamin A, the molecular name for which is retinol. Found in carrots, used for general healthy living, can be stored in the liver. During World War II pilots performing nighttime tactical bombing runs were asked to eat carrots to improve their sight at night. Deficiency can result in night blindness.
  • Vitamin B1, aka thiamine. Used for Growth, carbohydrate metabolism and normal functioning of the heart. Deficiency can lead to a condition called Beri-Beri (which is easy to remember as it has two B's).
  • Vitamin B2, aka riboflavin. For Keeping skin and mouth healthy. Deficiency can result in Cheilosis.
  • Vitamin B5 aka niacin. For healthy skin, sound mental health. . Deficiency can result in Pellagra.
  • Vitamin B6 aka Pyridoxine. Processing of proteins and for nervous system, Lack of this in a childs diet can cause convulsions.
  • Vitamin B12 aka Cyanocobalamin. Required for formation and maturation of RBCs. Lack of this in an otherwise balanced diet can cause Pernicious anemia.
  • Vitamin C aka ascorbic Acid (not citric acid!) is used for keeping teeth, gums and joints healthy. It is thermolable meaning it is broken down by heating and cooking. Lack of this in you diet can cause Scurvy. People in the US used to call people from the UK "Limeys” this is because UK sailors used to carry limes with them on long sea journeys to protect them from scurvy.
  • Vitamin D aka calciferol. For normal bones and teeth, can be stored in liver. Lack of this in your diet can result in Rickets, which is a disease, which causes bent bones.
  • Vitamin K aka phylloquinone. Used for normal clotting of blood lack of which can cause a bleeding condition called Hemophilia.

Energy Transformations within Your Cells

So how do you go from eating a tasty hamburger and fries and it ending up being broken down in your stomach and translated into usable cellular energy. Well, once all the hard work is done of munching the tasty burger and it ending in your stomach enzymes breakdown the complex carbohydrates into simpler constituent parts, which can be easily absorbed into the blood stream. These smaller molecules are then transported via the arteries and veins to all of the different cells in the body. Once at the cell, these energy packed molecules have to pass across the cell membrane, which functions as a semi permeable barrier, like the exterior walls of a house, the plasma membrane lets nice things in and keeps bad things out. Various proteins that span the cell membrane permit specific molecules into the cell.

Enzymes

Enzymes are not only used in the digestive process but inside the cells as well to make the most of what you have ingested. Molecules from food are packed with energy, as they have chemical bonds which when broken can transfer this to the cell. Cells release this potential energy stored in their food molecules through a series of oxidation reactions which is aided by enzymes.

An enzymeis a catalyst that brings about a specific biochemical reaction by lowering the activation energy (which is the energy required to kick start a chemical reaction). Oxidation describes a type of chemical reaction in which electrons are transferred from one molecule to another, changing the composition and energy content of both the donor and acceptor molecules. Food molecules act as electron donors. During each oxidation reaction involved in food breakdown, the product of the reaction has a lower energy content than the donor molecule that preceded it in the pathway. At the same time, electron acceptor molecules capture some of the energy lost from the food molecule during each oxidation reaction and store it for later use. Eventually, when the carbon atoms from a complex organic food molecule are fully oxidized at the end of the reaction chain, they are released as waste in the form of carbon dioxide. In a sense, there are two distinct types of enzymes, which are classified based on the way that they work:

  • Anabolic - this is the building up of molecules, i.e. starting with simple molecules enzymes help to bring them together into macromolecules.
  • Catabolic - this is the opposite to anabolic, so instead of building things up it's breaking down into their constituent parts.

Sometimes difficult to remember anabolic and catabolic. One way to remember anabolic is to remember "anabolic” steroids, which some bodybuilders use to build up muscle.

Substrate

Figure 8-9: Enzyme-Substrate interations.

This simplified diagram (Figure 8-9) shows an enzyme interacting with the substrate and its active site to create two products. An easy way to remember this is E + S → ES → P + E, where E is the enzyme, S is the substrate and P is the product. The first stage of the enzymatic pathway is for the substrate to enter into the active site, the enzyme changes its shape as it binds to the substrate which in turn leads to the substrate being converted in to the new products.

How can you easily spot an enzyme? Well that's easy! Most if not all have the suffix -ase, common examples include polymerase (replicates DNA) or amylase (in saliva)

This process is pretty straightforward however, there are some environmental factors which can affect the rate at which enzymes convert substrates in to products. The study of rates of enzyme activity is called enzyme kinetics. The most important factors include:

  • Substrate concentration - as there would be more substrate in the solution, it would mean that the probability of the molecules bumping into each other is greater and therefore have a better chance to react technically
  • Temperature - increasing temperature increases the Kinetic Energy that molecules possess. In a fluid, this means that there are more random collisions between molecules and therefore quicker reactions (see figure 8-10).
  • pH - enzymes have different pH values (i.e. concentration of hydrogen ions) at which the bonds within them are changed in such a way that the shape of their active site is the most complementary to the shape of their substrate. At the pH, the rate of reaction is at an Optimum, so this is the Optimum pH.
  • Inhibitors - slow down rate of reaction of enzyme when necessary there are two main types competitive and non-competitive. Competitive Inhibitorshave a shape similar to substrates, the enzyme cannot tell the difference so the inhibitor competes with the substrate for active site but no product is actually produced. Inhibitors that do not resemble the substrate are called Non-competitive inhibitors and the binds to the enzyme other than at active site this changes the enzyme's active site and prevents access to it.

If any of these factor are extreme, such as high-temperature or low pH the structure of the enzymes active site starts to break down making it dysfunctional making it less complimentary to the substrate, when this occurs the enzyme is said to be denatured.

Temperature for enzymes 

Figure 8-11: The relationship between temperature and enzyme activity,

Mitochondria

The majority of energy releasing reactions occur in mitochondria, the "power houses” of cells. They generate pretty much all of the ATP a cell needs, in addition to the other functions such as the cellular differentiation, signaling and cell death. The most important structural aspect of the mitochondirion (this is the singular) is that it has overlapping membranes, which provide a large surface area for reactions to occur.

Mitochondria 

Figure 8-12: The structure of a mitochondrion.

The key structures of the mitochondria, which you need to know for the PCAT, include:

  • Double membrane - the inside of the mitochondria can be loosely described as a large wrinkled bag packed inside of a smaller, unwrinkled bag. The two membranes create distinct compartments within the organelle, and are themselves very different in structure and in function. The inner membrane folds over many times (cristae). That folding increases the surface area inside the organelle.
  • Outer membrane - is a relatively simple phospholipid bilayer, which allows ATP, ADP, etc. to pass through it with ease.
  • Mitochondrial DNA - strangely enough mitochondria have their own DNA, which they used to replicate independently of the cell.

The ubiquitous ATP

Cells do not use the energy from oxidation reactions as soon as it is released. Instead, they convert it into small, energy-rich molecules such as ATP or nicotinamide adenine dinucleotide (NADH), which can be used throughout the cell to power metabolism and construct new cellular components. In addition, workhorse proteins called enzymes use this chemical energy to catalyze, or accelerate, chemical reactions within the cell that would otherwise proceed very slowly. Enzymes do not force a reaction to proceed if it wouldn't do so without the catalyst; rather, they simply lower the energy barrier required for the reaction to begin.

Squirreling ATP for the winter

When energy is abundant, eukaryotic cells make larger, energy-rich molecules to store their excess energy. The resulting sugars and fats -- in other words, polysaccharides and lipids -- are then held in reservoirs within the cells, some of which are large enough to be visible in electron micrographs. Animal cells can also synthesize branched polymers of glucose known as glycogen.

PCAT Practice Questions

1. Which of the following is the best definition for Transcription:

A. The transfer of genetic material between DNA and RNA

B. The conversion of RNA to a particular protein

C. The creation on DNA

D. The conversion or genetic information between ribosomes and RNA

2. Which of the following vitamins can protect you from scurvy and night blindness?

A. Vitamin A

B. Vitamin B

C. Vitamin C

D. Vitamin K

3. A good source of iron from dietary sources includes which of the following?

A. Carrots

B. Green vegetables

C. Milk

D. Egg plant

4. The basic formula for carbohydrates is which of the following?

A. Cn(H3O)n+1

B. Cm(H2O)n

C. Cn(N3O)n

D. Cn(H3C)n+1

5. How many homologous dress chromosomes are there in a nucleus?

A. 23 homologous pairs

B. 47 homologous pairs

C. 46 homologous pairs

D. 16 homologous pairs

6. Which of the following is a correct definition for a stage in the cell cycle?

A. The S1 phase stands for the standard first stage

B. The G1 phase stands for the first gap phase of the cell cycle.

C. The T1 phase stands for the first gap phase of the cell cycle.

D. The G1 phase stands for the second gap phase of the cell cycle.

7. Which of the following protein structures would you expect to see an alpha helical structure?

A. Primary

B. Secondary

C. Tertiary

D. Quartenary

8. What is the main difference between RNA and DNA?

A. The have very distinct structures

B. RNA contains Deoxyribose instead of just ribos

C. RNA contains Uracil as a base

D. RNA is supported on a sugar-phosphate backbone whereas DNA only contains phosphorous as a back bone.

9. Which of the following is NOT a possible lipid configuration?

A. Liposome

B. Bilayer

C. Micelle

D. Alpha helix

10. The statement "natural, gradual and non-random process of evolution" is the correct explanation of which of the following terms?

A. Mutation

B. Natural Selection

C. Gene Flow

D. Genetic Drift

11. Which of the following is the best term to describe photosynthesis?

A. Hypobolic

B. Hyperbolic

C. Catabolic

D. Anabolic

Answers and Explanation

1. A

Option A is the correct answer here transcription is the transfer of genetic information between DNA and RNA. Option (B), represents translation which is the conversion of RNA to a particular protein, good way to remember that the difference between the two is that transcription you're pretty much just copying the same information however translation you're creating a protein from RNA.

2.C

The answer here is options C, which is actually vitamin C! A deficiency of its Vitamin A (A) any can lead to night blindness of deficiency in vitamin B  be can lead to Beriberi and a deficiency of it and K, option (K)can lead to set a bleeding disorders

3. B

The best option here are green vegetables which is option (B). Milk is a good source of vitamin D and calcium. Eggplants and carrots do have other vitamins that are not very rich in iron.

4. B

Answer here of course is option (B). This is because this is the only option which has a ratio between carbon hydrogen and oxygen molecules of 1:2:1.

5. A

In normal cells (human), there are 46 chromosomes present in 23 homologous pairs of chromosomes. One member of each of these chromosome pairs is derived from the maternal parent and another one is from the paternal parent.

6. B

The G1 phase stands for the first gap phase of the cell cycle, so the correct answer here is (B).

7.B

An alpha helix is quiet a simple structure, however, not as simple as a primary structure protein which just contains a series of interconnected amino acids. The alpha helix is not one of the larger three-dimensional proteins such as tertiary, so the answer must sits in between primary and territory structure, so therefore it is secondary, so option (B) would be the best choice here.

8. C

(A) DNA and RNA have very similar structures to this rules out this option. (B) this option is actually the other way round RNA contains ribose and DNA contains deoxyribose. (D) this statement is incorrect as both DNA and RNA have a sugar phosphate backbone. This only leaves option (c) which shows that RNA contains uracil and DNA does not.

9. D

Option D is a classic protein structure and not a lipid structure.

10.B

The tricky part here in getting the right answer is trying to figure out what the difference between natural selection and genetic drift is. Selection is a gradual natural nonrandom selective process where is genetic drift is a random process of evolution.

11. D

Anabolic reactions create and then store energy, so the best answer here would be (D) photosynthesis. During photosynthesis energy is stored into high energy bonds and saved for later. Conversely, catabolic reactions break down high energy bonds to release energy to power a cell, an example would be cellular respiration where glucose is broken down to release energy.


Last modified: Thursday, 4 July 2013, 03:10 AM
Last modified: Friday, 3 March 2017, 4:38 AM