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Macromolecules and Key Biological Principles

Mollie Hilton
1) This particular sequence has been formed from the DNA strand by the first stage of protein synthesis, transcription. The RNA polymerase enters the nucleus, attaches to the DNA and begins transcription of nucleotides from the TATA box downstream, 5 prime to 3 prime. The polymerase opens and closes the complimentary base pairs of the DNA as it travels, copying codes for a particular protein. This process comes to a stop when it reaches the termination signal and the RNA polymerase pulls away from the DNA. With uracil bonded to adenine instead of thymine, the copied strand of nucleotides results with the creation of mRNA. The mRNA strand is then sealed and protected at both ends, 5 prime by the 5 prime cap and the 3 prime by the poly-a tail. The mRNA package then travels through the nuclear pores into the cytoplasm where translation takes place.
2) The second stage to protein synthesis is called translation and this is where the ribosomes connects and threads through the mRNA strand. The ribosomes read through fragments of three mRNA bases at a time which equals to one codon to make the process easier to read. The ribosome then selects the correct complimentary base pair tRNA anticodon sequence to match the mRNA codon. When this process occurs with the two nucleic acids connecting, this produces an amino acid. The amino acid produced is then added on to the next tRNA along that has just connected to the mRNA. A sequence of amino acids is formed and all connected by peptide bonds, which when complete, the chain is signalled to stop and the particular protein is complete. The rRNA inside the ribosomes contain no genetic information but provides a binding site for the construction of proteins.
Part 1:
In 1890 Austrian Monk Gregor Mendel experimented on pea plants to discover a new theory on inheritance. He began by conducting monohybrid cross on two different pure parental lined pea plant flowers, one red and one white. He discovered that the first generation (F1) of plants showed heterozygous dominant alleles on all the flowers, because the dominant gene always shows. (See punnet square)
F1
(Parent Red flower) PP X pp (Parent White flower)
Red flower
PP
Pp
Pp
Pp
Pp
p
White flower
p
The second generation (F2) exposed a 3:1 ratio of allele’s recessive traits as the first generation was heterozygous, holding one dominant and one recessive trait therefore resulting in all dominant alleles. Mendel discovered this as he let the F1 plants self-fertilise resulting in a 25% chance of one allele to show the recessive trait (see Punnett square)
F2
(Red flower) Ff X Ff (Red flower)
F f
FF
Ff
Ff
ff
F
f
The first law of Mendel’s theory is ‘The Law of Segregation’ and states that each parents alleles split during meiosis and one trait from each parent is passed down to the next generation. The particular genes passed during this process happens randomly.
Mendel’s second law ‘The Law of Independent Assortment’ states that there are many genes but all alleles are separate and unconnected for example eye and hair colour. Alleles are passed down generations but are independent and not direct of one another. This was founded when Mendel dihybrid crosses of the pea plant resulting in 9:3:3:1 ratio of genotypes.
Part 2:
When performing a monohybrid cross with a heterozygous tongue roller (Rr) and a homozygous recessive non tongue roller (rr) the alleles of each parent go through meiosis producing a child or multiple children. The outcome would result in creating a 50% chance of the offspring inheriting the tongue rolling trait. If the parents had four children the chance of half of them receiving the tongue rolling gene would be 50%, therefore inheriting the mutant alleles. The non-tongue rolling gene would also be 50% but receiving the homozygous recessive trait. This is demonstrated in the Punnett square below.
Heterozygous Tongue Roller
R r
Rr
rr
Rr
rr
r
Homozygous Non
Tongue Roller
r
Part 3:
When conducting a monohybrid cross with the chemical Phenylthiocarbamate on two heterozygous parents the results will show that there is a 50% chance of the offspring also be heterozygous dominant and 50% being homozygous, half of which dominant and the other recessive making all phenotypes possible. With the children created from these heterozygous parents the percentage of them obtaining the dominant Phenylthiocarbmate chemical would be 75% and the remaining 25% would be homozygous recessive. If the parents had four children the chance of them having the dominant gene would be a ratio of 3:1, resulting in three phenotype children and one complete recessive allele. (See Punnett square)
Parent 1 – Pp X Pp – Parent 2
PP
Pp
Pp
pp
Pp
P
p
Part 4:
A man who is a heterozygous tongue roller and a heterozygous PTC taster and woman being both a homozygous tongue roller and a non PTC taster had 16 children the outcome would prove that 100% of the children would be tongue rollers due to both parents having dominant tongue rolling traits. Although 50% of the tongue rolling children would be heterozygous, matching their farther. The amount of children that will taste the PTC will be 50% as half prove to be homozygous and the other half heterozygous. This results in all the children obtaining the tongue rolling traits and 50% of them not being able to taste the chemical Phenylthiocarbamate. (See Punnett squares below)
Woman: Homozygous Tongue Roller
T
T
T
T T
T T
t
T t
T t
Man: Heterozygous
Tongue Roller
Woman: No PTC taster
p
p
P
P p
P p
p
p p
p p
Man: Heterozygous PTC
Taster
As the results show:
Genotypes
Phenotypes
TTPp/TTPp/ TTPp/TTPp/
TtPp/TtPp/ TtPp/TtPp
Tongue roller and PTC taster
TTpp/TTpp/ TTpp/TTpp
Ttpp/Ttpp/ Ttpp/Ttpp
Tongue roller and non PTC taster

Lipids
Carbohydrates
Proteins
Chemical Structures
Lipids involve carbon, hydrogen and oxygen. Triglycerides are glycerol and three chains of fatty acids, one at either end and one in the middle. Phospholipids has a similar structure but removing one fatty acid chain from the glycerol and replacing it with a phosphate group, creating a polar and a non-polar end. Steroids structure involves three cyclohexane interlinked, attached to one cyclopentane.
Carbohydrates are carbon, hydrogen and oxygen. Monosaccharides is the most simple and can contain 3 to 10 carbon atoms depending on the type. Disaccharides compose of two monosaccharides connected by a glycosidic bond through a condensation reaction. Polysaccharides are chains of many saccharides on a larger scale linked together.
Amino acids are the backbone of proteins. Primary structure creates the correct sequence of polypeptides for a specific protein, linking amino acids from the carboxylic group of one to the amino group of the next. The secondary structure bends and twists the polypeptides with hydrogen bonds stabilising a formation, helix or beta pleated. The tertiary structure is when the chains take to 3D shapes. The quaternary structure comprises of more than one polypeptide chain bonding and creating a complete protein.
Roles in nature
The body stores fatty acids creating adipose tissue for energy and insulation. ‘The body does not have the potential to store excess glucose, beyond this amount, in a form that is recoverable as glucose. Any excess glucose that is not immediately metabolized, or converted to glycogen, is turned (irreversibly) into fatty acid for storage’ (Atti, P, 2012). Phospholipids have polar heads and non-polar tails to help create a barrier controlling molecules. Cholesterol is the precursor to hormonal developments such as estrogen and testosterone.
Carbohydrates create energy and storage for all living organisms, cell to cell interaction and structure. Photosynthesis produces the monosaccharide glucose for food, and also creates the polysaccharide cellulose which give the plant stability. Polysaccharides are used mainly store energy. ‘In animals, glycogen is stored inside the liver and it released when the amount of glucose in the blood circulation is too low.’ (D’Onofrio, A, 2015).
Proteins are complex and function having specific codes for particular roles within the body, from movement in muscles to transporting molecules inside and outside of a cell. ‘Muscles are composed of two major protein filaments: a thick filament composed of the protein myosin and a thin filament composed of the protein actin. Muscle contraction occurs when these filaments slide over one another in a series of repetitive events.’(Chin, G, 2015). Enzymes break down foods with saliva, support structures with collagen, send signals to the immune system, and help regulate insulin levels. Proteins are very important and are involved in basically every function within the body. ‘Proteins are worker molecules that are necessary for virtually every activity in your body. They circulate in your blood, seep from your tissues, and grow in long strands out of your head.’ (National Institute of General Medical Sciences, 2011).
Enzymes are specific to each individual substrate group. An enzyme substrate complex is created when a specific substrate binds with a particular enzyme either by lock and key method or by an induced fit. Tertiary and quaternary are the structures of the active site providing its form and is lined with amino acids providing the exact chemical reaction process needed but extremely concentrated therefore speeding up a biological catalysts reaction. A metabolism comprises of all the chemical reactions within the body creating energy, and without this speed and catalytic power that requires less energy due to the faster reactions, organisms and body would not function at all. ‘Build-up of new tissue, replacement of old tissue, conversion of food to energy, disposal of waste materials, reproduction – all the activities that we characterize as “life.” (Worthington Biochemical Corporation, 2015)
The enzyme combines two chemical substrates creating an anabolic reaction, releasing a different chemical substrate. The enzyme substrate complex can also perform a catabolic reaction creating two separate chemical energy’s by breaking down one. The complex then breaks down the substrate to simpler chemicals called energy conversation which is essential within all organisms for the metabolism to work. Enzymes can deform by not working in optimum temperature or PH balance that is specific to them causing enzymes to denature. ‘Therefore, when the metabolism slows down, people often develop dry skin, unhealthy nails, dry hair, hair loss, irritability, poor recall, fluid retention, decreased sex drive, and up to 60 other puzzling and, until now, baffling symptoms. This is the body’s way of insuring that depleted energy reserves are used to maintain the most important functions, such as vision, hearing, heart function, breathing, and all the other bodily functions necessary for survival.’ (Wilson, D, 2015). If enzymes denature, change shape or deform slightly, they can be inhabited by being embedded with a non-competitor, damaging the active site but not inhabiting it. This can alter and distort the active site of the enzyme and is receptacle to competitive and uncompetitive inhibition causing a block. When competitive inhibition takes place the inhibitor bonds to the active site and can remain until the enzyme can be relieved of the obstruction, due to the increase of the substrate concentration competing for the active site.
The two major pathways involved in producing energy within a cell is aerobic involving glucose and oxygen generating carbon dioxide, water and energy, and anaerobic respiration, glucose producing lactic acid. Both types of respirations are needed for the body to use chemical energy for growth and sustainment of the lifecycle. When chemical energy is released by ATP it becomes ADP as it loses a phosphate group, but, for a cell to survive it needs to produce energy and maintain a constant phosphorylation. Chemical energy is produced within the mitochondria’s cytoplasm at the first stage, glycolysis. Anaerobic respiration begins when glucose enters the cell, an enzyme moves a phosphate group from an ATP. A divide creates two 3-carbon sugar phosphates, with hydrogen removed by NAD and the ADP removing two phosphates, resulting in 2 ATP and two 3-carbon pyruvate molecules per separation. The pyruvic acid produced with anaerobic respiration causes lactic acid usually in the muscles as the co-enzyme, NADH provides a hydrogen compound. The lactic acid is the result of the chemical reaction by the body if not enough oxygen has been produced. ‘When you do vigorous exercise and your body can not supply enough oxygen to your muscles, they start doing anaerobic respiration. Glucose is converted to energy and lactic acid.’ (The King’s School, Worcester, 2015).
Aerobic respiration continues to the Krebs cycle which takes place in the matrix of the mitochondria where the pyruvic acid take on some chemical changes and eventually converts in to a citric acid. A number of chemical reactions take place resulting in producing NADH and FADH2 that enter into the final stage of respiration, oxidative phosphorylation. The phosphorylation process of ADP to ATP occurs when the electron transport chain splits the molecules by removing the hydrogen. This produces an H electron that continues along the chain, producing energy to push the H ions that remain in the matrix to the intermembrane space. This accumulates a concentration of the H ions which eventually move back into the mitochondria. The cellular respiration cycle of each ATP is repeated up to 300 times a day producing a maintained production of energy supplied initially by glucose and oxygen.
Bibliography
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Chin, G. (2015). Muscle Contraction: Actin and Myosin Bonding. Available: http://education-portal.com/academy/lesson/muscle-contraction-actin-and-myocin-bonding.html. Last accessed 11th Feb 2015.
D’Onofrio, A. (2015). Macromolecules of Life. Available: http://www.biology101.org/biologystudyguides/buildingblocksoflife.php. Last accessed 11th Feb 2015.
National Institute of General Medical Sciences. (2011). The Structures of Life. Available: http://publications.nigms.nih.gov/structlife/chapter1.html. Last accessed 11th Feb 2015.
The King’s School, Worcester. (2015). EFFECT OF EXERCISE. Available: http://www.ksw.org.uk/senior-school-resources/biology/fifth-form/effect-of-exercise. Last accessed 11th Feb 2015.
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Worthington Biochemical Corporation. (2015). Enzymes and Life Processes. Available: http://www.worthington-biochem.com/introbiochem/lifeProcesses.html. Last accessed 11th Feb 2015.
References
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CrashCourse. (2012). DNA, Hot Pockets,

Auxin Gravitropism Effect on Root Growth

To investigate how the Auxin gravitropism affects the growth of roots and shoots in seedlings.
Hypothesis:
If gravity affects the direction of growth in seedlings, then the roots will grow towards the direction that gravity is pulling them, and the shoots will grow in the opposite direction of gravity.
Introduction: Hormones are one of the bodies many and greatest communication systems. Hormone molecules can be released by any of about a dozen glands in the human body. Once released, the molecules travel through the bloodstream until they find a receptor cell that it recognizes. The molecule enters the receptor cell and ‘tells’ the cell to undergo a certain action. Plants hormones basically work the same way, but travel through the xylem and phloem because plants do not have blood streams. Hormones are involved in many biological processes such as growth, reproduction, and immune function.
Plants and animals both have hormones inside of them to help regulate biological processes such as growth. There are 5 groups of plant hormones: Auxins, Gibberellins, Cytokinins, Ethylene, and Abscisic Acid. Auxins are responsible for stimulating cell division and cell elongation in stems and roots. Auxins also aid in the ripening and dropping of food, as well as cell growth in response to gravity and light.
Gibberellins are responsible for activating stimulating cell division and preventing the ageing of leaves
Cytokinins also stimulate cell division, and also stimulate the germination of seeds.
Ethylenes affect the sweetness of fruit, as well as the texture and colour. It also promotes the ripening of the fruit.
Finally, Abscisic Acid can stop shoot growth, and induce aswell as maintain seed dormancy. Finally, this group of hormones promotes stomata closings, in order to overcome situations where water levels are very low.
The effects of hormones on plants are numerous. Hormones can put seeds into dormant states until the environment is well enough for the seed to grow, hormones ‘tell’ a fruit tree how and when to ripen their fruit, and then when to drop it. In this investigation, we will discuss how the hormone gravitropism affects the growth of shoots and roots in seedlings. This hormone causes roots to grow towards gravity because the roots have a high concentration of gravitropism inside of them. This hormone does not affect the stems as much because less gravitropism is found in them. This is why shoots and stems grow upwards while roots always grow downwards.
Another important hormone is phototropism. It is the hormone responsible for a plant bending towards sunlight. The side of a plant that is in shade has an increased Auxin concentration, resulting in the cells elongating which causes the plant to bend towards the light.
Hormones are very important because, as stated above they are the body’s greatest communication system. Hormones tell the different parts of the body how to function and when to change functions. This is important for all living things, so that all cells know what to do in order for the organism to live, grow and prosper. This is why hormones are so important.
Discussion: In What Direction did the Majority of the Roots and Stems Grow Once the Corn Kernels (Saplings) Germinated?
The initial upward direction was at 12, and the initial downward direction was 6. Once the seedlings germinated the majority of roots generally grew towards 6 which was downward and towards gravity, and the majority of shoots generally grew towards 12 which was upwards and against gravity.
After rotating the Petri dish, which way did the roots and stems grow? Did they change direction? If yes, then what was their new direction?
After rotating the petri dish on the fourth day, using 3 as the new upwards direction, the direction of root and shoot growth did change. The majority of roots began to clearly grow towards 9 which was the new downward direction. In addition, the majority of the shoots clearly began to grow towards 3 which was the new upwards direction.
Why was it important to place the seeds in a circle?
It was important to place the seeds in a circle so that we could number each seed position like the numbers on a clock. This allowed us to rotate the petri dish and have clearly defined points where up and down were so that we could observe how and if gravitropism affected the shoot and root growth. The numbering system also helped in the observations because it made it possible for the numbers to be used as defined growth directions
a) What is Gravitropism?
Auxin’s are plant hormones which affect cell division and elongation in stems and roots. Auxins also regulate cell expansion in plants responses to light and gravity. Finally, Auxins help in the ripening and dropping of roots. Gravitropism is a type of Auxin. It affects the growth or turning of a plant in regards to the external factor of gravity.
Do roots show a positive or negative Gravitropism? Explain your answer.
Roots show positive gravitropism, which means they always grow towards the pull of gravity. This is observed in all plants, their roots always grow towards the pull of gravity and never away from it. This is necessary so that the roots grow In the soil which is where the roots can uptake nutrients for the plants survival.
Do stems show a positive or negative Gravitropism? Explain your answer.
Stems show negative gravitropism, they grow away from the pull of gravity. This is also observed in all plants and is necessary because the leaves which grow from the shoots need sunlight to undergo photosynthesis which is necessary in a plants survival. Sunlight is only available above ground level, which is why the shoots grow upwards.
Scientists are very interested in how plants will grow in space. Explain why it would be important to know this.
It would be important to know how plant would grow in space so that we could possible use plants as a source of oxygen or as a source of food on a spaceship, space station, or any other enclosed area in space where there would be a need for oxygen and food. Scientists first need to discover how the many hormones in plants are adjusted to the environmental factors on earth. Gravity is a large factor in this case because the force of gravity on Earth is very high compared to that of space. Through this lab, scientists now know that the lack of gravity in space will result in the shoots and roots growing randomly for the most part. This may result in some plants growing no roots in the soil or no shoots above the ground so that no nutrients can be taken up and no photosynthesis can take place.
Sources of Error: A source of error that was identified during this lab was that the petri dishes were not big enough to let the roots grow naturally towards a direction. Once a seed got too long, it would start curling up on the side of the petri dish, and once this occurred the direction could not change easily. This caused some error because some roots were stuck in one position for most of the lab. A way to fix this error would be to use a larger petri dish. If the diameter increased by about 6 Cm the roots and shoots would mostly have as much space as they need.
Conclusion: The hypothesis stated that if gravity affected the direction of growth in seedlings, then the roots would grow towards the direction that gravity was pulling them, and the shoots would grow in the opposite direction of gravity. The observations showed that the root and shoot growth was partially affected by gravity, based on the short observation length, and the tendency of the roots to curl up around the edges of the petri dish
Therefore, the hypothesis was accepted.

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