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Biomolecules · Bioelements and biomolecules

Bioelements and Inorganic Biomolecules

Before you start, make sure you know: The characteristics of living things (Secondary Year 1)
Before you start, make sure you know: The hydrosphere (High School Year 2 (semesters 3 and 4))

When a tortilla burns on the comal, it leaves a black layer and, in the end, some gray ashes. What elements was the part that went off as smoke made of, and which ones make up the ashes? The same thing happens with any living tissue: almost all of it leaves as gases, and only a small mineral portion remains.

Bioelements: primary, secondary, and trace elements

Only about twenty elements of the periodic table are part of living matter. Four of them (C, H, O, and N) alone make up more than 95% of the mass of any living thing.

Three horizontal boxes comparing the abundance of bioelements: the primary box is the widest, the secondary box is intermediate, and the trace-element box is the narrowest. relative abundance in living matter (nonlinear scale) primary: C, H, O, N, P, S (more than 95%) secondary: Ca, Na, K, Cl, Mg 0.1 % a 2 % trace elements: Fe, Zn, Cu, I… less than 0.1% the width of each box does not represent its importance, only its amount (nonlinear scale)

Now let's look at the values for each element. This bar graph shows the approximate abundance of the main bioelements in living matter (for example, the human body).

Horizontal bar graph with the approximate percentage of the mass of living matter for each bioelement: oxygen 65, carbon 18.5, hydrogen 9.5, nitrogen 3.3, calcium 1.5, phosphorus 1, potassium 0.4, sulfur 0.3, sodium 0.2, and chlorine 0.2 percent. approximate percentage of the mass of living matter O 65 % C 18.5 % H 9.5 % N 3.3 % Ca 1.5 % P 1 % K 0.4 % S 0.3 % Na 0.2 % Cl 0.2 % blue: primary · green: secondary

Notice that O, C, H, and N together make up about 96% of the mass. They are the four most abundant, and all are primary.

Go back to the beginning: what goes off as smoke is mostly C, H, O, and N (primary) in the form of gases such as $\mathrm{CO_2}$, water vapor, and nitrogen oxides. The ashes are salts of secondary elements and trace elements.

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Explain the difference between primary bioelements, secondary bioelements and trace elements, and give a specific example of each of the three groups.

Explain the difference between primary bioelements, secondary bioelements and trace elements, and give a specific example of each of the three groups.

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Look at the bar chart showing the abundance of the main bioelements in living matter. State which group of bioelements the four most abundant elements belong to,…

Look at the bar chart showing the abundance of the main bioelements in living matter. State which group of bioelements the four most abundant elements belong to, approximately what percentage of living matter they represent as a whole, and why they are considered essential for forming biomolecules.

O C H N Ca P Fe, Zn, Cu… 62 % 20 % 10 % 3 % 2 % 1 % < 1 % primary secondary trace elements

You can do it on paper and send a photo with your answer.

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The elemental composition (% dry mass) of two unknown samples is analysed in the laboratory: Sample 1: Oxygen 62.4%, Carbon 19.8%, Hydrogen 9.5%, Nitrogen 3.1%, Calcium…

The elemental composition (% dry mass) of two unknown samples is analysed in the laboratory:

  • Sample 1: Oxygen 62.4%, Carbon 19.8%, Hydrogen 9.5%, Nitrogen 3.1%, Calcium 1.4%, Iron 0.005%, Zinc 0.003%.

  • Sample 2: Oxygen 46.6%, Silicon 27.7%, Aluminum 8.1%, Iron 5.0%, Calcium 3.6%, Carbon 0.03%.

  1. a) Reasonably deduce which of the samples comes from living matter and which from the Earth's crust, justifying your choice based on the physicochemical properties of carbon that make it more suitable than silicon for forming biomolecules.
  2. b) From the data of the biological sample, classify its elements into primary, secondary, and trace elements according to their relative abundance.
  3. c) Justify why a trace element like zinc is just as essential for maintaining cellular life as carbon, despite being present in a proportion thousands of times lower.
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Water: a polar molecule held together by hydrogen bonds

Bent water molecule: the oxygen (δ⁻) joined by covalent bonds to two hydrogens (δ⁺) at an angle of about 104.5°; the electric dipole arrow points from the hydrogens toward the oxygen. angle ≈ 104.5° O (δ⁻) H (δ⁺) H (δ⁺) electric dipole from δ⁺ toward δ⁻ (the O) Central water molecule joined by four hydrogen bonds (dashed lines) to four neighboring molecules. Each water molecule can form up to 4 hydrogen bonds O O O O O dashed line: hydrogen bond (between molecules)

Maximum density at 4 °C

Almost all liquids become denser as they cool. Water does not: its maximum density (1.000 g/cm³) is at 4 °C. Why?

  • Above 4 °C, thermal agitation constantly breaks and re-forms hydrogen bonds, and the molecules pack together compactly. As the water cools, they move closer together and the density rises.

  • Below 4 °C, the agitation is already low and the hydrogen bonds stabilize: each molecule tends to end up bonded to four neighbors in an open geometry. The lattice takes up more space and the density drops.

  • At 0 °C the crystal lattice of ice is completed, with hexagonal gaps, and the density falls to 0.917 g/cm³.

That is why, in a lake that is cooling, the coldest water (near 4 °C) sinks and the water near 0 °C stays on top and freezes first. The bottom stays at about 4 °C.

Practice★☆☆Not started
State two functions of water in living organisms that are a direct consequence of its polarity, and briefly explain each of them.

State two functions of water in living organisms that are a direct consequence of its polarity, and briefly explain each of them.

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Unlike almost all liquids, whose density increases continuously as they cool until solidifying, water reaches its maximum density at 4 °C (1.000 g/cm³) and decreases to…

Unlike almost all liquids, whose density increases continuously as they cool until solidifying, water reaches its maximum density at 4 °C (1.000 g/cm³) and decreases to 0.917 g/cm³ when freezing at 0 °C.

  1. a) Explain the molecular cause of this thermal anomaly of water, describing how hydrogen bonds are reorganised in the transition from liquid water to ice.
  2. b) Imagine a hypothetical scenario in which water did not present this anomaly and ice were denser than liquid water. Reasonably predict the thermal and physical evolution that a 20 m deep mountain lake would undergo during a winter with temperatures of -10 °C, and justify how it would affect the survival of benthic and nektonic aquatic organisms.
Solve

Properties of water and their biological functions

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Relate the high specific heat capacity of water to thermoregulation in organisms and give an example showing this function in a specific living organism.

Relate the high specific heat capacity of water to thermoregulation in organisms and give an example showing this function in a specific living organism.

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Mineral salts: dissolved and precipitated

Comparison between dissolved salts, with free Na⁺, K⁺, Cl⁻, and Ca²⁺ ions surrounded by water, and precipitated salts, which form a solid crystal lattice of calcium and phosphate or carbonate ions. dissolved precipitated Na⁺ Cl⁻ K⁺ Ca²⁺ mobile ions in water solid crystal: bone, shell
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A cell accumulates $\text{K}^+$ ions inside itself and maintains $\text{Na}^+$ ions on the outside. Explain what form these mineral salts are in within the cellular…

A cell accumulates $\text{K}^+$ ions inside itself and maintains $\text{Na}^+$ ions on the outside. Explain what form these mineral salts are in within the cellular medium (dissolved or precipitated) and name two functions they can perform.

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The human skeleton contains calcium salts in precipitated form. Name a specific mineral salt that forms it and explain what advantage is gained by it being precipitated…

The human skeleton contains calcium salts in precipitated form. Name a specific mineral salt that forms it and explain what advantage is gained by it being precipitated rather than dissolved.

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In an experimental hydroponic culture, the effect of bioelement deficiency on tomato seedlings is studied. Batch 1 grows in a medium lacking nitrogen and batch 2 in a…

In an experimental hydroponic culture, the effect of bioelement deficiency on tomato seedlings is studied. Batch 1 grows in a medium lacking nitrogen and batch 2 in a medium lacking iron. After two weeks, both batches suffer severe chlorosis and growth arrest. A student claims that the consequences in batch 2 should be insignificant compared to batch 1, arguing that nitrogen accounts for around 3% of the dry mass of the plant (primary bioelement), while iron accounts for less than 0.01% (trace element).

  1. a) Refute the student's argument by explaining the fundamental difference between the biological role of primary bioelements and that of trace elements.
  2. b) Justify at a biochemical level why the deficiency of such a minuscule amount of iron blocks chlorophyll synthesis and photosynthesis with a severity comparable to the lack of nitrogen.
Solve

Buffer systems and pH stability

If you add a little hydrochloric acid to a liter of pure water, the pH drops from 7 to 3. If you add the same amount to blood plasma, the pH hardly changes. How do biological fluids avoid abrupt changes in acidity?

A buffer combines a species able to pick up $\mathrm{H^+}$ (a base) and its protonated form, which can release them (an acid). It cushions changes in pH, but with limited capacity. The bicarbonate system in the extracellular medium and the phosphate system in the intracellular medium stand out.

$$\mathrm{H_2PO_4^-\rightleftharpoons H^++HPO_4^{2-}}$$ A phosphate buffer: when there is an excess of H⁺ the base HPO₄²⁻ picks up a proton and becomes H₂PO₄⁻; if H⁺ is lacking, H₂PO₄⁻ releases a proton and returns to HPO₄²⁻. Excess H⁺: the base picks them up H⁺ + HPO₄²⁻ H₂PO₄⁻ H⁺ lacking: the acid form releases them H₂PO₄⁻ HPO₄²⁻ + H⁺

Summary

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