Topic 2. Molecular Biology

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2.1 Molecules to metabolism

Lesson one : Introduction to molecular biology

Objectives:

Keywords:

  • metabolism: the sum total of all reactions happening in cells, involving enzymes.
  • molecule: a particle made from more than one atom, covalently bonded together
  • anabolism: synthesis of complex molecules from simple molecules eg. joining together monomers to form macromolecules by condensation reactions.
  • condensation reaction: a reaction that removes water to form a bond
  • monomer: a small molecule, that can be joined together to form a macromolecule
  • catabolism: the breakdown of complex molecules into simpler molecules eg. hydrolysis of macromolecules into monomers.
  • hydrolysis: a reaction that adds water to break a bond
  • Organic molecule: based on carbon and found in cells, e.g.. lipid, carbohydrate, protein, nucleic acid

Activator: Can you think of any molecules in the movie ‘Superhealth’ me that were discussed by Morgan Spurlocks doctors? How do you think they might be classified, as lipids, carbohydrates, protein, or nucleic acids?

Biochemistry is based on the element carbon. Carbon is unique because an atom of carbon can form four covalent bonds with other atoms. This allows it to become an effective building block for macromolecules.

Screen Shot 2017-11-06 at 08.58.00

 

 

Building and breaking down organic molecules (anabolic and catabolic reactions)

Anabolic reactions happen when we grow. Building proteins is an essential part of making you taller, building muscles, growing hair, etc. Effectively what happens when you build a protein is that monomers called amino acids are joined together to form a macromolecule called protein. This happens through a condensation reaction, where water is removed and a bond is formed in the place of where the OH and the H groups were that made water.

Catabolic reactions happen when we digest food. Breaking down molecules is also important in detoxification, and recycling. Effectively what happens when you break down macromolecules, is water is added to the molecule where the bond occurs, dividing the macromolecule into monomers. This kind of breakdown adding water, is hydrolysis.

It is worth adding that both anabolic and catabolic reactions rely on enzymes. For example the enzyme pepsin catalyses the digestion of proteins into amino acids.

Figure: A dipeptide being formed and broken down from two amino acids.

image credit bbc

image credit bbc

 

Task: Make a table of monomers and polymers for the following: Proteins, Starch, Glycogen, Cellulose. 

 Introduction to the main organic molecules:

Proteins – used for structural purposes. Also a wide variety of uses including enzymes, hormones, toxins

Carbohydrates – energy storage, and also structure in plants in the case of cellulose

Lipds – energy storage, insulation, protection

Nucleic acids – Short term energy storage (ATP), controlling the functions and characteristics of life i.e. DNA

 Lesson two: Drawing Organic Molecules:

objectives: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid.

Key skills:

  • Numbering carbohydrate rings. This is done by numbering the carbon after the oxygen as carbon 1, and then continuing in a clockwise direction
  • Showing the carbon backbone as lines. This is done by using a corner to represent a carbon atom. This avoids showing all of the atoms which are there, and is represents a conventional shortcut amongst biochemists.

 

https://www.educreations.com/lesson/embed/34659618/?s=YtbLrD&ref=app

 

Drawing Triglycerides

Structure of a Triglyceride: A complete triglyceride structure consists of three fatty acid chains, joined through a 3-carbon molecule called glycerol. Glycerol on its own, is a component of skin moisturisers, low-fat deserts, shampoo and the liquid in the new electronic cigarette.

A generalised triglyceride structure looks like this:

Triglyceride

The difference between milk fat, and almond oil, is determined by the length and number of double bonds in the three fatty acid chains. The glycerol remains the same. A slightly more detailed look at the same molecule would be:

triglyceride detailed

 

This time you can see the actual atoms of carbon, hydrogen, and oxygen that make up this example of a triglyceride. You can see that the bonds between the molecule glycerol, and the three fatty acids are formed by the elimination of water. This is a common theme in organic chemistry.

Recognising organic molecules. You need to be able to recognise the following basic types of organic molecules:

  • Single and double sugars
  • Complex carbohydrates (like starch)
  • Amino acids
  • Triglycerides

 

 

 

 

 

2.2 Water.

Lesson One – the properties of water

Water is not an organic molecule. It is arguably the most important compound for life on Earth. We are going to look at why water is so useful: as a component of cells and body systems, and as an abiotic component of a habitat.

Key vocabulary:

Polarity: having a negative or / and a positive charge.

Adhesion: Forces which allow water to ‘stick’ to surfaces

Cohesion: Forces which allow water to ‘stick’ to each other

Latent heat of vaporisation of water: the energy required to make water evaporate

Specific heat capacity of water: the energy required to make water increase in temperature

Solvent: a substance which allows solutes to dissolve in it (solutes eg. sugar, dissolve in solvents)

The slides in the powerpoint below will be used in the lesson

Task: Download and fill in the table on water properties (click)

Task one- The Properties of water

 

Lesson two: Water lab

Objectives: practice paper three style questions. Learn how to estimate osmolarity (and therefore osmotic potential). Interpret a graph of osmolarity.

Instructions (click below)

Potato Osmolarity Lab

 

Lesson three: Food analysis lab (McDonald’s experiment)

 

In order to prepare for this lab it is recommended you watch this video, showing the lab standard food tests.

 

 

 

Hand-out for lab Paper 3 Practice McDonalds lab

Paper 3 practice McDonalds lab

 

2.3 Metabolising carbohydrates and lipids

Carbohydrates and lipids are both sources of energy that the body uses. Your body will rely on both as a source of energy.

What is the difference?

Complex carbohydrates eg. glycogen. Can be broken down relatively rapidly to form single sugars, like glucose. They store less energy per gram than lipids. Glycogen, the human carbohydrate used for energy storage, requires water to help store it, which makes it less efficient as an energy store per weight. In summary, they are a good short-term energy store.

Lipids, eg. cholesterol and triglycerides. Cannot be mobilised rapidly, it takes time to break them down. They store far more energy per gram than carbohydrates (about 6 times more). They do not require water to help store them, which makes them more efficient as an energy store per weight. In summary, they are a good long-term energy store.

AND unlike complex carbohydrates, in humans they also have secondary uses:

– thermal insulation in the sub-cutaneous adipose tissue (fatty tissue underneath skin keeps us warm).

-Shock absorption for major organs (all of our major organs have a layer of fat to protect them)

-Waterproofing and conditioning (sebum, natural oil found on human skin and in human hair).

Breaking down and Building carbohydrates and lipids

In order to get the energy from complex carbohydrates and lipids, we need to break them down. In order to store the extra energy in our food, we need to build them.

1) Anabolic reactions – build, remove water.   2) Catabolic reactions – destroy, add water.

Both types of reactions depend on enzymes to help them work faster (catabolic reactions rely on digestive enzymes, eg. amylase, which breaks down amylose (a kind of starch), into maltose ( a double sugar).

 

Lipids diary: Analysis

http://www.mydailyintake.net/energy/ 

 

2.3 Optional  Project: ‘ Superhealth Me’

2.4 Proteins

Proteins are polymers made from the sub-units amino acids, joined together to make polypeptides chains. The name ‘polypeptide’ comes from the individual bonds between amino acids, which are called ‘peptide bonds’. One protein may be made from more than one polypeptide chain linked together.

 Haemoglobin molecule – made from 4 polypeptide chains.

image credit biotutotorial.com

image credit tutotorialpoint.com

 

A peptide bond

Peptide bonds are formed by condensation (the elimination of water), and broken by hydrolysis (the addition of water).

peptide bond

image credit boundless.com

 

Amino acids – the mystery and wonder

http://www.nasa.gov/topics/solarsystem/features/left_hand_aminoacids.html read this fascinating article

  • Amino acids have been found on asteroids, sampled in outer space according to NASA scientists.

Q) What could be the possible explanation for this phenomenum? 

  • Its possible for any amino acid to appear in two forms, a left-handed and a right-handed version. For some reason, all of the amino acids on Earth are left-handed.

Q) Is this evidence for the common ancestry of all life on Earth? If aliens life-forms exist, could their proteins be based on right-handed amino acids?

image credit: NASA

image credit: NASA

 

  • Scientists can make amino acids!

 

  • ‘In 1952, US scientist Stanley Miller  conducted one of the most famous experiments in all of science. They repeatedly sent electric sparks through flasks filled with the gases thought to resemble Earth’s early atmosphere, including water vapor, hydrogen, methane, and ammonia. After 1 week of zapping the mixture, they found organic compounds including amino acids in the mixture.

read more:

http://www.sciencemag.org/news/2011/03/long-neglected-experiment-gives-new-clues-origin-life

image credit: science mag.org

image credit: science mag.org

Q) Is this the same as creating life in a laboratory? How is it different?

Essential and non-essential amino acids

There are twenty amino acids, from which all of all of the proteins on the Earth are formed. Ten are essential, meaning we have to have them in our diet. Ten are non-essential, meaning we can synthesise them in our body from essential ones. The process of changing an essential amino acid into a non-essential amino acid is called transamination

This explains why vegetarians have to eat certain foods, like nuts, to get the essential amino acids that their metabolism requires.

 

image credit ptinterest.com

image credit ptinterest.com

 

Essential and non-essential amino acids

image credit compoun.chem.com

image credit compoun.chem.com

 

 

Proteome

Because all of us have differences in our sequence of DNA (with the possible exception of identical twins), every individual has a unique combination of proteins.

All the proteins produced by a cell, tissue or an organism is called the proteome.

by contrast, all the genes of a cell, tissue or an organism is called the genome.

 

Q). How would you study a proteome? Using gel electrophoresis, in the same way that you would analyse a genome.

Watch this khan academy video for a good introduction to the technique of gel electrophoresis. Take some personal notes on the process of gel electrophoresis.

Suggestions:

Q) What is gel electrophoresis

Q) How does it work?

Q) What is it for?

remember the story of the discovery of cyclins (cell division) by Tim Hunt? He was looking at the proteome of sea urchin eggs when he made his big discovery.

Denaturation: Why can proteins be ‘cooked?’

Raw salmon vs. Cookes salmon – both tasty, but what’s the difference?

image credit: sansaire.com

image credit: sansaire.com

Proteins have a complex, three dimensional structure which is stabilised by bonds between the R groups of amino acids within the molecule. Most of these bonds are easily broken by heat, or extremes of pH. These results in a breakdown of this three-dimensional structure, or change in the ‘conformation’.

We call this change in conformation ‘denaturation’. Denaturation is permanent, a protein will not return to its proper shape if allowed to cool down! If it can be restored to its original structure, which is rare – this is called ‘renaturation’.

image credit: memegenerator.net

image credit: memegenerator.net

how to flirt with a biochemist! – use at own risk.

Cooking an egg.

Albumen is the main protein found in egg white. The structure is globular (like a ball or globe), and like other proteins with this general shape, it is soluble in water and hence can be mixed with milk and used for baking recipes.

Once cooked, the globular structure breaks down, and a new structure forms which is much less dense. What is interesting is that new bonds called sulphur bridges form, linking all the albumen molecules into a continuous sheet. Sulphur bridges occur between amino acids that contain sulphur eg. methionine and cysteine. The SH refers to Sulphur hydryl groups, which are oxidised to make the S-S sulphur bridges in the process of denaturation.

image credit thinglink.com

image credit thinglink.com

 

Revision summary and links to next topics: Enzymes, transcription and translation

2.5 ENZYMES

Lesson one: Altering the rate at which enzymes work

Keywords:

  • Substrate: the substance being acted on by an enzyme
  • Active site: the part of the enzyme molecule that binds with an enzyme
  • Enzyme activity: the measure of how fast an enzyme is working
  • Enzyme-substrate complex: the combination of an enzyme and a substrate, bound by the active site
  • Inhibition: when a substance interferes with the formation of an enzyme substrate complex (eg. cyanide as a poison inhibits key enzymes in respiration)
  • Concentration: number of particles (Mols) of a substance per litre of solute.

 

Enzymes are globular proteins that work as catalysts.

Globular means, they are literally shaped like a ball. The molecule will have hydrophilic groups around the outside of the molecule, in order to be soluble – as water is the medium for metabolic reactions. A catalyst is a substance that speeds up the rate of a chemical reaction, without being altered itself. An enzyme molecule can therefore be reused as often as is needed.

As enzymes are proteins, they can also be denatured by heat of extremes of pH.

image credit: sally buy

 

Common enzymes:

1) Catalase – Occurs in a huge variety of cells, breaks down toxic by-product of respiration hydrogen peroxide into harmless water and oxygen.

2) Amylase – Breaks down starch (amylose), into maltose (a disaccharide) in the mouth and in the pancreas.

3) Rubisco (ribulose biphosphate carboxylase) – an enzyme involved in photosynthesis, and probably the most common protein on the planet.

The ‘lock and key’ mechanism

Each enzyme has a part of its molecule called an ‘active site’, which binds to the molecule it is working on, the ‘substrate’.

image credit: wikipedia.org

image credit: wikipedia.org

 

Enzymes are ‘specific’, in that only one particular substrate ‘fit’ into the active site.

 http://highered.mheducation.com/sites/0072943696/student_view0/chapter2/animation__how_enzymes_work.html

 Factors affecting enzyme activity

The rate at which an enzyme works is called ‘enzyme activity’.

Enzyme activity is affected by:

  • temperature
  • pH
  • substrate concentration

Temperature: As temperature increases, there are more collisions between faster moving enzyme and substrate molecules – making enzyme activity faster. Denaturation starts to occur, and after an optimum temperature (for human enzymes usually 40 C), the activity decreases sharply as the enzyme is denatured.

 

 

image credit: revisionworld

image credit: revisionworld

 

pH: At a low or a high pH, enzyme activity is low. Enzymes can even be denatured by extreme pH values. Enzyme activity rises to an optimum pH ( for human enzymes usually 7) in the middle. The digestive system enzymes have varying optimum pH values.

 

 

 

image credit: study.com

image credit: study.com

 

Substrate concentration: Enzyme activity increases when there is more substrate available, until a point when all the active sites are occupied (saturation point). After this further increases in substrate concentration will have no effect on enzyme activity.

sites: sachina.org

sites: sachina.org

 

Watch the video, and make a list of all the commercial uses of enzymes that you remember:

Q) What is meant by the term ‘immobilised enzymes?’

 

Immobilised enzymes are enzymes that have been ‘fixed’ to a solid media eg. glass beads. This means that they are not added to the solutions, but the reaction mix is passed through the media containing the enzyme.

Immobilised enzymes being used to create lactose-free milk

Discuss: What are the advantages of using immobilised enzymes?

image credit bpi schools

image credit bpi schools

 

The

 

 

 

 

 

 

 

Advantages:

  • Enzyme can be separated easily from the products of the reaction, stopping the reaction at an ideal time and preventing contamination of the final product with left-over enzyme
  • Enzyme can be used again and again (recycled)
  • Enzymes are less likely to be denatured if they are immobilised.
  • It is possible to use higher enzyme concentrations, speeding up reaction rates.

 

2.6 The structure of DNA

DNA is made from the sub-units nucleotides. One nucleotide consists of a ribose sugar (pentose), a phosphate group, and a nitrogenous base.

To join the nucleotides together into a chain, strong covalent bonds are formed between the phosphate and ribose of adjacent nucleotides.

image credit: mrothery.co.uk

image credit: mrothery.co.uk

Skill: Draw a nucleotide, showing the detail of the carbon atoms in the ribose, and the phosphate group.

Skill: Identify the 3′ and the 5′ end of a nucleotide, based on what you know of the numbering system for carbon atoms in a sugar. Be able to identify the 3′ and 5′ end of a chain of nucleotides.

Assembling a DNA molecule:

There are four nitrogenous bases found in DNA:

  • Adenine (A)
  • Guanine (G)
  • Thymine (T)
  • Cytosine (C)

These bases are paired in DNA structure, according to the following base pair rules:

1) A-T

2) G-C

Weak hydrogen bonds form between the nitrogenous bases, assembling an anti-parallel double helix.

DNA_Structure

The above molecule is twisted to form a double helix:

DNA_helix 2

 

2.7 DNA replication, transcription and translation

 

DNA replication means doubling the DNA content of a cell, by making DNA molecules out of every DNA molecule present.

DNA replication is semi-conservative; this means that the new DNA molecules each contain 50% of the original DNA, that is – one of the original strands. The new DNA molecules each have one of the original DNA strands, and a new strand that has been synthesized from free nucleotides in the cytoplasm.

Mechanism in detail:

-DNA unwinds and separates into two separate strands (unzips). This means that the hydrogen bonds are broken in between the base pairs.

-The enzyme helicase helps to separate the two strands, and requires ATP to break the bonds.

-Each of the separated original strands serves as a template for building new strands.

-The new strands are formed by joining free nucleotides one by one, that are complimentary to the original strand sequence.

-The enzyme DNA polymerase functions by joining nucleotides to the new strand. By joining the nucleotides one by one, fewer mistakes are made. The enzyme always joins nucleotides in the 5′-3′ direction.

 

This first animation shows very neatly how DNA is coiled into chromosomes. The second part shows DNA replication, but at a level needed only for higher level. Watch it, focusing not on the names of the enzymes, but only on the process of forming the new strands. Watch how joining to the 3′ end causes a problem in one of the new strands. 

 

This video shows the same process – DNA replication at the HL Biology, but the explanation is clearer. It doesn’t hurt to get a head start by taking  a look at it now. The main points for SL biology are:

-DNA polymerase builds the new strands

-The enzyme only works in 5′ to 3′ direction. This causes an interesting problem with one of the new strands.

 

 Meselson and Stahl’s famous experiment

Meselson and Stal provided the evidence in 1958 which led the widespread acceptance of the theory of semi-conservative replication. They used isotopes of nitrogen (N-15) to create special heavy nucleotides.

Because the new strands use the nucleotides from the cytoplasm, the double stranded molecule could only build the new strands from the heavier N15 nucleotides.

This meant that the new strands were half light N-14, and half heavy N-15. Their weights were above the weight of the original DNA made with N-14.

They measured the weights using centrifugation (a spinning test tube). The heavier the DNA is, the more it moves down the test tube and forms a band lower down.

Original        B              C             What they found

dnad

 

Thinking exercise: If they had got results B, or C, what would that have meant about how DNA is replicated?

Key word: Conservative : Both original strands are maintained

Idea: Is there another explanation for the results? Some scientists believed the DNA could be 50% mixed, but within the same strands. This is called dispersive, by allowing the DNA replication to happen for one more cycle, Meselson and Stahl showed that this is not the case.

Follow the link to review DNA replication:

https://www.youtube.com/watch?v=7u05FsiUYdU

  Transcription and Translation

 

Transcription means the synthesis of an MRNA copied from the  DNA base sequence by RNA polymerase

Transcription takes place in the nucleus:

  1.  DNA strands unwind, separating into two strands, the anti-sense, and the sense strand. RNA polymerase will bind to the anti-sense strand
  2.  RNA polymerase moves along the anti-sense strand, adding complimentary nucleotides one at a time to form MRNA, in the direction of 5′ to 3′ of the mRNA strand.
  3.  Transcription will end when the end of the gene is reached. The two DNA strands reform the double helix
  4.  The mRNA molecules leaves the nucleus, via a nuclear pore, and enters the Rough Endoplasmic Reticulum.

Figure 2.71 Transcription Note: in image coding strand =sense strand, other strand =anti-sense

image credit: online.science.psu.ed

image credit: online.science.psu.ed

 

 Fig 2.72 Transcription

YZKKAgq

  • Think: Why does mRNA make a complimentary copy of the anti-sense strand, as opposed to the sense strand?
  • Why is it necessary to make a copy of the DNA?

Movie: Transcription: Real time

Translation

Translation is the synthesis of polypeptides on ribosomes. Proteins are made from more than one polypeptide (e.g. collagen is made from three polypeptide chains woven into a triple helix).

Translation occurs in ribosomes (either free ribosomes or in the rough endoplasmic reticulum:

  1. mRNA binds to the small sub-unit of a ribosome. The first codon (triplet of bases) on the mRNA matches an anti-codon (complimentary triplet) on a tRNA molecule.
  2. The tRNA molecule with the matching anti-codon, binds to the ribosome.
  3. This tRNA carries a specific amino acid with it. In this way, each codon on the mRNA codes for a specific amino acid
  4. A second tRNA molecule bonds to the ribosome, having an anti-codon which is complimentary to the next codon in the sequence.
  5. The second tRNA brings another specific amino acid. The ribosome transfers the amino acid carried by the first tRNA to the amino acid on the second tRNA, forming a peptide bond between them.
  6. The mRNA moves along the ribosome, causing new tRNAs to bond, bringing with them new amino acids, which are added to the growing polypeptide chain.

Figure 2.73 Translation

image credit: boundless.com

image credit: boundless.com

 

Movie: Translation (real-time)

 

Think: Compare transcription and translation (5 marks)

This is a copy of the mRNA code for translation:

image credit: iupui.edu

image credit: iupui.edu

 

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