Biology unit two module one

biological molecules

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Carbohydrates

Energy storage and supply, structure (in some organisms)

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Proteins

Structure, transport, enzymes, antibodies, most hormones

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lipids

Membranes, energy supply, thermal insulation, protective layers/padding, electrical insulation in neurones, some hormones

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Vitamins and minerals

Form parts of some larger molecules and take part in some metabolic reactions, some act as coenzymes or enyme activators

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Nucleic acids

Information molecules, carry instructions for life

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Water

Takes part in many reactions, support in plants, solvent/medium for most metabolic reactions, transport

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Biological elements and compounds in the body

  • Water (H2O) 70%
  • Chemicals 30%
    • DNA 1%
    • Phospholipids 2%
    • Polysaccharides 2%
    • Ions, small molecules 4%
    • RNA 6%
    • Proteins 15%
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Covalent bonds

are formed when electrons are shared between atoms. These bonds are very strong. Covalently bonded atoms form new molecules

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Double bonds

In some cases, carbon forms two bonds with another atom. Key examples in biology include C=C double bonds in hydrocarbon chains, and C=O double bonds found in many molecules, including organic acids

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Monomers and polymers

The term monomer refers to a single, small molecule, many of which can be joined together to form a polymer. Although they are made of smaller molecules bonded together, lipids are not polymers because the smaller molecules are very different to each other.

Carbohydrates - Monosaccharides (simple sugars) - Polysaccharides

Proteins - Amino acids - Polypeptides and proteins

Nucleic acids - Nucleotides - DNA and RNA

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Condensation and hydrolysis

In condensation reactions:

  • A water molecule is released
  • A new covalent bond is formed
  • A larger molecule is formed by the bonding together of smaller molecules

In all hydrolysis reactions:

  • A water molecule is used
  • A covalent bond is broken
  • Smaller molecules are formed by the splitting of a larger molecule
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Hydrogen bonds

Hydrogen bonds form when a slightly negatively charged part of a molecule comes close to a slightly positively charged hydrogen atom in the same (or another) molecule. This is most easily seen in water.

Hydrogen bonds are not strong bonds. They are often described as 'interactions'. However, in some polymers many thousands of hydrogen bonds can form and this helps to stabilise the structure of the molecule.

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carbohydrates in living organisms

  • energy source - released from glucose during respiration
  • energy store - e.g. starch
  • structure - e.g. cellulose

Some carbohydrates also form part of larger molecules (e.g. nucleic acids, glycolipids)

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Simple sugars

There are a number of different monosaccharides, containing between three and six carbon atoms. All have very similar properties - they:

  • Are soluble in water
  • Are sweet tasting
  • Form crystals

The monosaccharides are grouped according to the no. of carbon atoms in the molecule

  • 3-carbon monosaccharides are known as triose sugars
  • 5-carbon monosaccharides are known as pentose sugars
  • 6-carbon monosaccharides are known as hexose sugas

The most common monosaccharides are hexoses. These include glucose and fructose.

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Joining monosaccharides an splitting disaccharides

Tow monosaccharide molecules can be joined together in a condensation reaction, forming a disaccharide molecule.A new covalent bond called a glycosidic bond forms, and water is eliminated. The reverse hydrolysis reaction uses a water molecule to break the glycosidic bond.

Building the polysaccharides starch, glycogen and cellulose, and breaking down larger molecules, for example during digestion, involves the making and breaking of glycosidic bonds. Note that disaccharides are still sugars.

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alpha and beta glucose

In alpha-glucose, the OH at C1 is below the plane of the ring; in beta-glucose, the OH at C1 is above the plane of the ring. Although both are glucose molecules, this difference in structure leads to some very different properties

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Respiration

glucose + oxygen -> carbon dioxide + water + energy that is used to form ATP

alpha-glucose can be respired, beta-glucose cannot

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starch

the energy storage polysaccharide in plants

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glycogen

the energy storage polysaccharide in animals

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features of starch and glycogen

Because both starch and glycogen are made by bonding many thousands of alpha-glucose molecules together, they are described as energy-storage molecules.

  • they do not dissolve, so the stored glucose does not affect the water potential of the cell. This feature is vital in both plants and animals, as glucose is stored in a cell as free molecules would dissolve and dramatically reduce the water potential
  • They hold glucose molecules in chains so that they can easily be 'broken off' from the ends to provide glucose for respiration when required
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cellulose

cellulose fibres are arranged in a very specific way to form plant cell walls. Because the glucose monomers contain so many OH groups, many hydrogen bonds can form between them. About 60-70 cellulose molecules become cross-linked by hydrogen bond to form bundles called microfibrils. These, in turn, are held together by more hydrogen bonds to form larger bundles called macrofibrils.

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Structure and function of plant cell wall

  • the cell walls around plant cells give great strength to each cell, supporting the whole plant
  • the arrangement og macrofibrils allows water to move through and along cell walls, and water can pass in and out of the cell easily
  • water moving into plant cells does not cause the cells to burst, as it does in animal cells - the wall prevents bursting, and in turgid cells it helps to support the plant as a whole
  • the arrangement of macrofibrils in cell walls determines how cells can grow or change shape. for example, guard cell walls have arrangements of macrofibrils that result in the openingand closng of stomata as water moves in or out of the cell
  • cell walls can be reinforced with other substances to provide extra support, or to make the walls waterproof
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proteins

proteins have many functions:

  • they are structural components, e.g. of muscle and bone
  • they are membrane carriers and pores, e.g. for active transport and facilitated diffusion
  • all enzymes are proteins
  • many hormones are proteins
  • antibodies are proteins
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All proteins are made from amino acids

Proteins are large molecules because they are polymers. They are made by joining together a large number of similair, smaller subunits (monomers). The monomers that are joined together to make proteins are called amino acids. A protein consists of a long chain of amino acids joined end to end.

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Amino acids

All amino acids have the same basic structure. They all ahve an amino group at one end of the molecule, an acid group at the other end of the molecule and a carbon in between.

There are 20 types of naturally occuring amino acid. Each one is based on the same structure, but there are differences between amino acids because they have different R-groups.

The R-group in glycine is a hydrogen atom bonded to the second carbon. come R-groups are large - larger than the C-C-N part of the molecule. Some are positively charged, some are negatively charged. Some are ydrophobic, some are hydrophilic.

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Joining amino acids together

All amino acids are joined in exactly the same way, no matter which R-group they contain. A condensation reaction between the acid group of one amino acid and the amino group of another forms a covalent bond between the two amino acids. A water molecule is also produced.

The new bond formed is called a peptide bond. The new molecule produced is called a dipeptide. The peptide bond can be broken by a hydrolysis reaction, which uses a water molecule in order to break the bond.

Two amino acids joined together is a dipeptide, as more and more join together, a polypeptide is formed

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Primary structure

An organism may contain 10,000 or so different proteins. Each protein has its own function within the organism. Each one is formed from amino acids joined by peptide bonds in a chain. A protein may be hundreds of amino acids long, but all proteins will have an amino acid group at one end and an acid group at the other.

The function of each protein is determined by its structure. The structure of each protein is determined firstly by its amino acid sequence. The unique amino acid sequence of a polypeptide or protein is called its primary structure.

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breaking down proteins and polypeptides

It is important to remember that the formation and breakage of peptide bonds (and other types of covalent bond) in organisms is catalysed by enzymes. Covalent bonds are very strong and do not simply 'appear' or 'fall apart' in the conditions found within cells

Enzymes that catalyse the breaking of peptide bonds are known as protease enzymes. These are not only found in the parts of an organism where food is digested - organisms continually break down and rebuild proteins. Two good examples are as follows.

  • Hormone regulation - it is vital that hormones are broken down so that their effects are not permanent and can be controlled. Any cell that is targeted by a hormone contains enzymes that can break down that hormone
  • Ageing - one of the features of ageing is that the skin loses elasticity and becomes wrinkled. This occurs because older skin is less abl to rebuild the protein collagen and other proteins that give young skin its smooth and elastic properties.
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Secondary structure

The proteins secondary structure is formed when the chain of amino acid coils or folds to form an alpha helix or a beta pleated sheet. Hydrogen bonds hold the coils in place. Although hydrogen bonds are quite weak, many are formed, so overall they gove great stability to parts of the protein molecule.

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Tertiary structure

The final three-dimensional shape of a protein is formed when these coils and pleats themselves coil or fold, often ith straight runs of amino acids in between. This three-dimensional shape is held in place by a number of different types of bonds and interactions. A proteins tertiary structure is vital to its function. for example, a hormone must be a specific shape in order to fit into the hormone receptor of a target cell. A structural protein, such as collagen, is shaped to be strong, with protein chains wound around each other in a specific way. An enzye must have an active site, the shape of which is complementary to that of its substrate.

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heating molecules

Heating a protein increases the kinetic energy in the molecule. This causes the molecule to vibrate and breaks some of the bonds holding the tertiary structure in place. this is denaturation. even if cooled, the bonds will not reform.

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globular and fibrous proteins

globular proteins

  • roll up to form balls
  • usually soluble
  • usually have metabolic roles

fibrous proteins

  • form fibres
  • usually insoluble
  • usually have structural roles
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Quaternary structure

Quaternary structure refers to the fact that some proteins are made up of more than one polypeptide subunit joined together, or a polypeptide and an inorganic component.

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Haemoglobin

Haemoglobins quaternary structure consists of four polypeptide subunits. two are called alpha chains, the other two are beta chains. the four subunits together form one haemoglobin molecule molecule, which is a water solube globular protein.

Haemoglobins function is to carryoxygen from the lungs to the tissues. it binds oxygen in the lungs and releases it in the tissues. A specialised part of each polypeptide, called a haem group, contains an iron (Fe2+) ion. The haem group is responsible for the colour of haemoglobin

Haemoglobin (purple-red) + Oxygen -> Oxyhaemoglobin (bright red)

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Haemoglobin and collagen

Haemoglobin

  • Globular Protein
  • Soluble In Water
  • Wide Range Of Amino Acid Constituents In Primary Structure
  • Contains A Prosthetic Group - Haem
  • Much Of The Molecule Is Wound Into Alpha Helix Structures

Collagen

  • Fibrous Protein
  • Insoluble In Water
  • Approximately 35% Of The Molecule's Primary Structure Is One Type Of Amino Acid
  • Does Not Have A Prosthetic Group
  • Much Of The Molecule Consists Of Left-Handed Helix Structures
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Lipids in living organisms

Lipids perform a number of functions within living organisms:

  • a source of energy - lipids can be respired to release energy to generate ATP
  • energy storage - lipids are stored in adipose cells (cells that store lipid) in 'fat stores' in organisms
  • all biological membranes are made from lipids
  • insulation - e.g. the blubber in whales is lipid that reduces heat loss; lipids also provide 'electrical insulation' around long nerve cells
  • protection - e.g. the surface (cuticle) of plant leaves is protected against drying out by a layer of lipid
  • some hormones (steroid hormones) are lipids
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glycerol and fatty acids

Glycerol is a 3-carbon molecule with three OH groups. Glycerol and fatty acids are found in all the fats and oils that perform roles in energy storage and supply, and those found in membranes. While the glycerol molecule is always the same, the fatty acid molecules found in lipids can differ significantly. As with amino acids, animals cannot make some of the fatty acids they need from the raw materials taken into their bodies. these are called the essential fatty acids. All fatty acids have an acid group at one end. this acid group is the same as that found on an amino acid. the rest of the molecule consists of a hydrocarbon chain.

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saturated or unsaturated

These terms refer to the hydrocarbon chain, and whether it is 'saturated' with hydrogen or not. Put simply, if all the possible bonds are made with hydrogen, the fatty acid is unsaturated.

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Triglycerides

A triglyceride consists of one glycerol molecule bonded to three fatty acid molecules. All fatty acid molecules are joined to glycerol molecules in exactly the same way. A condensation reaction between the acid group of a fatty acid molecule and one of the OH (hydroxyl) groups of the glycerol molecule forms a covalent bond. a water molecule is also produced.

the new bond formed is called an ester bond

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Phospholipids

Essentially, a phospholipid molecule is almost identical to a triglyceride molecule. it consists of a glycerol molecule with fatty acid molecules bonded by condensation reactions to produce ester bonds

In phospholipids, the third fatty acid is not added to the glycerol molecule. Instead, a phosphate group is covalently bonded to the third OH group on the glycerol.

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Phospholipids and membrane fluidity

the fatty acids that make up a phospholipid may be saturated or unsaturated. Organisms can control the fluidity of membranes using this feature. For example, organisms living in colder climates have an increased number of unsaturated fatty acids in their pospholipid molecules. This ensures that membranes remain fluid, despite the low temperatures.

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cholesterol

cholesterol is vital to living organisms, so many cells (especially in the liver) can make it. Excess cholesterol may be a problem in humans because:

  • in bile, cholesterol can stick together to form lumps called gallstones
  • in blood, cholesterol can be deposited in the inner linings of blood vessels causing atherosclerosis, which can result in a number of circulatory problems.
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properties of water

  • solvent
  • liquid
  • cohesion
  • freezing
  • thermal stability
  • metabolic
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Nucleic acids in living organisms

nucleic acids come in two forms: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). In living organisms these molecules hold the coded information to build that organism.

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Nucleotides are monomers of nucleic acids

The monomer of all nucleic acids is called a nucleotide

Each single nucleotide is itself made by the joining of three subunits:

  • one phosphate group
  • one sugar molecule
  • one organic nitrogenous base

the three subunits are joined by covalent bonds to form a single nucleotide molecule

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Organic bases are either purines or pyrimidines

The five organic bases are grouped. Three are called pyrimidines and two are called purines. pyrimidines are smaller than purines.

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DNA is a stable polynucleotide

DNA is a long-chain polmer of nucleotide monomers. This polymer is called a polynucleotide.

Hydrogen bonds between the bases in opposite uprights strengthen the rungs of the ladder. This makes DNA a very stable structure

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base pairing

The chains are always the same distance apart because the bases pair up in a specific way. Where a pyrimidine appears on one side, a purine appears on the other. A pairs to (is complementary to) T. C pairs to (is complementary to) G.

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Making copies

In order to make a new copy of a DNA molecule:

  • the double helix is untwisted
  • hydrogen bonds between the bases are broken apart to 'unzip' the DNA - this exposes the bases
  • free DNA nucleotides are hydrogen bonded onto the exposed bases according to the base pairing rules
  • covalent bonds are formed between the phosphate of one nucleotide and the sugar of the next to seal the backbone
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structure to function in DNA

  • the sequence of bases is an example of information storage. The information is in the form of codes to build proteins
  • the molecules are long, so a large amount of information can be stored
  • the base-pairing rules mean that complementary strands of information can be replicated
  • the double helix structure gives the molecule stability
  • hydrogen bonds allow easy unzipping for copying and reading information
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RNA is different

RNA is structurallly different from DNA in a number of important ways:

  • the sugar molecule that makes up the nucleotides is ribose
  • the nitrogenous base uracil (U) is found instead of the organic bas thymine (T)
  • the polynucleotide chain is usually single stranded
  • three forms of RNA molecules exist
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Three forms of RNA

  • messenger RNA (mRNA) - is made as a strand complementary to one strand of DNA
  • ribosomal RNA (rRNA) - is found in ribosomes
  • transfer RNA (tRNA) - carries amino acids to the ribosomes, where they are bonded together to form polypeptides
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all enzymes are proteins

All enzymes are very similair in many ways:

  • they are globular proteins - generally soluble in water
  • they act as catalysts - speeding up chemical reactions, but not being 'used up' as part of the reaction
  • they are specific - catalysing a reaction involving only one type of substrate
  • the globular structure contains a 'pocket' or cleft area called an active site
  • their activity is affected by temperature and pH
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substrate and product

lactase - the breakdown of lactose into glucose and galactose monomers

catalase - the breakdown of hydrogen peroxide into water and oxygen gas

ribulose biphosphate carboxylase (rubisco) - catalyses the binding of carbon dioxide to ribulose biphosphate

ATP-ase - the breakdown of ATP into ADP and a phosphate group

glycogen synthetase - the building up of glycogen by catalysing the joining together of glucose molecules.

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Lock and key, or induced fit

lock and key - the active site of the enzyme is shaped to fit a specific substrate

induced fit - the active site of the enzyme changes shape slightly to fit the substrate

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competitive inhibitors

competitive inhibitor molecules have a similair shape to that of the substrate molecules. this means that they can occupy the active site, forming an enzyme-inhibitor complex. these changes are not permanent

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Non-competitive inhibitors

Non competitive inhibitors do not compete with substrate molecules for a place in the active site. Instead, they attach themselves to the enzyme in a region away from the active site. This distorts the tertiary structure of the enzyme, altering the shape of the active site. These changes are permanent

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cofactors

A cofactor is any substance that must be presen to ensure enzyme-controlled reactions take place at the appropriate rate. some cofactors are a part of the enzyme (prosthetic groups); others affect the enzyme on a temporary basis (coenzymes and inorganic ion cofactors)

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deadly poisons

Many poisonous substances have their effects because they inhibit, or even overactivate anzymes. Potassium cyanide, for example, inhibits cell respiration. It does this because it is a non-competitive inhibitor for a vital respiratory enzyme called cytochrome oxidase, found in mitochondria. Inhibition of this enzyme decreases the use of oxygen so ATP cannot be made. The organism can only respire anaerobically, which leads to a build up of lactic acid in the blood.

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Comments

charlotte ryan

These are really good.. Thanks

harry

These are great! :)

Don't you learn with colour? :P

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