Biological Molecules Flashcards
Polysaccharides
Polysaccharides
Polysaccharides contain monosaccharides. They are formed by condensation reactions linked by glycosidic bonds.
Mainly used as energy stores and structual components of cells.
Major polysaccharides include starch and cellulose in plants and glycogen in animals.
What is starch and what is its function?
Formed from two polymers of alpha glucose - amylose and amylopectin
Found in starch grains inside plant cells (inside chloroplasts)
Function - is an insoluble store of glucoser
How is starch formed.
Formed from two polymers of alpha glucose - amylose and amylopectin
Amylose - condensation reaction which forms a 1-4 glycosidic bond.
Amylose features
Amylose
condensation reaction which forms a 1-4 glycosidic bond.
• 1-4 glycosidic bonds
• Unbranched chains
• Helical structure
Amylopectin
Amylopectin
• 1-4 and 1-6 glycosidic bonds
• Highly branched chains due to the placement of the bonds.
Where is starch stored
Starch is a major carbohydrate in plants.
It is usually stored as intracellular starch grains in organelles called plastids. The plastids include green chloroplasts and colourless amyloplasts.
Explain how the structure of cellulose leads to its function
Many hydrogen bonds provide collective strength
Insoluble so wont affect water potential
What is cellulose and its function
Formed from beta glucose
Found in cell wall of plant cells
Function provides structual strength to cell wall.
Hydrogen bonds in cellulose
Hydrogen bonds give molecules great tensile strength which is ideal for providing structual support to plant cells.
Hydrogen bonds then form between chains via the OH group to form microfibres and cellulose fibres.
Very rigid which is ideal for structual components such as plant cell walls.
What is gylcogen
Polymer of alpha glucose.
Functionm - is an insoluble store of glucose
Highly branched and can be compacted easily
Where are glycogen found
These branches of glucose form glycogen grains which are found in cytoplasm of muscle and liver cells.
Formation and structure of glycogen
Formed from many condensation reactions between alpha glucose
containing alpha 1-6 glycosidic bonds that produce and even more 1-6 bonds making a very branched structure.
Properties of lipids
Properties of lipids:
• made up of carbon, hydrogen and oxygen
• Proportion of carbon to oxygen and hydrogen is smaller than carbohydrates.
• Insoluble in water
• Soluble in organic solvents such as alcohol and acetone
Roles of lipids
Roles of lipids
• contribute to flexibility to cell membranes
• Source of energy
• Waterproofing
• Insulation
• Protection
What are triglycerides
They are produced from a condensation reaction between 3 fattu acids and one molecule of glycerol.
This forms 3 ester bonds and 3 h2o molecules
Whatfunctional group does fatty acids contain
There are over 70 different fatty acids and they all have the COOH carboxillic acid group with a hydrogen chain attached.
The length of chain determines how saturated the fat is. The more double bonds in the tail means the more unsaturated the fat is.
What is a phospholipid
Made of a glycerol molecule, two fatty acid chains and a phosphate group attached to the glycerol.
The two fatty acids also bond to the glycerol via two condensation reactions resulting in two ester bonds
Energy storage in triglycerides
Due to the large ratio of energy stpry carbon hydrogen bonds compared to the number of carbon atoms, alot of energy is stored in the molecule.
Triglycerides in water
They do not affect water potential and osmosis.
This is because they are large and hydrophobic making them insoluble in water
How many amino acids are in the body
There are over 20 amino acids found in biology.
What are the two sulphyr containing amino acid
There are only two sulphur containing amino acids, these include cysteine and methionine. The sulfur atoms in the cysteine molecules can form a covalent bond. This is a disulphide bonds. Not broken by high temps or ph changes
What is a polypeptide
If we join three or more amino acids, we make a polypeptide. One molecule of water is formed from every peptide formed.
We can reverse this reaction and break the peptide bond by hydrolysing the molecule (adding water) which can be done by protease in the digestive system.
What is the difference between the polypeptide and the protein?
A polypeptide has to fold into a complex 3d shape to carry out its function - we would refer to it as a protein molecule
Primary structure in proteins
The sequence of amino acids bonded by covalent peptide bonds is the primary structure of a protein
DNA of a cell determines the primary structure of a protein by instructing the cell to add certain amino acids in specific quantities in a certain sequence.
This affects the shape and the function of the protein.
The primary structure is specific for each protein.
Tertiary structure in proteins
Further conformational change of the secondary structure leads to additional bonds forming between the R groups (side chains)
The additional bonds are:
- Hydrogen (these are between R groups)
- Disulphide (only occurs between cysteine amino acids)
- Ionic (occurs between charged R groups)
- Weak hydrophobic interactions (between non-polar R groups)
This structure is common in globular proteins
Quaternary structure in proteins
Occurs in proteins that have several polypeptide chain working together as a functional macromolecule.
Each polypeptides are called subunits by scientists.
The quaternary structure shows how the individual subunits are arranged to form a larger three dimensional structure.
Also shows position of any prosthetic groups.
Prosthetic Groups
Some proteins contain other non protein molecules forming part of the structure.
These are called prosthetic group which help carry out their function.
Proteins with a prosthetic group are called conjugated proteins.
What happens when mutations occur
if it mutates the protein base may function, some can cause catastrophic and some may have little impact.
Bonding in proteins - Hydrogen bonds
They fold so hydrophilic groups are on the outside and hydrophobic groups are on the inside.
Some R groups are polar so the hydrogen bond may form between them.
Due to the slight positive and negative charges on the hydroxyl, the bond can form between R groups.
Weak bonds and easily broken by PH or temperature changes.
Disulphide bonds - bonding in protein
Disulfide bonds are strong covalent bonds that form between two cysteine R groups (as this is the only amino acid with an available sulfur atom in its R group)
These bonds are the strongest within a protein, but occur less frequently, and help stabilise the proteins
These are also known as disulfide bridges
Can be broken by reduction
Disulfide bonds are common in proteins secreted from cells eg. insulin
Bonding protein - Ionic bonds
Ionic bonds form between positively charged (amine group -NH3+) and negatively charged (carboxylic acid -COO-) R groups
Ionic bonds are stronger than hydrogen bonds but they are not common
These bonds are broken by pH changes
Bonding proteins - Hydrophobic reactions
between non polar side chains. Several amino acids are not charges so are called non polar.
Hydrophobic R groups tend to cluster together to exclude water molecules.
Hydrophobic interactions form between the non-polar (hydrophobic) R groups within the interior of proteins
Globular proteins
Globular proteins form a spherical mass with (tertiary) a specific 3D shape and a quaternary. They are soluble in water. They contain hydrophilic amino acids on their surface which will interact with water molecules making them soluble. Hydrophobic amino acids are deep in the centre of the protien.
How does haemoglobin bond with oxygen
The presence of the haem group (and Fe2+) enables small molecules like oxygen to be bound more easily because as each oxygen molecule binds it alters the quaternary structure (due to alterations in the tertiary structure) of the protein which causes haemoglobin to have a higher affinity for the subsequent oxygen molecules and they bind more easily
What subunit does haemoglobin contain
The prosthetic haem group contains an iron II ion (Fe2+) which is able to reversibly combine with an oxygen molecule forming oxyhaemoglobin and results in the haemoglobin appearing bright red
Making haemoglobin an example of a conjugated protien.
What structure is haemoglobin
It has a quaternary structure as there are four polypeptide chains. These chains or subunits are globin proteins (two α–globins and two β–globins) and each subunit has a prosthetic haem group.
What is collagen
Collagen is the most common structural protein found in vertebrates
In vertebrates it is the component of connective tissue which forms
Collagen is an insoluble fibrous protein
Why is collagen insoluble
They have a large proportion of amino acids with hydrophobic R groups makes them insoluable in water which makes them useful for structure and support.
Where is collagen found
Collagen is found in skin, teeth, bones, tendons, blood vessels and warts.
How is collagen formed?
Collagen is formed from three polypeptide chains closely held together by hydrogen bonds to form a triple helix (known as tropocollagen)
Each polypeptide chain is a helix shape (but not α-helix as the chain is not as tightly wound) and contains about 1000 amino acids with glycine, proline and hydroxyproline being the most common
What are the two isomers of glucose?
Alpha glucose is where the hydroxyl group is on the bottom
Beta glucose is where the hydroxide group is on the top
What are some common monosaccharides?
Glucose fructose and galactose
What are proteins?
Proteins are polymers (and macromolecules) made of monomers called amino acids
The sequence, type and number of the amino acids within a protein determines its shape and therefore its function
What is an Amino Acid
Amino acids are the monomers of proteins
There are 20 amino acids found in proteins common to all living organisms
What is the general structure to an amino acid?
The general structure of all amino acids is a central carbon atom bonded to:
An amine group -NH2
A carboxylic acid group -COOH
A hydrogen atom
An R group (which is how each amino acid differs and why amino acid properties differ e.g. whether they are acidic or basic or whether they are polar or non-polar)
How are amino acds joined together to form a peptide bond.
Condensation reaction
Water is removed
Peptide bond forms between OH of carbpxyl and H or amine group
What is the primary structure of a protein
The order of amino acids in the polypeptide chain - this is a polymer
What happens during hydrolysis reaction in polypeptides?
During hydrolysis reactions, the addition of water breaks the peptide bonds resulting in polypeptides being broken down to amino acids
How many levels of structure are in protiens and what do they relate to
There are four levels of structure in proteins:
three are related to a single polypeptide chain and the fourth level relates to a protein that has two or more polypeptide chains
Polypeptide or protein molecules can have anywhere from 3 amino acids (Glutathione) to more than 34,000 amino acids (Titan) bonded together in chains
When does the secondary structure occur in protiens?
The secondary structure of a protein occurs when the weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds.
Causes folding in the molecule to:
α-helix
β-pleated sheet
When does the α-helix occur in secondary structure
The α-helix shape occurs when the hydrogen bonds form between every fourth peptide bond (between the oxygen of the carboxyl group and the hydrogen of the amine group)
When does the β-pleated sheet occur in proteins
The β-pleated sheet shape forms when the protein folds so that two parts of the polypeptide chain are parallel to each other enabling hydrogen bonds to form between parallel peptide bonds
What is the impact of interactions with polypeptide chains
A polypeptide chain will fold differently due to the interactions (and hence the bonds that form) between R groups. This forms the tertiary structure of a protein.
Each protein has a unique R group and therefore many different interactions can occur creating a vast range of protein configurations and therefore functions.
What is the tertiary structure
The further folding of the secondary structure for form a unique 3D shape
Held in place by bonds :
disulfide (sulfur must be present) and ionic - inbetween r groups of amino acids
Weak hydrogen
Ionic
What type of test is the buiret test
The Biuret test is qualitative - it does not give a quantitative value as to the amount of protein present in a sample
How to carry out the test for protein:
A liquid solution of a sample is treated with sodium or potassium hydroxide to make the solution alkaline
A few drops of copper (II) sulfate solution (which is blue) is added to the sample
Biuret ‘reagent’ contains an alkali and copper (II) sulfate
The test for proteins: colour change observed
If a colour change is observed from blue to lilac/purple, then protein is present.
The colour change can be very subtle, it’s wise to hold the test tubes up against a white tile when making observations)
The test for proteins: no colour change observed
If no colour change is observed, no protein is present
For this test to work, there must be at least two peptide bonds present in any protein molecules, so if the sample contains amino acids or dipeptides, the result will be negative
Why do globular proteins have a spherical shape?
Globular proteins form a spherical shape when folding into their tertiary structure because:
their non-polar hydrophobic R groups are orientated towards the centre of the protein away from the aqueous surroundings and
their polar hydrophilic R groups orientate themselves on the outside of the protein
Why are globular proteins soluble in water
Their orientation enables globular proteins to be (generally) soluble in water as the water molecules can surround the polar hydrophilic R groups
The solubility of globular proteins in water means they play important physiological roles as they can be easily transported around organisms and be involved in metabolic reactions
Why do globular proteins have a specific shape
The folding of the protein due to the interactions between the R groups results in globular proteins having specific shapes.
This also enables globular proteins to play physiological roles, for example, enzymes can catalyse specific reactions and immunoglobulins can respond to specific antigens
What are fibrous protiens?
Fibrous proteins are long strands of polypeptide chains that have cross-linkages due to hydrogen bonds
They have little or no tertiary structure
Fibrous proteins have a limited number of amino acids with the sequence usually being highly repetitive
Why are fibrous proteins insoluble in water?
Due to the large number of hydrophobic R groups fibrous proteins are insoluble in water
Why are fibrous proteins suitable for structural roles?
The highly repetitive sequence creates very organised structures that are strong and this along with their insolubility property, makes fibrous proteins very suitable for structural roles.
For example, keratin that makes up hair, nails, horns and feathers and collagen which is a connective tissue found in skin, tendons and ligaments
How are the four globin subunits held together and arranged?
The four globin subunits are held together by disulphide bonds and arranged so that their hydrophobic R groups are facing inwards (helping preserve the three-dimensional spherical shape) and the hydrophilic R groups are facing outwards (helping maintain its solubility)
Why are the arrangements of the R groups is important to the functioning of haemoglobin.
If changes occur to the sequence of amino acids in the subunits this can result in the properties of haemoglobin changing. This is what happens to cause sickle cell anaemia (where base substitution results in the amino acid valine (non-polar) replacing glutamic acid (polar) making haemoglobin less soluble)
What is the function of haemoglobin?
Haemoglobin is responsible for binding oxygen in the lung and transporting the oxygen to tissue to be used in aerobic metabolic pathways
As oxygen is not very soluble in water and haemoglobin is, oxygen can be carried more efficiently around the body when bound to the haemoglobin
What else can the iron II ion allow oxygen to do?
The existence of the iron II ion (Fe2+) in the prosthetic haem group also allows oxygen to reversibly bind as none of the amino acids that make up the polypeptide chains in haemoglobin are well suited to binding with oxygen
The primary structure of collagen
In the primary structure of collagen almost every third amino acid is glycine
This is the smallest amino acid with a R group that contains a single hydrogen atom
Glycine tends to be found on the inside of the polypeptide chains allowing the three chains to be arranged closely together forming a tight triple helix structure
What bonds are present in collagen
Along with hydrogen bonds forming between the three chains there are also covalent bonds present
Covalent bonds also form cross-links between R groups of amino acids in interacting triple helices when they are arranged parallel to each other.
What are fibrils?
The cross-links hold the collagen molecules together to form fibrils.
The collagen molecules are positioned in the fibrils so that there are staggered ends (this gives the striated effect seen in electron micrographs)
When many fibrils are arranged together they form collagen fibres
Collagen fibres are positioned so that they are lined up with the forces they are withstanding
Why does collagen have great tensile strength?
Flexible structural protein forming connective tissues
The presence of the many hydrogen bonds within the triple helix structure of collagen results in great tensile strength. This enables collagen to be able to withstand large pulling forces without stretching or breaking
The staggered ends of the collagen molecules within the fibrils provide strength
Why is collagen a stable protein
Collagen is a stable protein due to the high proportion of proline and hydroxyproline amino acids result in more stability as their R groups repel each other
Why is collagen insoluble in water
Length of collagen molecules means they take too long to dissolve in water (collagen is therefore insoluble in water)
What type of proteins are enzymes?
Enzymes are globular proteins
Critical to the enzyme’s function is the active site where the substrate binds
This means their shape (as well as the shape of the active site of an enzyme) is determined by the complex tertiary structure of the protein that makes up the enzyme and is therefore highly specific
Enzymes and metabolic pathways
Metabolic pathways are controlled by enzymes in a biochemical cascade of reactions
Virtually every metabolic reaction within living organisms is catalysed by an enzyme – enzymes are therefore essential for life to exist
How can enzymes be intracellular and extracellular
Enzymes can be intracellular or extracellular referring to whether they are active inside or outside the cell respectively
Intracellular enzymes are produced and function inside the cell
Extracellular enzymes are secreted by cells and catalyse reactions outside cells (eg. digestive enzymes in the gut)
The active site of an enzyme:
The active site is specific and unique in shape due to the specific folded and bonding in the tertiary structure of the protien.
Due to this specific active site, enxymes can only attatch to substrates that are complimentary in shape
What is the specificity of an enzymes active site determined by
The shape of the active site (and therefore the specificity of the enzyme) is determined by the complex tertiary structure of the protein that makes up the enzyme:
Proteins are formed from chains of amino acids held together by peptide bonds
The order of amino acids determines the shape of an enzyme
If the order is altered, the resulting three-dimensional shape changes
What is the specificity of an enzyme a result of
The specificity of an enzyme is a result of the complementary nature between the shape of the active site on the enzyme and its substrate(s)
Catabolic reactions in enzymes
Catabolic reactions involve the breakdown of complex molecules into simpler products, which happens when a single substrate is drawn into the active site and broken apart into two or more distinct molecules
Examples of catabolic reactions include cellular respiration and hydrolysis reactions
Anabolic reactions in enzymes
Anabolic reactions involve the building of more complex molecules from simpler ones by drawing two or more substrates into the active site, forming bonds between them and releasing a single product
Examples of anabolic reactions include protein synthesis and photosynthesis
Lock and key model
This model suggests that the enzyme is like a lock and that the substrate is like a key that fits into it due to their complementarity in shape.
This model suggests that the enzyme active site is a fixed shape and that due to random collisions the substrate can collide and attach to the enzyme. This forms an enzyme-substrate complex.
Once the enzyme-substrate complex has formed the charged groups within the active site are though to distort the substrate and therefore lower the activation energy. The products are then released, and the enzyme active site is empty and ready to be reused.
The induced fit hypothesis
Induced fit is when the enzyme active site is induced, or slightly changes shape, to mould around the substrate.
When the enzyme-substrate complex occurs, due to the enzyme moulding around the substrate it puts strain on the bonds and therefore lowers the activation energy. The products are then removed, and the enzyme active site returns to its original shape.
The induced fit model is the accepted model for how enzymes function.
What happens as the enzyme denatures due to temperature
Bonds (eg. hydrogen bonds between amino acids) holding the enzyme molecule in its precise shape start to break
This causes the tertiary structure of the protein (ie. the enzyme) to change
This permanently damages the active site, preventing the substrate from binding
Denaturation has occurred if the substrate can no longer bind
How do high temperatures speed up reactions
Higher temperatures speed up reactions:
Molecules move more quickly
Higher frequency successful collisions between substrate molecules and active site of enzyme
More frequent enzyme-substrate complex formation
Substrate and enzyme collide with more energy, making it more likely for bonds to be formed or broken (allowing the reaction to occur)
How do lower temperatures slow down the reactions
Molecules move relatively slow
Lower frequency of successful collisions between substrate molecules and active site of enzyme
Less frequent enzyme-substrate complex formation
Substrate and enzyme collide with less energy, making it less likely for bonds to be formed or broken (stopping the reaction from occurring)
Why are enzymes denatured at extreme PH
high or too low a pH will interfere with the charges in the amino acids in the active site. This can break the bonds holding the tertiary structure in place and therefore the active site changes shape.
Therefore the enzyme denatures and fewer enzyme-substrate complexes form.
Different enzymes have a different optimal pH
Where an enzyme functions can be an indicator of its optimal environment:
Eg. pepsin is found in the stomach, an acidic environment at pH 2 (due to the presence of hydrochloric acid in the stomach’s gastric juice)
Pepsin’s optimum pH, not surprisingly, is pH 2
Enzyme concentration impact on rate
The higher the enzyme concentration in a reaction mixture, the more number of active sites available and the likelihood of enzyme-substrate complex formation
If there is insufficient enzyme active sites will become satruated with substrate and unable to work any faster
Substrate concentration impact on rate
The greater the substrate concentration, the higher the rate of reaction:
As the number of substrate molecules increases, the likelihood of enzyme-substrate complex formation increases
However, all available active sites eventually become saturated and any further increase in substrate concentration will not increase the reaction rate
Competitive inhibitors
Are the same shape as the substrate and can bind to the active site. This prevents the substrate from binding and the reaction occurring. If you add more substrate this will flood/out-compete the inhibitor, knocking them out of the active site.
Non competitive inhibitors
bind to the enzyme away from the active site, the allosteric. site. This causes the active site to change shape, and therefore the substrate can no longer bind, regardless of how much substrate is added.
What do reversible inhibitors do?
Metabolic reactions must be very tightly controlled and balanced, so that no single enzyme continuously and uncontrollably generate more
of a particular product
can be controlled by using the end-product of a particular sequence of metabolic reactions as a non-competitive, reversible inhibitor
What do reversible inhibitors do?
Metabolic reactions must be very tightly controlled and balanced, so that no single enzyme continuously and uncontrollably generate more
of a particular product
can be controlled by using the end-product of a particular sequence of metabolic reactions as a non-competitive, reversible inhibitor
How do non-competitive, reversible inhibitors work?
the process is slowed down as the end-product of the reaction chain binds to an alternative site on the original enzyme, changing the shape of the active site and preventing the formation of enzyme-substrate complexes
The end-product detaches from the enzyme and be used elsewhere, allowing the active site to reform and the enzyme to return to an active state
This means that as product levels fall, the enzyme begins catalysing the reaction once again, in a continuous feedback loop
This process is known as end-product inhibition
Impact of increasing concentration of the inhibitor
Increasing the concentration of an inhibitor, therefore, reduces the rate of reaction and eventually, if inhibitor concentration continues to be increased, the reaction will stop completely
Impact of increasing concentration of the inhibitor
Increasing the concentration of an inhibitor, therefore, reduces the rate of reaction and eventually, if inhibitor concentration continues to be increased, the reaction will stop completely
Concentration and competitive inhibitors
competitive inhibitors, countering the increase in inhibitor concentration by increasing the substrate concentration can increase the rate of reaction once more (more substrate molecules mean they are more likely to collide with enzymes and form enzyme-substrate complexes)
Concentration and non competitive inhibitors
For non-competitive inhibitors, increasing the substrate concentration cannot increase the rate of reaction once more, as the shape of the active site of the enzyme remains changed and enzyme-substrate complexes are still unable to form
Structure of cellulose
Polymer forms long straigjt chains. Chains are held in paralell by many hydrogen bonds to form fibrils.
Structure of starch
Made of 2 polymers
Amylose an unbranched helix
Amylopectin - a branched mlecule
Explain how the structure of starch leads to its functiom
Helix can compact to fit alot of glucose in a small space.
Branched structure increases surface area for rapid hydrolysis back to glucose.
Insoluble wont affect water potential.
Explain how the structure of glycogen leads to the function
Branched structure increases surface area for rapid hydrolysis back to glucose
Insoluble wont affect water potential
Examples of monosaccharides
Glucose fructoe and galactose
Examples of disaccharides
Sucrose, maltose and lactose
Examples of polysaccharides
Startch cellulose and glycogen
What is a disacharide
Made up of two monosaccharides
Joined together by a glycosidic bond
Formed via a condensation reaction
Disacharide formed by two glucose molecules
Maltose and water
Disaccharide formed by glucose amnd galactose
Lactose
Disaccharide formed by glucose and fructose
Sucrose and water
How does a condensation reaction work
H20 is removed
And a 1-4 glycocidic bond is formed
What are the R groups in a triglyceride and what are the two types
Saturated fatty acids - the hydrocarbon chain has only single bonds between carbons.
Unsaturated fatty acids- the hydrocarbon chain consists of at least one double bond between carbons
How do triglycerides act as a metabolic water source
Due to high ratio f hydrogen to oxygen atoms they act as a metabolic water source.
Tirglycerides can release water if theyre oxidised. This is essential of animals in the desert such as camels.
What is the relative mass of lipids?
Lipids have a relatively low mass. Therefore alot can be stored without increasing mass and preventing movement.
Properties of phospholipids
Hydrophilic head of a phospholipid can attract with water as it is charged.
Due to the phosphate being charged, it repels other fats.
The fatty acid chin is not chagred. It is known as the hydrophobic tail and repels water but will mix with fats
How are phospholipids positioned in water
They have two charged regions so is a polar molecule
They are positioned so that the heads are exposed to the water and the tails are not. This created the phospholipid bilayer which makes up the plasma membrane around cells.
What is the quartenary structure
A protein made up of more than one polypeptide chain eg haemoglobin has four polypeptide chains
What does it mean if a protein is denatured
The bonds which hold the tertiary and secondary structure in shape break and therefore the unique 3d shape is lost
Conditions
High temp (too much kinetic energy)
Too high or too low Ph
The importance of the primary structure in proteins
If even one amino acid in the sequence is different then it will cause the ionic/hydrogen/disulfide bonds to form in a different location.
This results in a different 3D shape
Impact:
Enzymes will have a different shaped active site (will be non-functioning)
Carrier proteins will have a different shaped binding site (molecules no longer complementary and cannot be transported across membranes
