Biological Molecules Flashcards
How many different amino acids are used in proteins?
20
What do all amino acids contain?
Carbon, hydrogen, oxygen, nitrogen
What do some amino acids also contain?
Sulfur
Do all amino acids have the same structure?
Yes, but R can be one of 20 different chemical groups
What holds a chain of amino acids together?
Strong peptide bonds
How many amino acids long can proteins be?
Up to several hundred
What determines the structure of a protein?
The order of amino acids
What does the structure of a protein determine?
How the protein works
What is the primary structure?
The sequence of amino acids
What is the secondary structure ?
-Hydrogen bonds form between the amino acids all along the polypeptide chain (this is due to the polarity of the CO and the NH groups).
-These hydrogen bonds cause the polypeptide chains to twist and fold into shapes .
-The twisted 3d shape formed can either be an alpha helix cylindrical shape or a beta pleated sheet .
-Both these structures are maintained by hydrogen bonds
What are globular proteins?
Proteins that have a roughly spherical shape
What elements do carbohydrates contain?
Carbon, hydrogen and oxygen
What do the different types of carbohydrates include?
Sugars, starch and cellulose
What are sugars?
Small, water-soluble molecules that taste sweet
What groups are sugars divided to?
Monosaccharides and disaccharides
Why are the single units from which all carbohydrates are built?
Monosaccharides
What are glucose and fructose?
Monosaccharides
What 2 forms does glucose have?
Alpha and beta
How are disaccharides formed?
When 2 monosaccharides are joined together by a chemical reaction. A molecule of water is also formed
What sort of reaction is the reaction between 2 disaccharides?
A condensation reaction
What 2 polysaccharides are starch molecules made up of?
Amylose and amylopectin
Why is starch good at storing glucose?
Because it insoluble
What is cellulose?
A polysaccharide made up of glucose molecules
How do cellulose molecules lie?
Long and straight
Several cellulose molecules can lie side to side to form….
Microfibrils
Microfibrils are held together by…
Weak hydrogen bonds
Is cellulose found in animal cells?
No, only plant cells
What do the microfibrils do to the plant cell wall?
Strengthen it
What do lipids contain?
Carbon, hydrogen and oxygen
What 2 things can lipids be?
Fats and oils
What 2 things can lipids be?
Oils and fats
What are plant oils and animal fats mostly made up of?
Lipids called triglycerides
What does a tryglyceride consist of?
A molecule of glycerol with 3 fatty acids attached to it
What is a fatty acid molecule?
A long chain of carbon atoms with an acid group (COOH) at one end
What are attached to the carbon atoms in a fatty acid?
Hydrogen atoms
What is a fatty acid with many double bonds called?
Polyunsaturated
What is a special type of lipid?
A phospholipid
What are phospholipids?
Lipids that have 2 fatty acid chains and a phosphate group
What are cell membranes made from?
A double layer of phospholipids
What are enzymes?
Biological catalysts that increase the rate of the reaction
What do enzymes do to the activation energy?
Lower it
What type of enzymes are all proteins?
Globular proteins
What are enzymes involved in?
Breaking down molecules or building molecules
Why are digestive enzymes important in the digestive system ?
Because they help to break down food into smaller molecules
What do enzymess involved in DNA replication do?
They help to build molecules
What is the active site?
A region on the surface of an enzyme molecule where a substrate molecule can attach itself
The shape of the substrate molecule and the shape of the active site are …
Complementary
What happens as soon as the enzyme substrate complex is formed?
The products of the reaction are released and the enzyme is ready to accept another substrate molecule
Only one substrate will fit the enzyme correctly , so each enzyme only catalyses one specific reaction, true or false?
True
What happens when the temperature of an enzyme is increased?
The enzyme reactions become faster because the molecules have more energy.
What happens to enzymes at really high temperatures?
-The enzymes atoms vibrate quicker and break the weak bonds that hold the tertiary structure together.
-The shape of the active site changes and the substrate can no longer fit in.
-The enzyme is said to be denatured
What can acids and alkalis do to enzymes?
Denature them. Hydrogen ions in acids and hydroxyl ions in alkalis disrupt the weak bonds and change the shape of the active site
What are monosaccharides?
The monomers of carbohydrates
What are examples of monosaccharides?
Glucose, galactose, fructose, ribose, deoxyribose, glyceraldehyde
What type of bond form when monosaccharides like glucose bond?
Glycosidic bonds
What make up maltose?
Alpha glucose + alpha glucose
What forms sucrose?
Alpha glucose + fructose
What is the molecular forma of sucrose?
C12 H22 O11
What forms lactose?
Alpha glucose + galactose
What does sucrose and sucrase make?
Alpha glucose + fructose
what does amylose and amylopectin make ?
Starch
Is amylose a monosaccharide or a polysaccharide?
A polysaccharide
Is amylopectin a monosaccharide or a polysaccharide?
A polysaccharide
What is the common formula for monosaccharides?
Cn(H20)n
What are some examples of polysaccharides?
Glycogen, starch and cellulose
What polymers are formed by the condensation of alpha glucose?
Glycogen and starch
What polymer is formed from the condensation of beta glucose?
Cellulose
What is the difference between alpha glucose and beta glucose ?
The differenc is the differing positions of the -OH groups. Alpha is a same-sided 1-4 hydroxyl group , while beta refers to opposite sided 1-4 groups.
Draw alpha glucose
Answer in book
Draw beta glucose
Answer in book
What is the difference between ribose and deoxyribose?
Ribose has a hydroxyl group at position 2, whereas deoxyribose has a hydrogen atom at position 2. Due to this, deoxyribose sugar is more stable than ribose sugar
Draw ribose
Answer in book
Draw deoxyribose
Answer in book
What is an isomer?
Something with the same molecular formula but a different structure
What is respiration?
The process in which glucose is broken down to release energy in the form of ATP
What is the word equation for respiration?
Oxygen + glucose-≥ carbon dioxide + water
What is the symbol equation for respiration?
6O2 + C6H12O6 -≥ 6H2o + 6CO2
What is glucose stored as in plants?
Starch
What is glucose stored as in animals?
Glycogen
Why can’t beta glucose be respired?
Because of its shape
Is starch a polysaccharide?
Yes
What is amylose?
A polymer of glucose joined by a -1,4- glycosidic bonds. Amylose is unbranched and helical
What is amylopectin?
polymers of glucose joined by -1,4- glycosidic bonds but with branches of 1,6 glycosidic bonds. This causes the molecule to be branched rather than helical
Why is starch good for storage?
Because it is insoluble (due to its lack of polar areas)
In starch, why can more energy be stored in a small space?
Because the helix is compact
Why is starch an excellent long term storage molecule?
Because there are only a few branches for the enzyme amylase to act on so the release of energy is relatively slow.
Which has more branches, amylopectin or glycogen?
Glycogen
What is glycogen made up of?
Alpha glucose molecules with much shorter 1,4 chains and many more branches of alpha 1,6 glycosidic bonds than amylopectin
Why does glycogen have more branches than amylopectin?
Because animals have a higher energy requirement and so more branches allows for more free ends, where glucose molecules can either be added or removed, allowing for condensation reactions to occur more rapidly
Why is cellulose strong?
-Because it’s alternate arrangement causes straight chains to form
-these chains are then cross linked by hydrogen bonds which form between the hydroxyl group
Why are microfibrils strong?
Because hundreds of them are arranged in overlapping sheets that run at different angles. The hydrogen crosslinks also make cellulose very resistant to hydrolysis
Where is chitin found?
In the exoskeleton of insects
Does chitin have complex crosslinks?
Yes
Does alternate molecules/inversion occur in chitin?
Yes
What are the side chains of peptidoglycan?
Amino acids
What is peptidoglycan similar in structure to?
Cellulose
Does cross linking occur in peptidoglycan?
Yes
Are there alternate molecules in peptidoglycan?
Yes
Does peptidoglycan contain nitrogen?
Yes
Why can amylose store a lot of energy?
because it is coiled and therefore it is a very
compact molecule
What are lipids?
Lipids are macromolecules that contain carbon, hydrogen and oxygen atoms. Unlike carbohydrates, lipids contain a lower proportion of oxygen
Are lipids polar or non polar?
non-polar
Are lipids hydrophobic or hydrophilic?
hydrophobic (insoluble in water)
What does hydrophobic mean?
Insoluble in water
What reactions form the ester linkage?
Condensation reactions
What are the main groups of lipids?
Phospholipids and triglyerides
What are the roles of lipids?
-Energy storage
-Insulation(electrical and thermal)
-Buoyancy(floating)
-Waterproofing
-Protection
-Membranes
-Source of water- from respiration
-Aids absorption
What is the only thing lipids are soluble in?
organic solvents, such as alcohols
Describe the structure of the triglyceride molecule
Has one molecule of glycerol and 3 fatty acids joined together by ester bonds (which are formed in a condensation reaction)
Are triglycerides polar or non-polar?
non-polar
what are the monomers of tryglycerides?
glycerol and fatty acids
What is glycerol?
an alcohol (an organic molecule that contains a hydroxyl group bonded to a carbon atom)
What is on either end of a fatty acid chain?
at one end is a methyl group, at the other end is a carboxyl group
what is the shorthand chemical formula for a fatty acid?
RCOOH
What is a difference between lipids from animals and those from plants?
Lipids from animals are saturated, whereas lipids from plants are unsaturated
What are the monomers of phospholipids?
glycerol and fatty acids
What is the structure of a phospholipid?
two fatty acids bonded to a glycerol molecule and a phosphate ion
is the phosphate in phosholipids polar or non-polar?
Polar and it is soluble in water (hydrophilic)
are the fatty acid ‘tails’ in phospholipids polar or non-polar?
non polar and therefore insoluble in water (hydrophobic)
why are phospholipids amphipathic?
because they have both hydrophobic and hydrophilic parts
what is a function of triglycerides?
energy storage
when does an ester bond form in a lipid?
when a hydroxyl (-OH) group from the glycerol bonds with the carboxyl (-COOH) group of the fatty acid
what 2 categories do triglycerides fall in to?
fats and oils
why do lipids help animals to float?
because fats have a low density
why are trigylcerides good at storing energy?
because they store more energy per gram due to their hydrocarbon chains
where are molecules of cholesterol synthesised?
in the liver and transported via the blood
what steroid-based hormones is cholesterol used to produce?
oestrogen, testosterone and progesterone
what does cholesterol affect in the cell membrane?
the fluidity and permeability
what is the structure of cholesterol?
contains 4 carbon based rings, a hydrocarbon tail, and a hydroxyl group
is the hydroxyl group in cholesterol water soluble or not?
it’s water soluble (hydrophilic)
is the hydrocarbon tail in cholesterol oil soluble?
yes and it is hydrophobic
what family of lipids is cholesterol part of?
sterols
what can the hydrophilic hydroxyl group on the cholesterol molecule interact with?
the head groups of phospholipids. the rest of the cholesterol molecule can interact with the hydrophobic fatty acid tails
what are the functions of cholesterol?
- producing steroid-based hormones
- making vitamin D, this process takes place in the skin in response to ultraviolet light.
-producing bile in the liver
-fluidity and permeability of cell membranes
what is vitamin d needed for?
the proper development of bones
what does bile do?
increases the rate of digestion of lipids by the enzyme lipase
do saturated lipids melt at higher or lower temperatures to unsaturated lipids?
higher
do unsaturated lipids melt at higher or lower temperatures to saturated lipids?
lower
What are the 3 main parts to an amino acid?
Tha amine group, the carboxyl group and the R group
Is the R group different for each of the 20 amino acids?
Yes
What is the R group in glycine
A hydrogen atom
What is the R group in alanine?
A methyl group
What is the R group in glycine
What does a dipeptide contain?
2 amino acids bonded together
What does a polypeptide consist of?
3 or more amino acids bonded together
Why is the primary structure very important?
Because it helps to determine the final 3D shape of the protein and so the protein function is dependent on the primary structure
What can changing a single amino acid in the primary structure lead to?
A change in the proteins function. The protein hence may not be able to carry out it’s function effectively
What is the tertiary structure?
The overall 3D shape of a polypeptide after proteins fold even further.additional bonds will be made between the r groups, such as ionic, hydrogen, disulfide and weak hydrophobic interactions . The function of the molecule also depends on the tertiary structure
What is an example of a tertiary structure?
An enzymes active site
What 2 changes can disrupt the tertiary structure and denature the protein?
pH and temperature
What is the quaternary structure existent?
In proteins that have more than 1 polypeptide chain working together as a functioning macromolecule
What is an example of a protein with a quaternary structure?
Haemoglobin
What is each polypeptide chain referred to as?
A subunit
Many proteins contain a p… group
Prosthetic
What prosthetic group does haemoglobin have?
Haem, which binds to oxygen
What is a protein with a prosthetic group called?
A conjugated protein
What are disulfide bonds?
strong covalent bonds that form between two cysteine R groups (as this is the only amino acid with a sulphur atom)
What is the strongest protein bond?
The disulfide bond
How can disulfide bonds be broken?
By oxidation
In which proteins are disulfide bonds common in?
proteins secreted from cells eg. insulin
Where do Ionic bonds form in a protein?
Ionic bonds form between positively charged (amine group -NH3+) and negatively charged (carboxylic acid -COO-) R groups
Are Ionic bonds broken by pH changes?
No
Where do hydrogen bonds form in proteins?
between strongly polar R groups.
What is the weakest type of bond that forms in proteins?
Hydrogen bonds, but they are also the most common as they form between a wide variety of R groups
Where do hydrophobic interactions form?
between the non-polar (hydrophobic) R groups within the interior of proteins
What is the difference between the hydrogen bonds in the secondary structure and the hydrogen bonds in the tertiary structure?
The hydrogen bonds in the secondary structure form only between the amino and carboxyl groups. Whereas the hydrogen bonds in the tertiary structure form between the R groups as well
Are fibrous proteins elongated or spherical?
Elongated
Are globular proteins elongated or spherical?
Spherical
Are fibrous proteins soluble or insoluble in water?
Insoluble
Are globular proteins soluble or insoluble in water?
Soluble
What are some examples of fibrous proteins?
Collagen, keratin, elastin
Describe the amino acid sequence of globular proteins
Irregular and wide range of R groups
Describe the amino acid sequence of fibrous proteins
Repetitive with a limited range of R groups
What type of functions do globular proteins have?
Physiological
What type of functions do fibrous proteins have?
Structural
What is a good way of distinguishing between fibrous and globular proteins?
SAFES (Shape, Amino acid sequence, Function, Examples and Solubility).
Do fibrous proteins have a tertiary structure?
They usually have little/ no tertiary structure
Do globular proteins have a tertiary structure?
They have a complex tertiary structure and usually a quaternary structure as well
What is chromatography?
A method used to separate mixtures of substances into their components.
These mixtures can be analysed and their components can be identified.
What is the stationary phase?
A solid or a liquid supported on a solid e.g chromatography paper, TLC
What is TLC?
Silica on plastic
What is the mobile phase?
A liquid or a gas(normally an organic solvent)
What happens during chromatography?
The mobile phase picks up the molecules and carries them through the stationary phase
What groups stick out of the stationary phase?
OH- groups
What does the distance the molecules in chromatography move depend on?
The hydrogen bonds they make with the stationary phase and their solubility in the mobile phase
What type of molecule sticks to the stationary phase more?
A polar molecule
How do you calculate Rf values?
Rf value = distance travelled by sample / distance travelled by solvent
what type of covalent bond is present in carbohydrates?
glycosidic
what type of covalent bond is present in proteins?
peptide
what type of covalent bond is present in lipids?
ester
what type of covalent bond is present in nucleic acids?
phosphodiester
.
.
all monomers of carbohydrates are reducing…
sugars
what is a monosaccaride?
a single sugar unit, all are reducing sugars
what is a disaccharide?
a sugar formed from 2 monosaccharides joined together by a glycosidic bond in a condensation reaction
what is a polysaccharide?
a polymer formed by many monsaccharides joined by glycosidic bonds in condensation reaction
is ribose a pentose or a hexose?
a pentose, with 5 carbon atoms
is glucose a pentose or a hexose?
a hexose, with 6 carbon atoms
give some examples of polysachharides
cellulose, starch, glycogen
where is sucrose found?
in plants, such as sugar cane
what elements do nucleic acids contain?
carbon, hydrogen, oxygen, nitrogen, and phosphorous (to form the phosphate groups)
what do reducing sugars do?
donate electrons and they reduce the soluble copper sulphate to insoluble brick-red copper oxide
what are some examples of reducing sugars?
glucose, fructose and galactose
what do non-reducing sugars do?
they cannot donate electrons, therefore they cannot be oxidised
what’s an example of a non-reducing sugar?
sucrose
how many carbon atoms does a triose have?
3
what’s an example of a triose?
glyceraldehyde
what is the most well-known carbohydrate monomer ?
glucose
what is the main function of glucose?
releasing energy for the production of ATP
what do riboses and deoxyriboses make up?
RNA and DNA
what glycosidic bond does maltose form?
a 1,4
what glycosidic bond does sucrose form?
a 1,2
what glycosidic bond does cellulose form?
b 1,4
what glycosidic bond does amylose form?
a 1,4
what glycosidic bond does amylopectin form?
a 1,4 and a 1,6
what catalyses hydrolysis reactions?
enzymes
what are examples of hydrolysis reactions?
the digestion of food in the alimentary tract and the breakdown of stored carbohydrates in muscle and liver cells for use in cellular respiration
what is maltose?
the sugar formed in the production and breakdown of starch
what is lactose?
a sugar found only in milk
are starch and glycogen soluble or insoluble?
insoluble, so they will have no osmotic effect, unlike glucose
why can starch be easily hydrolysed for use during cellular respiration?
because the amylopectin in starch has branches that result in many terminal glucose molecules that can easily be hydrolysed for use during cellular respiration
summarise the test for proteins
- Add sodium
hydroxide solution. - Add copper (II)
sulphate solution.
Colour change should be from blue to purple
summarise the test for starch
- Add iodine in
potassium iodide
solution.
Colour change from
brown-orange to
blue-black.
summarise the test for lipids
- Add ethanol.
- Pour solution into
water.
A cloudy emulsion forms
summarise the test for reducing sugars
- Add Benedict’s
reagent to a sample and
heat in a water bath
that’s brought to a boil.
Sample goes from blue to
green to yellow to orange
to brick red precipitate,
depending on the
concentration
summarise the test for non reducing sugars
- Add dilute HCl.
- Put in a water bath
brought to a boil. - Neutralise with
sodium hydrogen
carbonate. - Do Benedict’s Test
for reducing sugars.
Sample goes from blue to
green to yellow to orange
to brick red precipitate,
depending on the
concentration
summarise the test for glucose
- Dip test strip in
solution.
Colour change will occur
if glucose is present.
Compare to chart of
known colour changes to
check for concentration.
what is an ion?
an atom (or sometimes a group of atoms) that has an electrical charge
what is a positive ion called?
a cation
what is a negative ion called?
an anion
what is an inorganic ion?
An inorganic ion is an ion that does not contain carbon
some inorganic ions act as cofactors.What are cofactors?
Cofactors are non-protein chemical compounds that are required for a protein to function
What are the functions of hydrogen ions?
-hydrogen bonding
-ATP formation
-control of blood pH
-transport of carbon dioxide
What are the functions of calcium ions?
-bone and enamel structure
-cofactor in blood clotting
- synaptic transmission of nerve impulses
-muscle contraption
What are the functions of iron ions?
-transport of oxygen via haemoglobin
-transfer of electrons
What are the functions of sodium ions?
-electrolyte
-nerve transmission
-reabsorption of water into the kidneys
What are the functions of potassium ions?
-electrolyte
-nerve transmission
-reabsorption of water into the kidneys
-opening of the stomata
What are the functions of ammonium ions?
- deamination of proteins
What are the functions of nitrate ions?
-source of nitrogen for plants
What are the functions of hydrogen carbonate ions?
-carbon dioxide transport in the blood
What are the functions of chloride ions?
-maintaining pH balance during carbon dioxide transport
What are the functions of phosphate ions?
-component of the cell membrane(phospholipids)
-component of bones (calcium phosphate)
-component of ATP and nucleic acids
What are the functions of hydroxide ions?
bonding between biochemical molecules
what are 2 products of atp?
Adenosine diphosphate and (inorganic) phosphate
What is the structure of collagen?
- Peptide bonds between amino acids
- Secondary structure is alpha helix
- Has high proportions of glycine
- 3 polypeptide chains and hydrogen bonds between them
- No hydrophilic R groups on the outside of the molecules
- Adjacent molecules joined by crosslinks
- Crosslinks form fibrils
What is the structure of heamoglobin?
- Peptide bonds between amino acids
- Secondary structure is alpha helix, with small regions of beta pleated sheets.
- Hydrophilic R groups on the outside of the molecule
- 4 polypeptide chains, 2 alpha, 2 beta
- 4 haem groups per molecule
- Made up of a wider range of amino acids
Describe the ways in which the structure of collagen is similar to the structure of haemoglobin?
- Both have an acid amino chain
- Both vae amino acids joined by peptides
- Both helical
- Both have a quaternary structure
- Both have more than 1 subunit
How much heamoglobin differ from collagen?
- Haemoglobin is globular, whereas collagen is fibrous.
- Haemoglobin has hydrophilic R groups on the outside, whereas collagen doesn’t.
- Haemoglobin has 4 polypeptide chains, whereas collagen has only 3.
- Haemoglobin has a high wider range of amino acids- not predominantly glycine like collagen is
What are the differences between glycogen and cellulose?
- Glycogen doesn’t have hydrogen bonding, whereas cellulose does.
- Glycogen has a- 1,4 bonds and a-1,6 bonds; whereas cellulose only has a-1,4 bonds.
- Glycogen is branched, whereas cellulose is helical.
- Glycogen doesn’t have fibrils, whereas cellulose does have fibrils.
-Glycogen has granules, whereas cellulose does not have granules.
-All glucose units in glycogen are in the same orientation, whereas adjacent glucose units in cellulose are in opposite orientation.
Why does glucogen make a good storage molecule?
- Glycogen is insoluble, so it doesn’t affect the water potential of the cell.
- Can be broken down easily.
- Has many branches for enzymes to attach to
- It’s compact and so stores a lot of energy
