Chapter 3 - Biological Molecules Flashcards
How are the electrons shared in O-H water bonds?
Not equally- oxygen has a much greater share
What primarily gives water its unique characteristics?
Hydrogen
Why is water such an important component in transport?
It acts as a solvent, which is essential for the movement of important solutes
Why is water a solvent?
Because it is a polar molecule, meaning molecules are attracted to the water (H2O molecules), allowing them to move as one mass
What is capillary action?
The process in which water can rise up a narrow tube against the force of gravity
What happens to the density of water when it freezes?
It becomes less dense
Why does the density of water decrease when it freezes?
Because it forms a crystalline structure, due to hydrogen bonds which fix the molecules slightly further apart than the average distance in liquid state
Are hydrogen bonds strong?
Individually, hydrogen bonds interactions are weak, however they occur in high numbers
What are hydrogen bonds in water?
The interactions between different water molecules. The delta positive hydrogens interact with the delta negative oxygens, and this electrostatic attraction forms hydrogen bonds
What causes water to have a ‘skin’ of surface tension?
Because water molecules are more strongly cohesive to each other than to air
What causes water to have cohesive properties?
Hydrogen bonds between water molecules
What are carbohydrates also known as?
Saccharides or sugars
If something ends is -ose, what are they?
Carbohydrates
What is a single sugar unit known as?
A monosaccharide
When monosaccharides are joined together, what do they form?
Polysaccharides
What is the chemical formula of glucose?
C6.H12.O6
How many carbons is glucose composed of and what does this make it?
6 carbons, making it a hexose monosaccharide
What are the two structural variations of glucose?
Alpha glucose and beta glucose
How are the carbons numbered in glucose?
Clockwise, beginning with the carbon to the right of the oxygen within the ring
What is the different between alpha and beta glucose?
The OH group on carbon 1 is in opposite positions
Why aren’t glucose molecules polar?
They are
Is glucose soluble in water- why?
Yes it is, because of hydrogen bonds that form between the hydroxyl groups (OH) and H2O molecules
What is a glycosidic bond?
The covalent bond formed in saccharides, which join carbohydrates
Why are reactions called condensation reactions?
Because they form water as one of the products
What type of reaction is the reaction between two glucose molecules?
A condensation reaction
What two molecules form sucrose?
Glucose and fructose
In a glycosidic bond, how do you get the prefix numbers (e.g 1,4 glycosidic bond)?
You find the two carbons the bond is between (e.g the first and fourth carbon)
Where is ribose present?
In RNA nucleotides
Where is deoxyribose found?
DNA nucleotides
What type of glucose molecule forms starch?
Alpha glucose
What are the two types of polysaccharides in starch?
Amylose and amylopectin
What is the structure of amylose?
Helix, which is further stranded by hydrogen bonding within the molecule
What are the effects of the structure of amylose on its properties?
It makes it more compact and much less soluble
When is amylose formed?
When alpha glucose molecules are joined only by 1,4 glycosidic bonds
What type of energy store is starch?
A chemical energy store
What is the structure of amylopectin?
It is also made by alpha glucose 1,4 glycosidic bonds, however (unlike amylose) there are also some 1,6 bonds, giving it a branched structure
How often do you see branching points in amylopectin?
Once every approximately 25 glucose molecules
Why is ice floating useful for living environments?
- Insulates environment below; water below does not freeze and is kept at higher temperature
- Habitat for certain animals e.g. polar bears
Why is water being a solvent useful for living environments?
- Solvent for important ions that organisms uptake
- e.g. nitrates for amino acids
Why does ice float?
Because when water freezes the molecules spread out and form a fixed lattice
How does ice insulating the water below help the survival of organisms?
- Organisms can still move
- Organisms do not freeze
- Allows nutrients to continue to circulate
Why is water an excellent solvent?
As it is polar, so attracts and binds to other polar/charged molecules e.g. ions
Why is water’s stable temperature useful for living environments?
- Large number of hydrogen bonds mean high specific heat capacity
- Temperature of enzymes remains constant, preventing them from working too slowly or denaturing
What bonds form between amino acids?
Peptide bonds
What type of reaction is the reaction between amino acids?
Condensation
What is the opposite of condensation reactions?
Hydrolysis
What are amine groups made up of?
H-N-H
What are carboxyl groups made up of?
O=C-O-H
What forms when many amino acids are joined together?
A polypeptide
What part of an amino acid distinguishes it from other amino acids?
Its R-group
What do different sequences of amino acids lead to?
Different protein structures with different shapes being produced
What is primary protein structure?
The base initial sequence in which amino acids are joined
What bonds are involved in the primary structure of proteins?
Only peptide bonds
What are R-groups in amino acids?
The part that can vary
What are two types of secondary structure?
Alpha helices
Beta pleated sheets
What is secondary protein structure?
When the amino acid chain structure change as a result of hydrogen bonding
Properties of globular proteins
- compact
- water soluble
- roughly spherical
When do globular proteins form?
When proteins fold into their tertiary structures in such a way that the hydrophobic R-groups on the amino acids are kept away from the aqueous environment, making them soluble
Give one example of a globular protein
Insulin
Insulin properties
- globular protein
- hormone involved in maintaining blood glucose levels
What does insulin need to be fulfill its purpose?
- soluble in blood to allow transportation
- precise shape to fit into specific receptors to have their effect
What are conjugated proteins?
Globular proteins that contain a non protein component called a prosthetic group
What make up triglycerides?
One glycerol molecule and three fatty acids
How do fatty acids and glycerol molecules react to form lipids?
The hydrogens from the glycerol molecule react with the hydroxyls from the fatty acids, forming water.
The glycerol oxygens then react with the carbonyl groups of the fatty acids, forming an ester bond
What is bond in triglycerides called?
Ester bond
What are saturated fatty acid chains and what are their structure?
Chains with no double bonds between carbons; form straight chains
What are monounsaturated fatty acid chains?
Chains with one double bond between carbons
What are polyunsaturated fatty acid chains and what are their structure?
Chains with more than one double bond between carbons, meaning they can’t pack together closely
In fatty acid chains, what do double bonds do?
Cause the molecule to bend
What state are polyunsaturated fatty acid chains at room temperature?
Liquid (i.e they are oils)
What are phospholipids made up of?
One hydrophilic phosphate head attached to two hydrophobic fatty acid tails
Why are phospholipids called surfactants?
Because they form a layer on the surface of water, with the hydrophobic fatty acid tails sticking out of the water
What are sterols also known as?
Steroid alcohols
What are sterols?
- Another type of lipid
- They are alcohols
- The OH group is hydrophilic, but the rest is hydrophobic
Example of sterol
Cholesterol
What is the general structure of an amino acid?
Carbon, which is attached to an amine group, a carboxyl group, an R-group and a hydrogen
What are proteases?
Enzymes that catalyse the hydrolysis reaction of peptides
What makes up a peptide bond?
C - N
What is catalase?
An enzyme that breaks down hydrogen peroxide
What are fibrous proteins?
Long insoluble proteins
2 difference between globular and fibrous proteins
- Globular are soluble, fibrous aren’t
- Fibrous aren’t folded into complex 3-D shapes, globular are
3 examples of fibrous proteins
- Keratin
- Elastin
- Collagen
Where is keratin found?
In hair, skin and nails
Where is elastin found?
In walls of blood vessels and aveoli
Where is collagen found?
Connective tissue found in skin, tendons, ligaments and the nervous system
What are the three components of a nucleotide?
- Phosphate group
- Pentose sugar
- Nitrogenous base
What are the bonds between nucleotides?
Phosphodiester bonds
What are the 4 types of base?
- Adenine
- Thymine
- Guanine
- Cytosine
What can the 4 types of base be divided into?
2 groups- pyrimidines and purines
What bases are pyrimidines?
Thymine and Cytosine
What bases are purines?
Guanine and Adenine
Which are bigger, purines or pyrimidines and why?
Purines, due to their double ring structure
How many hydrogen bonds do A and T form?
2
How many hydrogen bonds do G and C form?
3
What is thymine replaced by in RNA?
Uracil
What is the sugar in DNA?
Deoxyribose
What is the sugar in RNA?
Ribose
What is the function of DNA helicase in semi-conservative replication?
Enzyme that cause the two strands of DNA to separate
What is the function of DNA polymerase in semi-conservative replication?
Enzyme that cause the nucleotides to join up (form phosphodiester bonds)
What is semi-conservative replication?
Where two new molecules of DNA are produced, each one consisting of one strand of the old DNA, and one strand of the new DNA
What is a codon?
A triplet code
What is transcription?
Process where DNA is turned into RNA
What is translation?
Process where mRNA is translated into a sequence of amino acids
What is the sense strand?
The strand of DNA that contains the desired sequence of bases to code for the amino acids
What is the antisense strand?
The complimentary strand to the sense strand- it acts as a template strand, so the complementary RNA strand carries the same base sequence as the sense strand
What is the function of DNA polymerase?
Enzyme that catalyses the formation of phosphodiester bonds
What does tRNA contain which is necessary for protein synthesis?
Anticodons
What do anticodons do?
Bind to their complimentary codon, which brings amino acids together in the correct sequence
Properties of ATP
- Soluble
- Small
- Contains bonds that release amount of energy suitable for most cellular needs, but not so much energy is wasted as heat
How is energy released by ATP?
Bond reforming from ADP + P to ATP
What type of energy store is ATP and why?
It is a good immediate energy store, as the interconversion of ATP to ADP is happening constantly, meaning they don’t need a large store of it
Why is ATP not a long term energy store?
Due to the instability of the phophate bonds
What is the structure of ADP?
3 phosphates - ribose - adenine
Why is haemoglobin a conjugated protein?
Because it contains the haem prosthetic group
What is glycogen functionally equivalent to?
Starch
What types of organisms is glycogen found in?
Animals and fungi
What are the key properties of amylopectin (found in plants) and glycogen (found in animals)?
Insoluble
Branched
Compact
What is glucose stored as in plants?
Starch
What is glucose stored as in animals?
Glycogen
What type of reactions must starch/glycogen undergo to release glucose for respiration?
Hydrolysis reactions
Why are beta glucose molecules unable to join together in the same way alpha glucose molecules do?
Because the hydroxyl groups on carbon 1 and 4 are too far away from each other to react and form a bond
What is the only way beta glucose molecules can be joined together?
Alternate beta glucose molecules are turned upside down, to bring the hydroxyl groups close enough together
What is the outcome of this bonding of beta glucose molecules?
The polysaccharide formed is unable to coil or form branches, so is a straight chain molecule
What is the name of the straight chain molecule formed from the join of beta glucose molecules?
Cellulose
What is the test for reducing sugars?
Warm with Benedict’s reagent
What are the different positive results for the test for reducing sugars and what does each tell you?
Blue - no reducing sugars
Green - low concentration
Orange - medium concentration
Red - high concentration
What will happen when non-reducing sugars and Benedict’s are mixed?
They will not react (the solution will remain blue)
How do you test for non-reducing sugars?
You must boil it with dilute hydrochloric acid, and then warm with Benedict’s reagent
In the test for non-reducing sugars, why must it first be boiled with dilute HCl?
Because the non-reducing sugar will be hydrolysed by the acid, turning into its reducing sugar components, hence giving a positive test
What is the test for starch and positive result?
Add iodine solution, and the positive test is a colour change from yellow to purple/black
How do you test for lipids and what is the positive result?
Emulsion test- sample mixed with ethanol and then shaken with water. If a white emulsion forms, lipids are present
How are peptide bonds formed?
A hydrogen from amino acid 1, and the OH from amino acid 2 join together to form water.
The nitrogen from amino acid 1 forms the peptide bond with the carbon from amino acid 2
What is tertiary protein structure?
The protein folding into its final shape
What 5 interactions are found in tertiary proteins?
- Dipole-dipole interactions
- London forces
- Hydrogen bonds
- Ionic bonds
- Disulphide bridges
Where do ionic bonds form between in tertiary proteins?
Between oppositely charged R-groups
What are disulphide bridges?
Covalent bonds that form between R-groups that both contain sulphur
What are quaternary proteins?
Where interactions form between two or more individual proteins (called subunits). These can be identical or different proteins
What interactions are present in quaternary proteins?
All the same interactions as in tertiary proteins, however they are between different protein molecules rather than within one molecule
Why is genetic code referred to as degenerate code?
Because different codons can code for the same amino acid
What enzyme causes phosphodiester bonds to be formed between RNA nucleotides?
RNA polymerase
What must happen to the DNA double helix for transcription to occur?
The DNA double helix must be unzipped (by DNA helicase)
Where does the mRNA first bind to during translation?
The start codon (AUG) binds to the small subunit of the ribosome
What does tRNA carry that is necessary in translation?
Each tRNA molecule carries an amino acid corresponding to the correct triplet code
What does the first tRNA molecule always carry?
The amino acid methionine
What happens between amino acids during translation?
They form peptide bonds between each other, which in turn causes the 1st tRNA to release the 1st amino acid
What does the ribosomes do during translation?
It moves along the mRNA
