Biological molecules Flashcards
Name two types of starch?
Amylose
Amylopectin.
How is it like glycosidic bond formed?
Condensation reaction between two monosaccharides
What is the condensation reaction between for a 1,4-glycosidic bond?
Between the hydroxyl groups at carbon 1 of one monosaccharide and carbon 4 of the other monosaccharide
What is the condensation reaction between for a 1,6-glycosidic bond?
Between the hydroxyl groups at carbon 1 of one monosaccharide and carbon 6 of the other monosaccharide
What is the structure of alpha glucose?
H at the top, OH at the bottom
What is the structure of beta glucose?
H at the bottom OH at the top
What glucose molecule is amylopectin made up of?
Alpha glucose
What glycosidic bonds is amylopectin made up of?
Alpha 1,4
Alpha 1,6
Describe the structure of amylopectin?
Highly branched due to the 1–6 glycosidic bonds
Elliptical
What does amylopectin being highly branched mean?
Rapid hydrolysis because many points for the enzyme to act on
What does the elliptical structure of amylopectin mean for it?
Compact
Amylopectin
- molecule
- bonds
- shape and structure
- benefits of structure
- benefits of shape
Alpha glucose Alpha 1-4, alpha 1-6 Highly branched due to 1-6 binds Elliptical Branched means rapid hydrolysis because lots of points for enzymes to act Compact due to elliptical shape
Amylose
- molecule
- binds
- shape
- spread out/ compact
- respiration
Alpha glucose
Alpha 1-4 glycosidic bonds
Alpha helix naturally coils (single chain)
Compact - fewer OH groups exposed on the helix so less of an osmotic effect
Slow hydrolysis for respiration because only 2 enzyme attachment points
Molecules that make up amylose?
Alpha glucose
Amylose bonds
Alpha 1-4 glycosidic bond
Amylose structure
Alpha helix which naturally coils up (single chain)
Amylose spread out/compact
Compact = few OH group is exposed on the helix so less of an osmotic affect
Amylose hydrolysis points
Slow hydrolysis for respiration because they’re only two enzyme attachment points
Glycogen
Molecule Bond Branched? Hydrolysis Compact/spread out? Compared to starch
Alpha glucose Alpha 1-4, alpha 1-6 glycosidic bonds Highly branched due to many 1,6 bonds Spherical Branches allow rapid hydrolysis to produce glucose because there are many enzyme attachment points Compact so more can be stored Less dense and more soluble than starch
Molecules that make up glycogen
Alpha glucose
Glycosidic bonds in glycogen
Alpha 1,4
Alpha 1,6
Describe glycogen structure?
Highly branched due to many alpha 1,6 glycosidic bonds
Spherical
Branched allow rapid hydrolysis because many enzyme attachment points
What molecules is cellulose is made up of?
Beta glucose
What glycosidic bonds does cellulose have?
Beta 1,4 glycosidic bonds
Is cellulose insoluble or soluble?
Insoluble
Describe the structure of cellulose
Straight chain with staggered ends so no overall points of weakness
Quality to cellulose
Intermolecular forces mean it’s very flexible
H bonds break and reform with other OH groups
Each chain linked by H bonds forming strong fibres
Cellulose
- molecules
- bonds
- soluble/insoluble?
- structure
- forces
Beta glucose
Beta 1,4 glycosidic bonds
Insoluble
Straight chain with staggered ends so no overall points of weakness
Intermolecular forces mean it’s very flexible
H bonds break and reform with other OH groups
Each chain linked by H bonds forming strong fibres
What are carbohydrates?
Naturally occurring sugars, starches and fibre.
What are all carbohydrates made up of?
Sugar molecules.
Sugar molecules can link together to form starches and fibre
In the body what (carbohydrates) is broken down
Starches and sugars are broken down in the digestive system to glucose
Name three examples of complex carbohydrates
Starch
Glycogen
Cellulose
What are the four carbohydrates we study at A-level
Starch (amylopectin and amylose)
Glycogen
Cellulose
Compare the monomers of amylopectin, amylose, glycogen and cellulose
Amylopectin - alpha glucose
Amylose - alpha glucose
Glycogen - alpha glucose
Cellulose - beta glucose
Compare the shape of amylopectin, amylose, glycogen and cellulose
Amylopectin - elliptical
Amylose - helical
Glycogen - spherical
Cellulose - straight chained
Compare the glycosidic bonds of amylopectin, amylose, glycogen and cellulose
Amylopectin - 1-4, 1-6
Amylose - 1-4
Glycogen - 1-4, 16
Cellulose - 1-4
Compare the branched/unbranched of amylopectin, amylose, glycogen and cellulose
Amylopectin - branched
Amylose - unbranched
Glycogen - branched
Cellulose - unbranched
Compare the monomers orientation in cellulose and glycogen
Cellulose - monomers upside down
Glycogen - monomers not upside down
What is small things are present in cellulose ?
Microfibres
Celulose is found in
Plants
Glycogen is found in
Animals and fungi
Amylopectin and amylose are found in
Plants
What do all of the four complex carbohydrates have in common?
Insoluble so do not affect water potential
Which complex carbohydrates are compact and what does this mean?
Compact because helical (amylose)
Compact because spherical (glycogen)
Compact because elliptical (amylopectin)
So more storage
Discussed the size of starch
Large so cannot pass out of the membrane
How is cellulose adapted to be strong and flexible for plant cell walls?
Strong due to chains linked by hydrogen bonds forming strong fibres
Flexible because hydrogen bonds can break and reform with different OH groups
What are the monomers of carbohydrates
Monosaccharides
Give an example of simple carbohydrate monosaccharides
Glucose, fructose, galactose
Talk about glucose
Type of sugar, mers
Glucose is a hexose sugar
There are two types of glucose - alpha glucose and beta glucose they are isomers of each other
How is sucrose formed?
Condensation reaction between glucose and fructose molecule
How is lactose formed?
Condensation reaction between a glucose molecule and galactose molecule
How is maltose formed?
Condensation reactions between two alpha glucose molecules
How are disaccharides formed?
Condensation reaction between
two monosaccharides so that a glycosidic bond forms between them and a molecule of water is released
What are glycosidic bonds between?
The OH group form one monosaccharide and the OH group from another monosaccharide
What is sugar a general term for?
Monosaccharides and disaccharides
What do reducing sugars include?
All monosaccharides and some disaccharides (maltose and glucose)
What can all sugars be classified as?
Reducing or non-reducing
What do non-reducing sugar is include
Some disaccharides and all polysaccharides
Explain how to test for reducing sugars
Add Benedictus reagent to sample
Heat in water bath
Positive result = coloured precipitate forms (bricks red)
How does the colour of the precipitate formed in a positive Benedicts test reflect the concentration of the reducing sugar?
Blue -> green -> yellow -> orange -> brick red
Higher concentration the further colour change along that spectrum
What is a more accurate way of looking at colour change for identifying the concentrations of reducing sugar is present after the benedicts test?
Filter solution and weigh precipitate
What could it mean if the result of the Benedict’s test is negative?
There might still be a non-reducing sugar present
If the result of the Benedict’s test is negative, what further test could you do to test for non-reducing sugars?
Add dilute hydrochloric acid.
Heat and water bath.
Neutralise with sodium hydrogen carbonate.
Carry out Benedict’s test
Positive = same results as benedicts (brick red)
What are we essentially doing when we need to test for non reducing sugars ?
Testing with benedicts and seeing there is no reducing sugar
Breakdown non-reducing sugar into monosaccharides
So if benedicts test positive we know we did break the disaccharide down and it was originally a non reducing sugar
When testing for non reducing sugars what does adding HCL do?
Hydrolyses the glycosidic bond to form monosaccharides
What are the monomers of proteins?
Amino acids
What is formed when two amino acid is joined together?
A dipeptide
What is a polypeptide
A change of multiple amino acid is joined by peptide bonds
What are proteins made up of?
One or more polypeptide chains.
Which three groups does an amino acid have?
The carboxyl group.
An amine group.
R group (also known as a variable group)
How do you amino acids differ?
By the R group
Which amino acid has a H for it’s R group?
Glycine
How are peptide bonds formed?
Condensation reaction between two amino acids releasing a molecule of water
Explain according to bonds how a peptide bond forms
Imagine two amino acids side by side
The OH from one and the H from another form water
Leaving:
O H || I —-C—N—
Draw a peptide bond
O H
|| I
—-C—N—
Describe the primary structure of a protein
Unique sequence of amino acids in a polypeptide chain
Peptide
Describe the secondary structure of a protein
Polypeptide chain folds into alpha helices or beta pleated sheets
Hydrogen bonds form between amino acids
Peptide
Hydrogen
Describe the tertiary structure of a protein
Polypeptide chain coils and folds further.
Peptide Hydrogen Ionic London Disulphide bridges
In a tertiary structure protein where do the disulphide bridges form?
Whenever two molecules of amino acid cysteine come close together – sulfur atom in one cysteine bonds to sulfur atom in the other
Describe the Quaternary structure of proteins
More than one polypeptide chain
Give three examples of Quaternary structure of proteins
Haemoglobin.
Insulin.
Collagen.
What are the four types of our groups that amino acids can have?
Polar and on charge
Polar and positively charged
Paula and negatively charged
Nonpolar and hydrophobic
Name for functions of proteins
Enzymes
Antibodies
Transport proteins
Structural proteins
When the R group changes …
Bonds will form in different places
What causes channel proteins to form a channel?
They contain hydrophobic and hydrophilic amino acids
Explain the test and results for proteins
How to sodium hydroxide solution (test solution needs to be made alkali)
Add copper to sulphate solution
Positive = solution turns purple negative = solution stays blue
When is substrate fits into an enzymes active site, what is formed?
An enzyme substrate complex
What about an enzyme substrate complex lowers activation energy for a reaction?
1) If two substrates need to be joined together, being attached to the enzyme has them closer together reducing any repulsion so the molecules bond more easily and less energy is required
2) If an enzyme is catalysing a breakdown reaction fitting the substrate into the active site puts strain on the bonds in the substrate so the substrate breaks more easily requires less energy
Describe features of the lock and key theory
Active site doesn’t change shape, it’s rigid
What does the locking key theory rely on?
And the substrate entering the active site of the enzyme at exactly the correct orientation
Describe the induced fit theory
The substrate does not have to be complimentary to the active site of the enzyme
The substrate binds to the active site and the active site changes shape to form an enzyme substrate complex
As the active site of the enzyme binds around the substrate it puts pressure on the substrate, distorting its bonds (hydrogen and ionic)
The substrate becomes less stable which reduces its activation energy
Substrate is released sometimes broken up and enzyme returns to its original shape to catalyse more reactions
What is a transition states? (Enzymes)
The least stable state of the substrate when it contains the most energy
Explain three ways that enzyme properties relate to their tertiary structure
Each enzyme has a different tertiary structure and so a different shaped active site. If the substrate it’s not complimentary to the active site, and enzyme substrate does not form
The tertiary structure of an enzyme can be altered by changes in pH or temperature
The primary structure of the enzyme is determined by gene if there is a mutation in the chain it could change the tertiary structure of the enzyme produced
What do enzymes do?
Actors biological catalysts
Lower activation energy
Provide an alternate route for the reaction
Describe the structure of triglycerides
One glycerol
Three fatty acids
What bond joins a glycerol molecule to a fatty acid in a triglyceride?
An ester bond
What makes lipids insoluble in water?
The fatty acid tales are hydrophobic
How does an Ester bond form?
A condensation reaction between a fatty acid and glycerol molecule where a molecule of water is released
How many condensation reactions must occur for a triglyceride to form?
Three because three ester bonds into form to join three fatty acids to the glycerol molecule
Explain where the ester bond between a fatty acid and glycerol molecule forms
Between the OH on the glycerol and the OH on the fatty acid
Leaving the O from the glycerol
Draw the basic structure of a fatty acid
O
II
OH-C-R
Carboxylic acid ??
The R group is the tail and the OH is what forms water along with the H from the glycerol
Describe saturated fatty acids
Don’t have any double bonds between the carbon atoms in the fatty acid tail
Describe unsaturated fatty acid
Have at least one double bond between carbon atoms in the fatty acid tail
Describe the structure of a phospholipid
One glycerol
Too fatty acid’s
One phosphate group
Describe which parts of a phospholipid are hydrophobic and hydrophilic
Hydrophilic phosphate head
Hydrophobic fatty acid tails
Describe the emulsion test and result for lipids
Shake test substance with ethanol until it dissolves
Poor solution into water
Positive result = milky emulsion
What is the main function of triglycerides?
Energy storage molecules
What is the main function of phospholipids
Make up the bilayer of cell membranes
How is the structure of triglycerides related to their function as energy storage molecules
The long hydrocarbon tells of the fatty acids contain chemical energy which can be released one broken down
Triglycerides are insoluble so do not affect water potential and osmosis in the cell. They form insoluble droplets as the hydrophobic fatty acid tales face inwards and the hydrophilic heads face outwards
Explain how the structure of phospholipids is related to their function in the bilayer of the cell membrane
The hydrophilic heads and hydrophobic tails mean that they form a double layer with their heads facing out towards water on either side
This also means the centre of the boiler is hydrophobic so it prevents water soluble substances from passing through the membrane which acts as a barrier to the substances
What is one of the main functions of RNA?
Transfer genetic information from the DNA to the ribosomes
What is the main function of DNA?
Store genetic information
What is a nucleotide made up of?
Pentose sugar
Nitrogen containing organic base
Phosphate
What are the monomers of DNA and RNA?
Nucleotides
What is the pentose sugar in a DNA nucleotide called?
Deoxyribose sugar
What is the pentose sugar in RNA nucleotides called?
ribose sugar
What are the four possible bases in a DNA nucleotide?
Adenine
Thymine
Guanine
cytosine
What are the four possible bases in a RNA nucleotides?
Adenine
Uracil
Cytosine
Guanine
What are the polymers of DNA and RNA?
Nucleotides
Explain how phosphodiester bond forms
Condensation reaction between the phosphate group of one nucleotide and the sugar of another nucleotide releasing a water molecule
How are two DNA polynucleotide strands joined together?
Hydrogen bonds between complimentary base pairs
How many hydrogen bonds form between adenine and thymine?
Two hydrogen bonds
How many hydrogen bonds form between guanine and cytosine?
Three
The two polynucleotide strands of DNA are said to be…
Anti parallel
Which bases are purine and which are pyrimidine?
Purine - adenine and guanine
Pyrimidine - thymine and cytosine
What is a purine base?
To carbon nitrogen ring bases
What is a pyramidine base?
One carbon nitrogen ring bases
Which scientists determined to the structure of DNA and when?
Watson and Crick
1953
Which scientists validated the theory of semiconservative DNA replication which was created by Watson and Crick, and when?
Meselson and Stahl
After 1953..?
Why are DNA strands antiparallel?
DNA polymerase can only catalyse adding a phosphate to the third carbon on the ribose sugar of the next nucleotide
Why is DNA double-stranded?
It is more stable and less reactive
It provides a template for repair
Why is RNA single-stranded?
Requires less space
consumes less energy to replicate and translate into proteins
Explain how semiconservative replication of DNA occurs (4)
Helicase breaks the hydrogen bonds between complimentary base pairs, unwinding the double helix
Each original single strand acts as a template for a new strand. Complimentary base pairing occurs as free-floating DNA nucleotides are attracted to the complimentary exposed bases on each original template strand.
Condensation reactions join the nucleotides of the new strands by phosphodiester bonds. This is catalysed by DNA polymerase. Hydrogen bonds form between the bases of the new and original strand
Each DNA molecule contains one strand from the original DNA molecule and one new strand
Explain how DNA polymerase works.
DNA polymerase can only work in the 3’ —> 5’ direction due to its specific active site.
It produces a continuous Strand (the leading strand) and they discontinue a strand (the lagging strand)
Lagging strand is replicated in Okazaki fragments which are stuck together by DNA ligase
Why are DNA strands antiparallel?
DNA polymerase can only catalyse adding a phosphate to the third carbon on the ribose sugar of the next nucleotide
Why is DNA double-stranded?
It is more stable and less reactive
It provides a template for repair
Why is RNA single-stranded?
Requires less space
consumes less energy to replicate and translate into proteins
Explain how semiconservative replication of DNA occurs (4)
Helicase breaks the hydrogen bonds between complimentary base pairs, unwinding the double helix
Each original single strand acts as a template for a new strand. Complimentary base pairing occurs as free-floating DNA nucleotides are attracted to the complimentary exposed bases on each original template strand.
Condensation reactions join the nucleotides of the new strands by phosphodiester bonds. This is catalysed by DNA polymerase. Hydrogen bonds form between the bases of the new and original strand
Each DNA molecule contains one strand from the original DNA molecule and one new strand
Explain how DNA polymerase works.
DNA polymerase can only work in the 3’ —> 5’ direction due to its specific active site.
It produces a continuous Strand (the leading strand) and they discontinue a strand (the lagging strand)
Lagging strand is replicated in Okazaki fragments which are stuck together by DNA ligase
Define semiconservative replication
Produces two copies of DNA, each one contains one original Strand and one new strand
Define Conservative replication
Produces a copy of DNA composed of two entirely new strands, leaving the original two DNA strands together
Explain how Meselson and Stahl validated the theory of semiconservative replication for DNA.
They grew bacterial cells in media containing different nitrogen isotopes. (One batch of bacteria grew in media containing N15, heavy isotope. Other batch of bacteria grew in media containing N14, light isotope)
Nitrogen is used in the creation of DNA because it makes up the nitrogenous bases. Therefore DNA made from heavy nitrogen isotope would have an overall heavy density but DNA made from the light nitrogen isotope would have an overall lighter density.
Bacterial DNA made from the heavy nitrogen isotope was put into an environment with light nitrogen isotopes present and DNA replication occurred.
The DNA molecules which were produced had half of the nitrogen heavy isotope and half of the light nitrogen isotope so an overall medium density.
This suggested that they were made from the original heavy nitrogen strand and the new nitrogen light isotope strand. This is evidence for semiconservative replication.
(Heavy made, light made, bacteria with just heavy DNA out into environments with light N floating around, final DNA was medium density bf contained heavy N and light N)
How would the strips across the centrifuge tube appear if conservative DNA replication was occurring?
Conservative replication starting with DNA made from heavy N isotope in environment with free light N isotopes
One band of DNA across top for light N
One band of DNA across bottom for heavy N
How would the strips across the centrifuge tube appear if semi conservative DNA replication was occurring?
DNA strand in middle of centrifuge tube because medium density as made up of both heavy and light N isotopes
