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Chemistry > Polymers of life > Flashcards

Polymers of life Flashcards

1
Q

What are amino acids made from ?

A

An amine group
A carboxyl group
R group (side chain)
A central carbon atom
H group

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2
Q

What is a zwitterion ?

A

An overall neutral molecule that has both a positive and negative charge in different parts of the molecule.

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3
Q

How can paper chromatography be used to identify unknown amino acids ?

A
  • Draw a pencil line near the bottom of a piece of paper and put a concentrated spot of mixture you want to investigate on it
  • Place the paper into a beaker containing a small amount of solvent so that the solvent level is below the spot of mixture. Place a watch glass on to stop any solvent evaporating out.
  • Different substances have different solubilities in the solvent. As the solvent spreads up the paper, the different chemicals in mixture move with it, but at different rates, so hey separate out.
  • When the solvents’ nearly reached the top, take the paper out and mark where the solvent has reached with a pencil. This is the solvent front.
  • Identify the positions of the spots of different chemicals on the paper. Some chemicals, such as amino acids, aren’t coloured so you have to make them visible.
  • Dip the paper into a jar containing a few crystals of iodine. Iodine sublimes from a solid straight to a gas, and the iodine gas in the jar causes the sports to turn brown.
  • You can work out the Rf value of the substance using this formula:
    Distance travelled by spot / Distance travelled by solvent
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4
Q

How are proteins made ?

A

In a condensation reaction between amino acid monomers with peptide bonds. The amine group of one amino acid reacts with the carboxylic acid of another in a condensation reaction.

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5
Q

What is it called when two amino acids are joined ?

A

A dipeptide

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6
Q

What is it called when many amino acids are joined together ?

A

A polypeptide chain

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7
Q

How can you break a proteins down ?

A

In a hydrolysis reaction.
Use hot aqueous hydrochloric acid, and heated under reflux for 24 hours. This produces the ammonium salts of the amino acid, the final mixture is then neutralised using a base.

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8
Q

What is the primary structure of a protein ?

A

The primary structure is the sequence of amino acids in the long chain that makes up the protein (the polypeptide chain)

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9
Q

What is the secondary structure of a protein ?

A

The peptide links can form hydrogen bonds with each other, meaning the chain isn’t a straight line. The shape of the chan is called its secondary structure. The most common secondary structure is called an alpha helix chain. Another common type of secondary structure is a beta-pleated sheet.

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10
Q

What is the tertiary structure of a protein ?

A

The chain of amino acids is itself often coiled and folded in a characteristic way that identifies the protein. Extra bonds can form between different parts of the polypeptide chain, which gives the protein a kind of three-dimensional shape. This is its tertiary structure.

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11
Q

What are the different bonds that hold proteins together ?

A

Id - Id bonds > weak attractions that can form between two non-polar side groups

Ionic interactions > formed between charged side groups

Hydrogen bonds > some R - groups contain functional groups that are able to form hydrogen bonds.

The amino acid cytosine contains a thiol group. Sulfide groups on different cytosine residues can join together by forming a disulfide bond

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12
Q

What can a three dimensional structure of a protein affect ?

A

Its properties

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13
Q

The dipeptides formed can be hydrolysed to give the original amino acids again. Give the reagents and conditions for this reactions.

A

Hot aqueous hydrochloric acid and heat under reflux.

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14
Q

Which of the following statements about proteins are incorrect ?
A. The tertiary structure of a protein is held together by forces that form between the R groups on amino acids.
B. The primary structure of a protein is its amino acid sequence.
C. Proteins can be hydrolysed to their constituent amino acids using a strong base.
D. An amino acid with the formula CH3CH(OH)CH(NH2)COOH is able to form hydrogen bonds to stabilize the three dimensional structure of a protein.

A

C

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15
Q

Is DNA a polymer of nucleotides ?

A

Yes

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16
Q

What is a DNA nucleotide made up of ?

A
  • A phosphate group
  • A pentose sugar
    Deoxyribose
  • A nitrogen containing base
    Adenine, Thymine, Cytosine, Guanine
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17
Q

Where does the bond for when nucleotides join together ?

A

Between phosphate group and the sugar of another.

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18
Q

What are two differences between RNA and DNA ?

A
  • RNA nucleotides have a different sugar. In DNA nucleotides its deoxyribose. In RNA nucleotides its ribose.
  • RNA has the base uracil instead of thymine.
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19
Q

How do nucleotides link together ?

A

Through condensation reactions

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20
Q

How is a phosphate-sugar backbone formed ?

A
  • When a phosphate and a sugar react, a water molecule of water is lost and a phosphate-ester link is formed.
  • There are still -OH groups in the phosphate-ester, so further ester links can be formed. So a polymer forms made up of an alternating phosphate-sugar chain.
  • The phosphate groups always attach to the -CH2OH group and the -OH group on the adjacent carbon.
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21
Q

How do bases connect to the sugar ?

A

The base molecules are connected to the sugars in the phosphate-sugar backbone by a condensation reaction. All of the bases have an -NH group somewhere in their structure. It’s the N atom of the -NH group that bonds to the sugar, eliminating an -OH group from the sugar and H from the -NH group to form water.

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22
Q

How does DNA form a double helix ?

A
  • DNA is made of two polynucleotide strands.
  • The two strands spiral together to form a double helix structure which is held together by hydrogen bonds between bases.
  • Each base can only join with one particular partner > this is called complementary base pairing.
  • Adenine always pairs with Thymine, and Guanine always pairs with Cytosine
  • The two strands of DNA are complementary - this means that they match up. So, whenever there’s an adenine base on one strand, and whenever there’s a guanine base on one strand, there will be a cytosine base and thymine on the other, and vice versa.
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23
Q

What is base pairing ?

A

When the opposite bases always pair up, Adenine and Thymine, Guanine and Cytosine. It happens because of the arrangement of atoms in the base molecules that are capable of forming hydrogen bonds.

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24
Q

How is a hydrogen bond formed ?

A

Between a hydrogen in a polar bond and a lone pair of electrons on a nearby O, N or F atom. To bond, the atoms have to be the right distance apart.

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25
Q

How many hydrogen bonds are between A and T ?

A

Two hydrogen bonds

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26
Q

How many hydrogen bonds are between C and G ?

A

Three hydrogen bonds

27
Q

What is it called when DNA can copy itself ?

A

Self-replication

28
Q

What is cell division essential for ?

A

Growth and reproduction

29
Q

How does DNA replicate ?

A
  • The hydrogen bonds break and the DNA double helix starts to split into two single strands.
  • Bases on free-floating nucleotides in the cytoplasm now pair up with the complementary bases on the nucleotides in the DNA. Complementary base pairing makes sure the correct nucleotide joins in the correct place.
  • An enzyme called DNA polymerase join the new nucleotides together to form a polynucleotide chain
  • This happens on each of the strands to make an exact copy of what was on the other strand. The result is two molecules of DNA, identical to the original molecule of DNA.
30
Q

What are the monomers that make up DNA and RNA called ?

A

Nucleotides

31
Q

What are the three components of these monomers ?

A

A phosphate group
A pentose sugar
A nitrogen containing base

32
Q

What is the difference between the phosphate-sugar backbone of DNA and RNA ?

A

DNA has a pentose sugar of deoxyribose.
RNA has a pentose sugar of ribose.

33
Q

Name the reaction by which the components in a nucleotide connect together ?

A

Condensation reaction

34
Q

Which type of intermolecular force holds the two strands of DNA together in a double helix ?

A

Phosphate-ester bond

35
Q

Describe the process that happens during DNA replication ?

A

The hydrogen bonds break and the DNA double helix unwinds, and splits into two strands, by DNA helicase.Bases on free nucleotides in the cytoplasm can now pair up with the complementary bases on the nucleotides in the DNA. Complementary base pairing make sure the correct nucleotides joins in the correct place. DNA polymerase joins the new nucleotides together to form a polynucleotide chain. THis happens on each of the stands to make an exact copy of what was on the other strand, The result is two molecules of DNA, identical to the original molecule of DNA.

36
Q

How does DNA contain the basis of the genetic code ?

A
  • DNA codes for specific amino acids with sequences of three bases, called ase triplets or codons. Different sequences or base code for different amino acids.
  • There are 64 possible base triplet combinations, but only about 20 amino acids in human proteins so there are some base triplets to spare.
  • The order in which the amino acids are connected together determines the secondary and tertiary structures of a protein, and so all the proteins properties.
37
Q

What are the different types of RNA ?

A

mRNA
tRNA
rRNA

38
Q

How does mRNA help make proteins ?

A
  • mRNA is a single polynucleotide strand.
  • It’s an exact reverse copy of a single strand section of DNA, except thymines replaced by uracil.
  • The amino acid codons in mRNA are complementary to the DNA codons as they form when complementary bases pair up.
39
Q

How does tRNA help to make proteins ?

A
  • tRNA is a single stranded polynucleotide strand that’s folded into a clover shae. At one end of the tRNA molecule there’s a sequence of three base pairs called an anticodon, The anticodon complements a codon on the mRNA, so will attach to parts of the mRN, where that codon is present by base pairing.
  • On the other end of the tRNA there’s a binding site where the amino acid that corresponds to the complementary mRNA codon can attach.
40
Q

How does rRNA help to make proteins ?

A

rRNA is made up of polynucleotide stands that are attached to proteins to make things called ribosomes. It is the largest type of RNA.

41
Q

How does transcription occur ?

A
  • The DNA double helix unwinds to reveal a single stranded portion.
  • The DNA bases attract free nucleotides with complementary bases.
  • The RNA nucleotides are joined to each other by the enzyme RNA polymerase. This forms a strand of mRNA.
  • The DNA coils up again, unaltered
42
Q

How does translation
occur ?

A
  • DNA transcription occurs to make a strand of mRNA
  • Ribosomes are large complexes made from rRNA and proteins. A ribosome attaches to the mRNA, and starts to move along it, looking for a start codon (AUG)
  • Once its found a start codon the ribosome temporarily pauses, until a tRNA with the correct anticodon bases pairs with the AUG codon inside the ribosome. The tRNA has a methionine amino acid attached to it.
  • The ribosome then moves three bases forward, and waits for a different tRNA to bring the next amino acid that the mRNA codes for into the ribosome. Now there are two amino acids inside the ribosome and the ribosome joins them together with a peptide bond.
  • The ribosome moves forward again. The first tRNA now leaves the ribosome and breaks away from its amino acid. A new tRNA brings in the third amino acid of the chain.
  • The process continues in this way until a stop codon is reached. The stop codon doesn’t code for an amino acid. The ribosome releases the polypeptide chain at this point.
43
Q

Whats a codon ?

A

Three bases, also known as a base triplet

44
Q

Whats made during transcription ?

A

mRNA

45
Q

Whats made during translation ?

A

Polypeptide chain

46
Q

The sequence of bases in a small portion of mRNA is as follows:
-AAGGUGCAUCGA-

a) Why couldn’t the sequence be from a portion of DNA ?

b) How many amino acids does this sequence code for ? Explain your answer ?

c) Write the sequence of bases for the DNA strand from which the portion of mRNA was transcribed ?

A

a) DNA does not contain uracil, only RNA contains uracil

b) 4 amino acids. Each amino acid is coded for by a triplet of bases.

c) -TTCCACGTAGCT-

47
Q

DNA contains a sequence of base triplets that represents a sequence of amino acids in a protein molecule. The first stage in making a protein is to make a molecule of mRNA from the DNA.

a) What is the name of this process and where in the cell does it occur.

b) A protein is made using the bases in mRNA by a process called translation.
i) What is the name of the protein-RNA complex called in this process ?
ii) Why do all proteins made in this way start with the same amino acid (methionine) ?

A

a) Transcription - happens in the cell nucleus

b) i) Ribosome

 ii) Translation begins when a ribosome reads a start codon. As this codon is always the same, it always causes the addition of the same amino acid.
48
Q

A codon on a section of the mRNA has the sequence of bases -GGU-, which corresponds to the amino acid glycine. The mRNA codes for a polypeptide chain which contains 73 amino acids. Explain how this glycine molecule is inserted into the polypeptide ?

A

A tRNA has an anticodon at one end and glycine attached at the other. The anticodon on the tRNA involved is -CCA-. The tRNA anticodon binds to the codon on the mRNA. The same thing happens with the next codon and a peptide bond is formed with the adjacent amino acid.

49
Q

What are enzymes ?

A

They are biological catalysts, that speeds up a chemical reaction

50
Q

Do enzymes have a high or low specificity ?

A

High specificity

51
Q

How do enzymes work ?

A

The substrate has to fit into the active site. Substrates are three-dimensional, and if their shape doesn’t match the active site shape, then the reaction won’t be catalysed. This is called the lock and key model. The substrate is help in the active site by temporary bonds such as hydrogen bonds and id-id forces. These temporary bonds form between the substrate and ‘R’ group of the enzymes amino acids.

52
Q

Why is the reaction slow at low temperatures ?

A

The reactant molecules have low kinatic energy

53
Q

What happens at high temperatures or pH ?

A

The reaction rates drop off dramatically because the enzyme becomes denatured. It stops working properly and can no longer effectively catalyse the reaction.

54
Q

Why do enzymes
denature ?

A

When they become too hot, or are exposed to too high a concentration of acid or alkali. The bonds that define the shape of the active site break, changing the tertiary structure of the enzyme molecule. The active site is no longer the correct shape for the substrate to fit into.

55
Q

What are competitive inhibitors ?

A

They are molecules with a similar shape to the substrate. They compete with the substrate to bond to the active site, but no reaction follows, Instead they block the active site, so no substrate can fir in.

56
Q

What can impact the amount of inhibition that can happen ?

A

The relative concentrations of competitive inhibitor and substrate - if there’s a lot more of the competitive inhibitor, it’ll take up most of the active sites and very little substrate will be able to get to the enzyme. The amount of inhibition is also affected by how strongly the inhibitor bonds to the active site .

57
Q

What happens in a simple, uncatalysed reaction ?

A

The substrate, S, might become a molecule of product, P

58
Q

What happens when the concentration of S increases ?

A

The reaction speeds up. As it is a first order reaction, doubling the concentration of S should double the rate of reaction.

59
Q

What happens when this reaction,
S –> P
is catalysed by a reaction ?

A

At first doubling the concentration of S still doubles the rate of reaction. Eventually, the reaction reaches a stage where it can’t go an faster, no matter how much you increase the concentration.

60
Q

How can you measure the volume of gas, using a gas syringe ?

A

If the reaction produces a gas, you can measure the volume evolved at regular time intervals using a gas syringe.

61
Q

How can you measure the volume of gas, using a mass balance ?

A

If the reaction produces a gas, you can measure the mass of gas lost at regular time intervals using a mass balance.

62
Q

How can you measure the concentration of a product, using a titration ?

A

You can take samples at regular intervals and use titrations to find the concentration of a substrate or product in the solution.

63
Q

The enzyme catalyse is found in potatoes, and catalyses the break down of hydrogen peroxide into oxygen and water. Describe an experiment to determine how the rate of the enzyme-catalysed break down of hydrogen peroxide into water and oxygen changes with the concentration of hydrogen peroxide.

A
  • To sealed conical flask that is connected to a gas syringe add 10 cm3 of pureed potato
  • Add 1 cm3 of 0.001 mol/dm3 hydrogen peroxide to the flask, replace the bung and gas syringe and immediately start timing with a stop watch.
  • Record the volume of oxygen in the gas syringe after 30s.
  • Repeat the experiment using the following concentrations of hydrogen peroxide:
    0.002 mol/dm3
    0.005 mol/dm3
    0.01 mol/dm3
    0.02 mol/dm3
    0.05 mol/dm3
  • Use the data to calculate the rate of reaction at different concentrations of hydrogen peroxide.
64
Q
A

Chemistry (8 decks)

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