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(A Level) Biology > Topic 2 - Protein Synthesis (2.6 to 2.10) > Flashcards

Topic 2 - Protein Synthesis (2.6 to 2.10) Flashcards

1
Q

What is the genetic code

A

A set of rules that define how the four letter code of DNA is translated into 20 proteinogenic amino acids

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1
Q

What is a triplet

A

A sequence of 3 DNA bases that are read together and determine 1 amino acid

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2
Q

What is a codon

A

A triplet of bases in mRNA that
are complimentary to anticodons

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3
Q

How many amino acids are there

A

There are 22 proteinogenic amino acids but only 20 in our genetic code

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4
Q

What is a polypeptide

A

another name for a protein

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5
Q

What are proteinogenic amino acids

A

Amino acids that are incorporated biosynthetically into polypeptides

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6
Q

How is the genetic code degenerate

A

Most amino acids can be coded for by multiple triplets

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7
Q

Why is the genetic code degenerate

A

There are only 20 proteinogenic amino acids in our genetic code but there are 64 possible triplet combinations

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8
Q

What is partial degeneracy of triplets

A

Where the first two nucleotides are the same but the third is different

e.g uug and uua code for leucine (both start with uu)

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9
Q

What is complete triplet degeneracy

A

Where any base can take the third position and still code for the same amino acid

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10
Q

What is a transcription unit

A

Any section of DNA that is used to transcribe a polypeptide

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11
Q

What are the 3 sections of a transcription unit

A

The promoter
The structural gene
The terminator

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12
Q

What is the purpose of the promoter

A

RNA polymerase binds upstream to the promoter

This allows RNA polymerase to assemble RNA nucleotides.

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13
Q

What is the structural gene

A

The part of the gene which is read and transcribed

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14
Q

What part of the structural gene is ‘read’ and transcribed

A

The antisense strand (3’ to 5’)

This is because RNA polymerase places from 5’ to 3’ (starting at the 3’ end of the antisense strand and moving towards the 5’ end)

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15
Q

What is the purpose of the terminator

A

It causes RNA polymerase to ‘break off’ which stops RNA nucleotides from being placed / forming phosphodiester bonds

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16
Q

What happens during transcription

A

-DNA unzips and unwinds at one gene

-DNA helicase breaks the hydrogen bonds between complimentary nitrogenous bases

-RNA polymerase binds to the promoter region catalysing RNA nucleotides to line up on the template strand (antisense strand)

-Hydrolysis of phosphorylated molecules such as ATP occurs and the energy is used to form phosphodiester bonds between adjacent nucleotides

-RNA polymerase reaches the terminator region and transcription ends leaving a single strand of mRNA

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17
Q

What does RNA polymerase do

A

It adds complimentary RNA nucleotides to the template strand (reads up writes down) and causes phosphodiester bonds to form between adjacent nucleotides

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18
Q

**How are RNA nucleotides activated ** (check w sir)

A

Through phosphorylation (adding phosphate to the nucleotide)

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19
Q

What is the sense strand (transcription)

A

This is the strand that is not used in transcription
5’ to 3’

The mRNA formed in transcription is a copy of the sense (or coding) strand

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20
Q

What is formed in transcription

A

Pre-mRNA

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21
Q

How is pre-mRNA made into mature-mRNA

A

The introns are removed through splicing and the exons are rearranged into any order

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22
Q

Why can one gene code for multiple polypeptides

A

As the exons can be rearranged into any order

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23
Q

What are Introns

A

Regions in mRNA that do not code for amino acids

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24
Q

What are Exons

A

Regions that code for amino acids

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25
Q

Where are the ribosomes located and what happens at them

A

In the cytoplasm

Translation occurs

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26
Q

How does mature-mRNA move to the ribosomes

A

It exits the nucleus via small nuclear pores and moves into the cytoplasm

It then binds to the small ribosomal subunit

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27
Q

What are ribosomes made of

A

Ribosomes are made from proteins
.
Two subunits

The small subunit (size 20s) binds to the mRNA and reads it

The large subunit (size 60s) contains 3 sites (P, A, E) which tRNA binds to. It also joins the amino acids to form a polypeptide

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28
Q

What direction does the small ribosomal subunit read mRNA

A

In a 5’ to 3’ direction

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29
Q

What amino acid is coded for at the start codon of all eukaryotes

A

Methionine

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30
Q

What happens during translation

A

-The small ribosomal subunit attached to the mRNA and begins scanning it (until reaching the start codon)

-The tRNA carrying methionine (the start codon) forms a hydrogen bond with the complimentary mRNA codon at the p-site

-The large subunit joins the small subunit at the start codon (translation elongation can now occur)

-As tRNA occupies the p-site the 2nd tRNA molecule and its amino acid bind to the A-site

-A peptide bond forms between the amino acids and the polypeptide chain is transferred to the amino acid in the A site

-The tRNA molecule no longer holding an amino acid moves into the e-site, and the tRNA in the A-site moves into the P-site

-The ribosome moved down one codon in the 5’ to 3’ direction (towards the 3’ end)

-tRNA in the E-site leaves and a new tRNA moves into the A-site

-This process is repeated and peptide bonds form between the amino acids

-the process ends when the A-site becomes occupied by a stop codon

The amino acid folds into a complex 3D polypeptide

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31
Q

What happens when the ribosomal a-site is occupied by a stop codon

A

A release factor protein is released which causes the ribosomal subunits to dissociate.

This releases the amino acid chain

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32
Q

What is the structure of a ribosome (subunits)

A

Small subunit

                  Large subunit
                          E P A

The tRNA complimentary to the mRNA start codon binds to the P site
The rest of the tRNA initially binds to the A-site

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33
Q

What two groups do amino acids always contain

A

A carboxylic acid group (COOH), and an amine group (NH2)

R group

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34
Q

What does amphoteric mean

A

They can both accept and donate hydrogen ions

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35
Q

Why are amino acids amphoteric

A

They have both an acidic carboxyl group and a basic amine group

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36
Q

What does the amino acids ‘R’ Group determine

A

It determines how the amino acids interact with each other
This determines the secondary and tertiary structure of the protein

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37
Q

Which amino acid is the only one to contain sulphur

A

Cystine

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38
Q

Why is cystine (the amino acid) important

A

It can form a di-sulphide bridge (bond) with other cystines

This is the strongest bond in a protein
The more di-sulphide bridges a protein has the harder it is to denature

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39
Q

What is a dipeptide

A

The molecule formed when two amino acids react together

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40
Q

What type of reaction creates a dipeptide

A

A condensation reaction

41
Q

What is a peptide bond

A

The bond formed when two amino acids react with each other.

The bond occurs between the carboxyl group of 1 amino acid and the amine group of another (OH from the carboxyl is removed and 1H from the amine is removed to make water)

O H
|| |
C - N

(Between two amino acids)

42
Q

What is a carboxyl group

A

COOH

43
Q

What is an amine group

A

NH2

44
Q

What reaction breaks peptide bonds

A

Hydrolysis

45
Q

What is a polypeptide

A

A chain of 3 or more amino acids

46
Q

What are the 4 structures of a protein

A

Primary Structure
Secondary structure
Tertiary structure
Quaternary structure

47
Q

What is the primary structure of a protein

A

The specific sequence of an amino acids that are held together by peptide bonds
(forming a polypeptide)

48
Q

What is / happens in the secondary structure of a protein

A

This structure is where the folding of the polypeptide begins

The way the polypeptide folds (alpha helix or beat-pleated sheet) depends on where hydrogen bonds form (between peptide bonds)

49
Q

What is an alpha helix and when is it formed

A

It is a single stranded helix
It forms in the secondary structure of a protein when hydrogen bonds form between every 4th peptide bond

50
Q

What is a beta-pleated sheet and when is it formed

A

A folded polypeptide chain, resulting in two (or more) parallel strands

Hydrogen bonds form between opposite peptide bonds

51
Q

What is the tertiary structure and what happens in it

A

It is the third structure of a protein where folding continues

This folding / bending depends on interactions between the R groups and the attraction of different amino acids

The different bonds (e.g hydrogen , covalent, disulphide, ionic) determine how the amino acid folds

52
Q

What is the quaternary structure of a protein

A

In this structure multiple polypeptide chains join together.

These chains are kept together by different bonds, such as hydrogen bonds or disulphide bonds

53
Q

Which structure do some proteins not have

A

Not all proteins have the quaternary structure

54
Q

What is the structure of an RNA nucleotide

A

A nucleotide containing Ribose sugar, a phosphate group and a nitrogenous base

55
Q

What nitrogenous bases are present in RNA

A

Adenine
Uracil (replaces thymine)
Cytosine
Guanine

56
Q

What is tRNA and where does it come from

A

Transfer RNA is a carrier of amino acids that is complementary to a codon of mRNA

It comes from the cytoplasm

57
Q

What is the structure of tRNA

A

tRNA is a monomer made of RNA nucleotides.

It has an anti codon which is complimentary to mRNAs codons

It also has a specific amino acid attachment site, that allows it to form ester bonds with a specific amino acid

58
Q

What are the differences in tRNA and mRNA structure

A

mRNA has a linear structure while tRNA has a 3d folded structure

mRNA is made of more nucleotides than tRNA

tRNA has a site for an amino acid

mRNA has no hydrogen bonds in its structure but tRNA does

59
Q

Name a protein with a quaternary structure

A

Hemoglobin

60
Q

What are globular proteins

A

Spherically folded proteins that are soluble in water

61
Q

Why are globular proteins soluble in water

A

They have hydrophilic R groups on the surface and these groups interact with the water

Most of their hydrophobic groups are found on the inside

62
Q

What type of protein is Haemoglobin

A

It is a globular protein

It has a quaternary structure, consisting of 4 subunits.
2 alpha subunits
2 beta subunits

63
Q

Why can oxygen bind to heamoglobin

A

Each hemoglobin subunit contains 1 haem group

This group contains a singular Fe 2+ ion in its center that 1 oxygen can bind to

This means that each heamoglobin molecule can carry 4 oxygen

64
Q

Why are enzymes and hormones globular proteins

A

Enzymes and hormones are transported around the body in transport mediums
To be carried in a transport medium they must be soluble

Globular proteins are soluble

65
Q

What are fibrous proteins

A

Insoluble proteins with a long rope-like structure

They are often used for structural roles in organisms (e.g collagen and keratin)

66
Q

Why are fibrous proteins insoluble

A

They have a high number of hydrophobic R groups on the surface of the protein.

67
Q

What is the structure of collagen

A

Collagen is made of 3 polypeptide chains wound into a triple-helix

Every 3rd amino acid is glycine, so the strands of the triple helix are held tightly by hydrogen bonds.

Covalent bonds (cross links)

68
Q

What is glycine

A

glycine is the amino acid with the smallest R group - only 1 H atom

This means it can for strong hydrogen bonds with itself - and keep a structure tight

69
Q

What are enzymes

A

Enzymes are biological catalysts

They lower the activation energy of reactions and are not used up

70
Q

what type of proteins are enzymes

A

They are globular proteins

This means they are soluble in water and can be transported in blood

71
Q

Why are enzymes needed

A

Certain reactions in the body have a higher activation energy than energy that is available

If the body temperature was increased to supply the kinetic for a reaction energy lipids and proteins in your cell would denature

Using enzymes lowers the activation without increasing the body temperature

72
Q

Who is Herman Emil Fischer

A

The man who came up with the lock and Key hypothesis

73
Q

What is the Lock and key Hypothesis

A

A theory that states

Only enzymes that have and active side with a complimentary shape to a substrate, can form an enzyme-substrate complex

74
Q

How many amino acids is the active site made of

A

6 to 10 amino acids

75
Q

What deterimes the shape of an enzymes active side

A

The tertiary structure of a protein

Amino acid R-groups interact with each other and fold into complex 3D shapes. This folding determines the active sites shape

76
Q

What deterimes which enzymes can bind to which substrates

A

The shape of the active site and the specific amino acid R groups in the active site

77
Q

What two factors can cause enzymes to denature

A

High temperatures (above their optimal temperature)

A change in pH away from their optimal pH

78
Q

What happens when an enzyme denatures

A

Bonds in the tertiary structure are broken so:

Its active site changes shape and is no longer complementary to a substrate

This process is irreversible

79
Q

What is the Induced fit model

A

A theory that:

When in the presence of a substrate, there are subtle change sin the amino acid r-groups, causing a precisce conformation of the enxyme that excatly fits the substrate

80
Q

What bonds hold the substrate to the enzyme

A

Weak non-covalent bonds (such as hydrogen bonds and and ionic bonds

81
Q

what happens when the substrate colloded with and binds to the enzyme

A

After it form an ESC the substrate is converted into a product and an enzyme product complex is formed (EPC)

82
Q

Why can the product be released (from an enzyme)

A

The product is a slightly different shape to the substrate, so the induced fit is undone and the product is released (as is not complementary)

83
Q

What happens when the enzymes product is released

A

It returns to its original state and binds to a new substrate

84
Q

What are catabolic enzymes

A

enzymes that break down substrates

85
Q

What are anabolic enzymes

A

Enzymes that build up substrates

86
Q

What is a conjugate protein

A

A protein containing at least one prosthetic group

87
Q

How does increasing only substrate concentration affect the rate of reaction

A

As there are more substrate molecules in a given volume.
More enzymes and substeates collide so more ESCs can form
This means more substrate is converted into product - so the rate of reaction increases

Eventually all the active sites (of enzymes) are occupied by substrate
No new ESCs form, so the Rate of Reaction stays the same

88
Q

What factors affect the rate of reaction (enzymes)

A

pH
Temperature
Substrate concentration
Enzyme concentration

89
Q

What is proteolysis

A

Process where old / denatured enzymes are broken down into amino acids

90
Q

How is enzyme concentration naturally increased

A

By increasing the rate of transcription

91
Q

How is the concentration of enzymes naturally decreased

A

By increasing the rate of enzyme degradation (proteolysis)

92
Q

Why are enzymes degraded

A

If they have an abnormal shape
If they are old

93
Q

How does increasing enzyme concentration affect the rate of reaction

A

It causes it to increase

Enzymes decrease activation energy

There are more enzymes so more active sites for substrate to bind to
More ESCs are formed, so more product is released

Eventually the increase stops
The substrate molecules are all occupied in the active site or have been converted into products

94
Q

How does the induced fit model explain activation energy

A

The enzyme puts a strain on the bonds in the substrate

This makes it easier for the substrate to break and form new bonds

95
Q

What is a competitive inhibitor (enzymes)

A

A molecule with the same shape as a substrate.
The enzyme can bind to the inhibitor instead of the substrate, reducing the rate of reaction

96
Q

What is a non-competitive inhibitor

A

An inhibitor which binds to the allosteric site of an enzyme

It binds at the same time as the substrate and causes the active site to denature

This stops the reaction from occuring

97
Q

What happens when increasing substrate in the presence of competitive inhibitors

A

The effectiveness of the inhibitors will reduce as they have to compete with more substrate

98
Q

What does it mean if the active sites are saturated

A

All the active sites are occupied

99
Q

Do competitive inhibitors completely stop a reaction

A

No

They only have a temporary effect, and substrate may still bind instead of the inhibitor

100
Q

How does pH have an effect in the rate of reaction (enzymes)

A

All enzyme reactions have an optimal charge
Deviations in pH cause the concentration of H+ ions to change.
This can cause the rate of collisions to decrease slightly

Extreme pH changes can cause hydrogen bonds to break

(A Level) Biology (8 decks)

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