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Biology Mock AS1 > Proteins > Flashcards

Proteins Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

what is a gene

A

sequence of nucleotide bases in DNA molecules that codes for the production of a specific sequence of amino acids to make up a specific polypeptide (protein)

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2
Q

what is transcription

A

DNA is transcribed and an mRNA (messenger RNA) molecule is produced

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3
Q

what is translation

A

mRNA is translated and an amino acid sequence is produced

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4
Q

what is the role mRNA

A

carry the information encoded in the DNA from the nucleus to the site of translation on ribosomes

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5
Q

explain transcription

A

Part of a DNA molecule unwinds and the hydrogen bonds between the complementary base pairs break

exposes the gene to be transcribed

A complimentary copy of the code from the gene is made by building a single-stranded nucleic acid molecule known as mRNA which is catalysed by RNA

Free activated RNA nucleotides pair up, via hydrogen bonds, with their complementary bases on the exposed strand of the ‘unzipped’ DNA molecule

The sugar-phosphate groups of these RNA nucleotides are then bonded together in a reaction catalysed by the enzyme RNA polymerase to form the sugar-phosphate backbone of the mRNA molecule

When the gene has been transcribed and the mRNA molecule is complete, the hydrogen bonds between the mRNA and DNA strands break and the double-stranded DNA molecule reforms

The mRNA molecule then leaves the nucleus via a pore in the nuclear envelope

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6
Q

what is the strand called which the RNA nucleotides pair with

A

antisense or template strand, and it is used to produce the mRNA molecule.

The other strand is known as the sense or coding strand

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7
Q

how does RNA polymerase move along template strand

A

in the 3’ to 5’ direction

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8
Q

what happens after the mRNA leaves nucleus

A

the mRNA molecule attaches to a ribosome in the cytoplasm

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9
Q

what is tRNA

A

tRNA is a single stranded molecule of RNA that folds into a clover-like structre

triplet of unpaired bases at one end, known as the anticodon, and a region at the other end where a specific amino acid can attach

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10
Q

what do tRNA molecules do

A

bind with their specific amino acids (also in the cytoplasm) and bring them to the mRNA molecule on the ribosome

The triplet of bases (anticodon) on each tRNA molecule pairs with a complementary triplet on the mRNA molecule called the codon

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11
Q

what is there at the beginning of each mRNA

A

Near the beginning of the mRNA is a triplet of bases called the start codon (AUG)
This is a signal to start off translation

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12
Q

what bond is formed between two amino acids and what is produced by the end

A

A peptide bond is then formed, via a condensation reaction

continues until a ‘stop’ codon on the mRNA molecule is reached

The amino acid chain then forms the final polypeptide

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13
Q

what direction does the ribosome move along the mRNA in translation

A

5’ - 3’

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14
Q

describe the genetic code

A

non overlapping
degenerate: multiple codons can code for same amino acid limiting effect of mutation
universal

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15
Q

what are proteins

A

polymers made of monomers called amino acids

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16
Q

what is the structure of an amino acid

A

amino group H-N-H
R group: H - C - R
carboxylic acid O=C-OH

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17
Q

what happens when a peptide bond is formed

A

A hydroxyl (-OH) is lost from the carboxylic group of one amino acid
A hydrogen atom is lost from the amine group of another amino acid
The remaining carbon atom (with the double-bonded oxygen) from the first amino acid bonds to the nitrogen atom of the second amino acid. This is a condensation reaction so water is released

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18
Q

what happens during a hydrolysis reaction

A

he addition of water breaks the peptide bonds resulting in polypeptides being broken down to amino acids

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19
Q

what are the first three levels of structure in proteins related to

A

Three are related to a single polypeptide chain
The fourth level relates to a protein that has two or more polypeptide chains

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20
Q

what is the primary structure

A

The sequence of amino acids bonded by covalent peptide bonds

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21
Q

what is the secondary structure

A

relates to hydrogen bonds forming between the amino group and the carboxyl group

weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds

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22
Q

when does α-helix shape occur

A

when the hydrogen bonds form between every fourth peptide bond

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22
Q

when does the β-pleated sheet form

A

when the protein folds so that two parts of the polypeptide chain are parallel to each other enabling hydrogen bonds to form between parallel peptide bonds

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23
Q

what is tertiary structure

A

change of the secondary structure leads to additional bonds forming between the R groups

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24
Q

what are examples of addition tertiary bonds

A

Hydrogen (these are between R groups)

Disulphide (only occurs between cysteine amino acids)

Ionic (occurs between charged R groups)
Weak hydrophobic interactions (between non-polar R groups)

is common in 3D globular proteins

25
Q

what is quaternary

A

Occurs in proteins that have more than one polypeptide chain working together as a functional macromolecule eg. haemoglobin

26
Q

what structures contain hydrogen bonds

A

secondary and tertiary

27
Q

what are the structure of globular proteins

A

Compact
Roughly spherical (circular) in shape

Globular proteins form a spherical shape when folding into their tertiary structure

28
Q

why do globular proteins form spherical shape when folding into tertiary structure

A

Their non-polar hydrophobic R groups are orientated towards the centre of the protein away from the aqueous surroundings

Their polar hydrophilic R groups orientate themselves on the outside of the protein

29
Q

what is the function of globular proteins

A

The orientation of their R groups enables globular proteins to be (generally) soluble in water as the water molecules can surround the polar hydrophilic R groups

easily transported around organisms and be involved in metabolic reactions

30
Q

give an example of a globular protein and explain its function and structure

A

Haemoglobin

It has a quaternary structure as there are four polypeptide chains

The four globin subunits are held together by disulphide bonds

haem group contains an iron II ion (Fe2+) which is able to reversibly combine with an oxygen molecule forming oxyhaemoglobin and results in the haemoglobin appearing bright red

binding oxygen in the lungs and transporting the oxygen to tissue to be used in aerobic metabolic pathways

31
Q

what is the structure of fibrous proteins

A

long strands of polypeptide chains that have cross-linkages due to hydrogen bonds

32
Q

do fibrous proteins have tertiary structure

A

little or no tertiary structure

33
Q

function of fibrous proteins

A

large number of hydrophobic R groups, fibrous proteins are insoluble in water

Fibrous proteins are strong suitable for structural roles

34
Q

examples of 2 fibrous proteins

A

Collagen is a connective tissue found in skin, tendons and ligaments

Elastin is found in connective tissue, tendons, skin and bone

35
Q

describe collagen

A

Collagen is an insoluble fibrous protein

formed from three polypeptide chains closely held together by hydrogen bonds to form a triple helix

In the primary structure of collagen almost every third amino acid is glycine

Along with hydrogen bonds forming between the three chains there are also covalent bonds present

36
Q

how are collagen positions

A

The collagen molecules are positioned in the fibrils so that there are staggered ends

When many fibrils are arranged together they form collagen fibres

37
Q

function of collagen

staggered ends????

A

structural protein forming connective tissues

The presence of the many hydrogen bonds within the triple helix structure of collagen results in great tensile strength

The staggered ends of the collagen molecules within the fibrils provide strength

38
Q

compare collagen and haemoglobin

A

triple helix / 4 polypeptide chains

long and thin / spherical round

structural / functional

receptive amino acid variation / variable

insoluble / soluble

39
Q

what does biological catalyst mean

A

they function in living systems

‘Catalysts’ because they speed up the rate of chemical reactions without being used up or undergoing permanent change

They speed up reactions by reducing the activation energy of reactions

40
Q

are enzymes globular or fibrous
with what type of structure

A

globular proteins with complex tertiary structures

made up of two or more polypeptides and therefore have a quaternary structure

41
Q

are enzymes globular of fibrous and what does this mean

A

globular proteins
This means their 3D shape is determined by the complex tertiary structure of the protein that makes up the enzyme and is therefore highly specific

42
Q

enzymes have a unique….

A

active site where specific substrates bind forming an enzyme-substrate complex

43
Q

for a reaction to occur what conditions?

A

Substrates collide with the enzymes active site and this must happen at the correct orientation and speed

44
Q

how does the 3d shape of active site change

A

Proteins are formed from chains of amino acids held together by peptide bonds
The order of amino acids determines the shape of an enzyme
If the order is altered, the resulting three-dimensional shape changes as determined by complex tertiary structure of protein that makes enzyme

45
Q

what does higher enzyme concentration lead to

A

The higher the enzyme concentration in a reaction mixture, the greater the number of active sites available and the greater the likelihood of enzyme-substrate complex formation

46
Q

what is a limiting factor

A

If the amount of substrate is limited, at a certain point any further increase in enzyme concentration will not increase

47
Q

method for investigating the effect of enzyme concentration on the rate of reaction

A

Add a set volume of hydrogen peroxide solution to a boiling tube
Add a set volume of buffer solution to the same boiling tube

Invert a full measuring cylinder into a trough of water
Place the end of the delivery tube into the open end of the measuring cylinder and attach the other end to a bung

Add a set volume of one concentration of catalase to the boiling tube and quickly place the bung into the boiling tube

Record the volume of oxygen collected in the measuring cylinder by the water displaced every 10 seconds for 60 seconds

Repeat the whole experiment for the different concentrations of catalase

48
Q

results of investigating enzyme concentration on the rate of reaction

A

As the concentration of catalase increases the volume of oxygen produced would increase
This is because there would be more available active sites for hydrogen peroxide to use

The volume of oxygen would plateau out after the initial rate of reaction due to the substrate decreasing, having been converted into the product (oxygen)

49
Q

how does primary structure of leptin allow it to be water soluble

A

{primary structure / sequence of the amino acids} determines the folding (of the polypeptide)
forming a globular structure
hydrophobic (R) groups located in the centre of the protein / hydrophilic (R) groups located on the outside of the protein
water forms hydrogen bonds with { protein / hydrophilic groups}

50
Q

How does removing and substituting have different affects on protein structure

A

deletion could affect every codon (on the mRNA) / substitution will only affect one codon (1)
deletion more likely to affect the position of { stop codon / start codon } (1)
deletion results in a different sequence of amino acids / substitution may not affect the sequence of amino acids (1)
substitution may code for the same amino acid (1)
(same amino acid) due to the degenerate nature of the genetic code (1)

51
Q

how doe substitution affect the function of haemoglobin

A

(because) {one tripletis affected / a different triplet code is produced } (1)
* (the mutation) could change one of the amino acids (1)
* this would (change the bonds formed betweer the R groups / cause a change in the tertiary structure! (1)
* the haemoglobin would no longer be able to bind to oxvaen (1)

52
Q

importance of primary structure for function of enzyme

A

(primary structure) determines interaction between {amino acids / R groups} (1)
(primary structure) determines { folding / tertiary structure }
(1)
(therefore) affecting the shape of the active site
(1)
* (active site is) complementary to ATP (1)

53
Q

how can a base mutation lead to altered primary structure of an enzyme

A

changes in base will alter the triplet code which changes the codon and hence different amino acid sequence in primary structure

54
Q

how can an enzyme break down polysaccharide

A

hydrolysis of glucosidic bonds

55
Q

compare structure of globular and fibrous

A

both are chains of amino acids joined by peptide bonds (1)

both contain named bonds (holding molecule in its three dimensional shape) (1)

globular proteins have hydrophilic groups on the outside whereas fibrous proteins have hydrophobic groups on the outside (1)

globular have tertiary or quaternary structures whereas fibrous have little or no tertiary structure (1)

globular are folded into compact shapes whereas fibrous have long chains (1)

56
Q

how amino acids would be incorporated into a surfactant protein

A

mRNA of surfactant protein is attached to ribosome

pairing of anticodons on tRNA and mRNA and a tRNA is specific to one amino acid. Amino acids join by peptide bonds and a tertiary structure is formed

57
Q

what is an allele

A

is it an alternative version of a gene found at the same locus on a chromosome

58
Q

Vinegar contains ethanoic acid. why would vinegar result in anthocyanin pigments leaving onion cell

A

increased permeability of (cell surface) membrane

the low pH would {change the shape of / denature} proteins (in cell surface membrane)

(as vinegar) affects bonds (in protein)

59
Q

explain how the primary structure of an enzyme determines its three dimensional structure and its properties

A

(primary structure) {position / sequence / order /eq} of the {amino acids / R groups} / eq;
idea that this determines the {positioning / type} of the {bonds / folding / eq} ;
determining the {shape / properties} of the active site / eq;
idea of interaction of active sites and substrates e.g. enzyme substrate complex forms
idea of {polar / hydrophilic} on the outside of enzymes / {non polar / hydrophobic} on the inside / eg;

60
Q

Describe the structure of an enzyme.

A

ref to an enzyme as a protein ;

  1. ref to {3D / tertiary / globular} structure ;
  2. ref. to named bonds (holding structure in
    place) ;
  3. between the R groups ;
  4. ref to active site ;
  5. idea of specificity of active site

Biology Mock AS1 (8 decks)

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