Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

OCR AS LEVEL BIOLOGY > Chapter 3- Proteins and Nucleic Acids > Flashcards

Chapter 3- Proteins and Nucleic Acids Flashcards

You may prefer our related Brainscape-certified flashcards:
AP® Biology flashcards Biology 101 flashcards
1
Q

protein functions

A

Is made of carbon, hydrogen, oxygen and nitrogen
Functions : cell growth; cell repair; replacement of materials; structural role (ex: cytoplasm, muscle, collagen and elastin in skin, collagen in bone and keratin in hair); protein. carrier molecules in cell membranes; antibodies; enzymes; hormones

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Basic building block of a protein

A

Amino acids are the monomers which form a protein

Sequence of amino acids determine the type of protein formed and hence its function.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Structure of an amino acid

A

At one end of the molecule, there is an amino group (NH2) and at the other end there is a carboxyl group or an organic acid group, (COOH). The carbon has a double bond with the oxygen as well as a single bond to the OH. These two groups are attached centrally with a carbon atom that carried a hydrogen atom at one side and an R group on the other.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is a R group

A

A side chain that acts as a functional group as it helps to determine the internal bonds and so the shape of the polypeptide and hence its final function.
It is called a residual group.
The R group is different in each of the 20 amino acids that make up proteins. Once the amino acids are joined to one another by peptide bonds, they are often referred to as amino acid residues.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Examples of amino acids

A

Glycine- there is only one hydrogen atom as its residual group
Alanine- CH3 is its residual group
Leucine- its residual group consists of CH at the centre with the groups: CH3, H3C, CH2 surrounding this.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Examples of Polar amino acids

A

Aspartic acid- its residual group is CH2 and COOH
Arginine- its residual group is (CH2)3, HN, CNH, NH3
Serine- its residual group is CH2OH.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Polar or charged R groups

A

All polar or charged R groups are hydrophilic groups

Non-polar amino acids are hydrophobic (ex: valine )

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Peptide bonds

A

Proteins are polymers
Two Amino acids are joined by condensation reaction, with one molecule of water lost.
This results in a peptide bond being formed. This new molecule is called dipeptide.
This bond can be broken by a hydrolysis reaction using one molecule of water.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Polypeptides

A

Long chains of amino acids joined by peptide bonds are called polypeptides.
A chain of amino acids joined by peptide bonds is peptide.

The condensation reaction between amino acids in a polypeptide is catalysed by the enzyme peptidyl transferase present in the ribosomes.
The different R-groups of the amino acids making up a protein interact with each other forming different types of bonds.

Peptides differ in number, type and order of amino acids.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Levels of protein structure

A

The shape of a protein is vital in determining the properties of that protein and its function in the living organism.

All proteins are organised at different levels- primary, secondary, tertiary and quaternary
Only some proteins have quaternary structure.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Primary structure

A

This is the sequence, type and number of amino acids in the amino acid chain, as well as the position of the disulphide bonds if present.
The sequence, type and number of amino acids determine it’s function and also differentiates every protein from each other.
The sequence of amino acids influences how the protein folds and hence its shape and final function.

If one amino acid is changed then the function can be disrupted or even stopped completely

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Secondary structure

A

The amino acid chain takes a particular shape by folding or coiling as a result of bonds that form between certain amino acids in the chain.
The order of amino acids determine where the hydrogen bonds form and so what shape occurs.

Two forms of secondary folding: the alpha helix and beta pleated sheet.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Alpha helix

A

The alpha helix is held permanently in place by hydrogen bonds between amino acids in one part of the chain and those a little further along the chain.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

The beta pleated sheet

A

The beta pleated sheet folds in a concertina-like way, with hydrogen bonds connecting to an adjacent pleated sheet.

Hydrogen bonds are weak bonds, but the number of them present in such protein molecule help them maintain the stability of the molecule overall.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Tertiary structure

A

A 3D shape of the protein molecule
Occurs after the secondary structure has become further coiled or twisted into a more complex shape
The final shape depends on how the structure twists or coils.
These complex shapes are held together by different types of bond that form because of the position of certain amino acids in the chain
The sequence of the amino acids in the chain determines the exact shape of the molecule.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are the two types of tertiary structures?

A

Globular and fibrous

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is a globular protein

A

When the protein folds and coils to form a 3D shape
This makes globular proteins important molecules in metabolic processes.
Ex: enzymes
The globular shape of an enzyme gives it its active site.
Globular proteins are usually soluble, long with enzymes, form protein-based hormones, plasma proteins, antibodies and the components of the cytoskeleton.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is a fibrous protein?

A

Has a long fibrous structure
Important in structural roles such as keratin in hair and nails, collagen in skin, bone and cartilage.
Ex: Fibrin, a blood-clotting protein is a fibrous protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Bonds and interactions that stabilise the tertiary structures

A 
Hydrogen bonds: individual bonds are weak but multiple help stabilise the structure
Ionic bonds 
Hydrophobic interactions 
Both of these occur between the R groups
Covalent bonds such as disulphide bonds
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Quaternary Structure

A

When more than one polypeptide chains are made. Two or more subnits
In this case, two or more chains are held together and function as a whole.
This protein will not function unless all subunits are together.
In some cases the polypeptide chains are identical, but in other cases they are not.
Enzymes often consist of two identical subunits.
In some an inorganic molecule or ion is also required for the protein to function.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is a prosthetic group

A

A non-protein part of a protein molecule that is permanently attached to the molecule and is vital for the normal functioning of the molecule.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What is a conjugated protein

A

A globular protein with a prosthetic group such as haem in haemoglobin.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Haemoglobin

A

Is a conjugated (globular) protein molecule with a quaternary structure and a haem (prosthetic) group containing an inorganic ion- the metal iron, which gives the typical red colour.
Human haemoglobin contains four polypeptide chains- two alpha chains and two beta chains- each linked with a haem group.
The four chains are held together by a number of different bonds to make a stable globular molecule with a specific shape designed to carry out the molecule’s function of oxygen transport.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Examples of other globular protein molecules

A

Enzymes (amylase, catalase)
Antibodies
Protein-based hormones such as insulin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

How do the enzymes carry out their function of catalysing chemical reactions?

A

They rely on their 3D shape

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What is insulin

A

Is a hormone produced by the beta cells of the Islets of Langerhans in the pancreas.

Made of two chains
21 amino acids in chain A
30 amino acids in chain B
These chains are held together by three disulphide bridges.
It is important hormone in controlling glucose levels in blood.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is Collagen?

A

Fibrous protein with a quaternary structure
Has three polypeptide chains twisted around each other like a rope
Each chain is made of three repeating amino acids.
This structure is supported by hydrogen bonds and covalent bonds between the chains.
Multiple chains form a collagen fibril by forming cross link between each other. Then multiple collagen fibrils for a collagen fibre.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Properties of collagen

A

Provides support and strength in many structures of the body such as the heart and arteries, tendons and bone, and cartilage and skin.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Other examples of fibrous proteins

A

Keratin and elastin
Elastin has the ability to stretch and return to its original shape.
It is found in connective tissue, tendons and bone.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Comparison between haemoglobin and collagen (helical structure)

A

Haemoglobin is folded into a right-handed alpha-helical structure

Collagen is wound into a left-hand helical structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Solubility of haemoglobin and collagen in water

A

Haemoglobin is soluble in water

Collagen is insoluble in water

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Types of amino acid in haemoglobin and collagen

A

In a haemoglobin molecule, most of the 20 different amino acids are present

The collagen molecules are formed by just a few different types of amino acid.
One of the three amino acids that form most of the collagen molecules is called glycine.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Role of haemoglobin and collagen

A

Haemoglobin is responsible for transporting oxygen

Collagen provides strength in many areas of the body such as artery walls, tendons, cartilage and bone, and also provides the elasticity of the skin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Biuret test for proteins

A

Add sodium hydroxide to the protein suspension.
Shake this mixture.
A small amount of copper sulphate was then added drop by drop, shaking between each addition.
The colour should change to purple.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Calcium ions

A

Part of bone and enamel structure as calcium phosphate
A cofactor in blood clotting
An ion involved in nerve transmission across the synapse and in muscle contraction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

Sodium ions

A

An electrolyte
Essential function in nerve transmission
Essential in water reabsorption in loop of Henle and collecting duct

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Potassium ions

A

An electrolyte
Essential in nerve transmission
Essential in water reabsorption in loop of Henle and collecting duct
Used in plant guard cells as part of the stomatal opening mechanism

38
Q

Hydrogen ions

A

Common bonds in biochemical molecules
Involved in ATP formation
Involved in the control of blood pH and in the transport of carbon dioxide

39
Q

Ammonium ions (NH4+)

A

An intermediate ion in the deamination of proteins

40
Q

Nitrate ion (NO3-)

A

Nitrogen source for green plants to manufacture proteins

It is the form taken up from soil

41
Q

Hydrogen carbonate (HCO3-)

A

Involved in carbon dioxide transport in the blood, with H+

42
Q

Chlorine ion

A

The shift of chloride ions into and out of red blood cells maintain pH balance during carbon dioxide transport

43
Q

Phosphate (PO43-)

A

as phospholipids, phosphates form part of cell membranes
Forms calcium phosphate, an important constituent of bone for giving strength
Constituent of ATP and nucleic acids

44
Q

Hydroxide (OH-)

A

One of the important ions in bonding between biochemical molecules

45
Q

Biosensors

A

Offer methods for obtaining quantitative results
Is very precise and accurate analytical device.
Converts biological response into an electrical signal using a highly specific and stable enzyme.

46
Q

Hydrophobic and hydrophilic interactions

A

If a protein is hydrophilic or hydrophobic depends on the R groups of the amino acids.
Hydrophilic groups are on the outside of the protein while hydrophobic groups are on the inside of the molecule shielded from the water in the cytoplasm.

47
Q

Breakdown of peptides

A

The enzyme, protease reverse peptides back to their constituent amino acids.
A water molecule is used to break the peptide bond in a hydrolysis reaction, reforming the amine and carboxylic acid groups.

48
Q

Insulin

A

Globular protein
Hormone involved in the regulation of blood glucose concentration
Transported in the bloodstream so need to be soluble.
Also need to fit into specific receptors on cell-surface membranes to have their effect and therefore need to have precise shapes.

49
Q

Keratin

A

A group of fibrous proteins present in hair, skin and nails
Contains a large proportion of the sulphur-containing amino acid, cysteine.
This results in many strong disulphide bonds (bridges) forming strong, inflexible and insoluble materials.
More disulphide bonds, less flexible the keratin molecule is

50
Q

Elastin

A

Fibrous protein found in elastin fibres
Present in the walls of blood vessels and in the alveoli of the lungs- they give these structures the flexibility to expand when needed, but also to return to their normal size.
Is a quaternary protein made from multiple tropoelastin molecules.

51
Q

Two types of nucleic acids

A

DNA (deoxyribonucleic acid)
RNA (ribonucleic acid)

These are polynucleotides

52
Q

What is the monomer molecule of a polynucleotide

A

Nucleotide

53
Q

What is the structure of nucleotide structure

A

Phosphate group
Pentose sugar molecule
Organic nitrogenous base

54
Q

What sugars do DNA and RNA have

A

DNA has deoxyribose

RNA has ribose

55
Q

Examples of Purines

A

Adenine
Guanine

Both purINEs have INEs in them

56
Q

How many rings do Purines have

A

Purines

Have two rings

57
Q

Examples of pyrimidines

A

Thymine
Cytosine

URACIL (only exists in RNA)

pYrimidines have a Y in their names (except uracil)

58
Q

How many rings do pyrimidines have?

A

One ring

59
Q

What are bonds between the components in a nucleotide

A

Phospho-diester bonds form between the phosphate groups and the pentose sugars. Glycosidic bonds form between the pentose sugars and the organic nitrogenous base. Both of these are covalent bonds, formed by condensation reactions.
Two condensation reactions occur- one between the sugar and phosphate group and another between base and sugar; thus forming two water molecules

60
Q

What is called the backbone of a DNA

A

The sugar-phosphate formation in a strand of DNA is known as the sugar-phosphate backbone.

61
Q

What structure does DNA have

A

A double-stranded helix

62
Q

What is different about the polynucleotide strands

A

They run in opposite directions- they are antiparallel

The DNA molecule twists to form the double helix structure

63
Q

What bond holds the two strands of DNA together

A

Hydrogen bonds
3 between G and C
2 between A and T

The importance of the base pairing is that the molecule becomes very stable and is always the same width along the chain, because the bases hold the backbones the same distance apart.

64
Q

Why do the base A pair up to T and G to C

A

Purine bases and pyrimidine bases have complementary shape

This is known as complimentary base pairing

65
Q

There is 30% of Guanine in the DNA strand. How much Adenine is there?

A

If there is 30% of Guanine, there will also be 30% of Cytosine. This is because they pair up.
There always be equal number of complimentary bases in a DNA strand.

So, 30 + 30= 60%
100-60= 40%
40/2= 20%

There will 20% of Adenine and 20% of Thymine

66
Q

At what phase of cell division, does DNA replicate itself?

A

Interphase

67
Q

What is DNA replication

A

Semi-conservative

68
Q

How does semi-conservative replication work

A

DNA first unzips and unwinds while breaking the hydrogen bonds between the bases. The enzyme Helicase is involved in the process of separating the two polynucleotide strands of DNA . These then act as template for the formation of a new molecule of DNA.
Free floating nucleotides in the nucleus arrange themselves opposite the exposed complimentary bases of the DNA templates as the two polynucleotide strands separate.
The enzyme, DNA polymerase catalyses the condensation reaction to covalently bond each nucleotide to the adjacent one along the sugar-phosphate backbone.
The pentose sugars and the phosphate group forms the covalent bond, phosphodiester bonds.

69
Q

What is the result of semi-conservative replication?

A

By the end of the replication there are two identical DNA polymers.
With each strand bonded with its complimentary strand.

70
Q

The four main differences between DNA and RNA

A

DNA’s sugar molecule is deoxyribose
RNA’s sugar molecule is ribose

The nitrogenous bases in a DNA strand are AGCT
The nitrogenous bases in a RNA strand are AGCU

There are two DNA strands
There is always one single RNA strand

There is only one type of DNA
There are three types of RNA

71
Q

Other differences between DNA and RNA (only refer to these when the question is worth more than 4 marks)

A

DNA are bigger polymers
DNA is also more stable
DNA is only found in the nucleus whereas RNA is present in nucleus and cytoplasm.
DNA has many base pairs but in RNAs, some bases are paired and some aren’t

72
Q

Similarities between DNA and RNA

A

Made up of nucleotides
Phosphodiester bonds form between each nucleotides by condensation reaction, forming a polymer (nucleic acid)

Order of nitrogenous bases form code on the nucleic acid.

73
Q

3 types of RNA and their location

A

mRNA (messenger RNA)
Made in the nucleus, travels to cytoplasm

tRNA (transfer RNA)
Cytoplasm

rRNA (ribosomal RNA)
In ribosomes
Free in cytoplasm or attached to RER

74
Q

What are ATP and ADP

A

These are phosphorylated nucleotides
Comprise of ribose (pentose sugar) adenine (an organic nitrogenous base) and inorganic phosphates.
They are energy storage molecules where the energy can be released by breaking the bonds between phosphates.
ATP has 3 phosphate groups and ADP has 2 phosphate groups

75
Q

Structure and function of ATP and ADP

A

ADP + phosphate group = ATP
This is formed by a condensation reaction

ATP - phosphate group (+ energy released) = ADP
This is formed by hydrolysis

ATP is the universal energy currency of all living organisms.

76
Q

Analogy for ATP and ADP

A

ATP is a like a charged battery which releases energy. However, when it breaks the bond between its third phosphate group, it turns into a dead battery (ADP)
The phosphate group acts as a charger

77
Q

What is DNA- nucleic acid

A

The nucleic acid forms when two polynucleotide chains join together, by hydrogen bonds between nitrogenous bases, to form a double-stranded molecule.

78
Q

What is the gene

A

DNA is an extremely long molecule that codes for numerous proteins. Each short length of DNA known as gene is a sequence of bases that code for the amino acids making up a single protein.
Because no two proteins are the same length, the length of the gene also varies.

79
Q

why could there be several triplets coding for the same amino acid

A

There are 20 different amino acids and 64 different combinations of triplet codes, therefore some triplets code for the same amino acid.

This is known as the degenerate code.
Ex: serine is coded by 6 triplets.

80
Q

What is the advantage of an amino acid being coded by multiple triplets

A

The advantage of having different codes for the same amino acid is that if a mutation causes a base to change, the triplet may still code for the same amino acid and therefore not change the protein produced.

81
Q

Examples of amino acids that only have one base triplet that code for

A

Methionine- AUG (this starts the amino acid chain)
Tryptophan

AGT, GAT and AAT code for full stops signalling the end of the message.

82
Q

Protein Synthesis- Transcription

A

In a gene that codes for a protein, one of the DNA strands is called a coding strand and the other is a template strand
When this protein needs to be made, RNA polymerase unzips the DNA by binding it its strand. Then RNA polymerase then moves along the template strand in the 3’ to 5’ direction. As it moves along it pairs free RNA nucleotides with complementary nucleotides on the DNA template strand.
These RNA nucleotides covalently bond through condensation reaction to form phosphodiester bonds. This creates a polynucleotide chain growing in the 5’ to 3’ direction, known as mRNA.
So the mRNA and the coding DNA strand will have the same sequence of nucleotides- except uracil instead of thymine

83
Q

Translation

A

The mRNA leaves the nucleus through the nuclear pore, and travels to the ribosomes in the cytoplasm, or in the ER.
These then sit on a ribosome, exposing its base triplets otherwise known as codons.
Free floating tRNAs in the cytoplasm have a specific amino acid molecule at one end and a sequence of three bases (known as anticodon) at the other. These anticodons code for the amino acid attached to the tRNA on one end; and are also complimentary to the codons on the mRNA.
The correct anticodon binds with its complimentary codon in the mRNA in the P site of the ribosome. Note that the E,P and A sites of the ribosome are formed when the two subunits (small subunit of 30s and large subunit of 50s) join. Another tRNA fills in the A site and its anticodon binds with the codon. The amino acids at the opposite end form peptide bonds. The tRNA on the P site detaches the amino acid from its structure and moves to the E site (which is next to the P site) and leaves. Simultaneously the tRNA in the A site with two amino acids shift to the P site. Another tRNA follows and fills in the A site. Its anticodon binds with the codon on the mRNA. Then the chain of two amino acids on the tRNA (in the P site) form another peptide bond with the amino acid on the tRNA (in the A site). This goes on until a stop codon is reached.
Note that the ribosome moves; not the mRNA strand.

84
Q

What enzyme is responsible for forming the peptide bonds

A

Peptidyl transferase

85
Q

How does a stop codon work

A

When the stop codon is reached while forming the peptide chain, it is thought that there are two possibilities that occur at this time.
First being that the anticodon of a tRNA with no amino acid molecule attached to it, binds with the codon. Thus stopping the chain.
Second possibility is that no tRNA binds with the codon. So, this isn’t translated.

86
Q

What happens after the peptide chain has been formed

A

These then are packaged off as transport vesicles to the Golgi Apparatus. Here they are modified (folded into its specific tertiary or quaternary structure).
They enter the Golgi Apparatus through a process called exocytosis. This is when the vesicle fuses to the membrane of the Golgi Apparatus.
After they are modified, they are sent off as secretory vesicles from the cis network of the golgi body. They travel through cytokinesis and fuse to the cell surface membrane by exocytosis.

After it has been modified, it is send off as a secretory vesicle; which travels through cytoskeleton to the cell surface membrane and fuses to it through exocytosis.

87
Q

Features of DNA compared to features of RNA- information code

A

DNA:
The base sequence is a code used to build proteins
RNA:
It copies the DNA code by hydrogen bonding RNA nucleotides to the DNA bases and forming a chain of mRNA

88
Q

Features of DNA compared to features of RNA-

Replication

A

DNA
Each DNA molecule has one of the old polynucleotide chains (template strand) and one new chain (coding strand). It is replicated by semi-conservative replication.

RNA
transcription

89
Q

Features of DNA compared to features of RNA- size of molecule and information stored

A

DNA- Large amounts of information can be stored because the strand is extremely long.

RNA- molecules are shorter because small amount of information is copied each time

90
Q

How is DNA chain held together (mark scheme)

A 
Phosphodiester bonds between the phosphate and sugar
Hydrogen bonds between the bases
Purines to pyramidines
3 H bonds between C and G
2 H bonds between A and T

OCR AS LEVEL BIOLOGY (22 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions