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IB HL Biology > 2.4 Proteins > Flashcards

2.4 Proteins Flashcards

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1
Q

What are polypeptides?

A
  • A number of linked peptides.
  • They are also called proteins – the names are often used interchangeably.
  • The basic unit of a polypeptide is an amino acid: a carbon-based compound with a carboxyl group (-COOH) and an amino group (-NH 2 ).
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2
Q

A generalized diagram of an amino acid (the R group varies in different amino acids).

A
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3
Q

Initially, two amino acids bind in a condensation reaction to form a ___

A
  • Dipeptide

- The carboxyl group and the amino group provide OH and H, respectively, for the formation of a water molecule.

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4
Q

Diagram of condensation reaction of two amino acids

A
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5
Q

What is the largest protein found in the body and how long is it?

A
  • Titin

- About 27,000 amino acids long.

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6
Q

What are the three names related to proteins that are frequently used in biology?

A
  • Polypeptides are synonyms for proteins.
  • Peptides are smaller than proteins. Peptides are defined as molecules that consist of between 2 and 50 amino acids.
  • Proteins are polymers that are made up of 51 or more amino acids.
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7
Q

There are __ different amino acids found in proteins

A

20

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8
Q

Diagram of the 20 amino acids found in nature. What do the different color balls represent?

A

(Insert diagram)

The different coloured balls represent the following atoms: black – carbon, blue – nitrogen, yellow – sulfur and red – oxygen; hydrogen atoms have been omitted for clarity.

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9
Q

The 20 amino acids can be linked together in any sequence to form ___

A
  • Polypeptides.
  • Theoretically, 20 n different types of polypeptides can be formed, where n is the number of amino acids per polypeptide.
  • Hence, if a polypeptide of 20 amino acids long is being made, there are 20 to the power of 20 (20 20 ) different ways to combine these amino acids, giving rise to a huge range of possible proteins: 1.04 × 10 26 different proteins.
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10
Q

Where does the synthesis of polypeptides take place?

A

On ribosomes, in a process called translation.

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11
Q

How do we obtain amino acids?

A
  • Some food products are rich in proteins, such as meat, legumes, and dairy products.
  • When you ingest proteins, they are later digested and absorbed into the bloodstream as amino acids.
  • Our cells can make new proteins using amino acids that are obtained from food.
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12
Q

Which chemical reaction is taking place when a dipeptide is converted to two amino acids?

A

Hydrolysis

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13
Q

Name the bond that forms when two amino acids react together in a condensation reaction.

A

Peptide bond

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14
Q

Which molecules are monomers for polypeptides?

A

Amino acids

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15
Q

What are genes?

A
  • Sections of DNA that contain the instruction for all polypeptides of an organism.
  • Genes normally code for one polypeptide, which is a sequence of amino acids linked together by peptide bonds.
  • These peptide bonds between each amino acid are the result of a condensation reaction.
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16
Q

Diagram of a gene in a segment of DNA that exists in a nucleus and has the code for a polypeptide.

A
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17
Q

A gene normally codes for _____

A
  • One polypeptide and each polypeptide has a function.
  • Furthermore, there are proteins that can be made of one or more polypeptides.
  • The genetic material is transcribed into the ribonucleic acid (RNA) called mRNA (messenger RNA).
  • This then carries the instructions for the amino acid sequence to the ribosome (found in the cytoplasm).
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18
Q

Diagram of (from gene to polypeptides)

A
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19
Q

A protein may just be one polypeptide, or it may consist of a _____

A
  • Number of polypeptides linked together.
  • Hemoglobin is an example of a protein that consists of four polypeptide chains and a non-protein part known as a heme group.
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20
Q

Diagram of haemoglobin

A
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21
Q

What is the role of DNA in the formation of proteins?

A

The structure of enzymes is determined by DNA.

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22
Q

What is the role of DNA in the formation of proteins?

A

The structure of enzymes is determined by DNA.

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23
Q

What are polypeptides?

A

Many amino acids linked together.

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24
Q

The order of the amino acids determines the ___

A

Shape and function of the protein.

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25
Q

How do the 20 amino acids differ?

A
  • By their R groups, which determine the types of bonds and interactions with other molecules that they can make.
  • This, in turn, defines how the polypeptide chain or chains fold up in the protein and so directly affect its three-dimensional structure, known as its conformation.
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26
Q

What can a single change in the order of amino acids cause?

A
  • Changes in a protein’s conformation, resulting in a change of shape or loss of function.
  • Gene mutations can cause these changes in the order of amino acids.
  • Even a single amino acid change can upset the conformation and functioning of a protein. In sickle cell anemia, the glutamic acid is substituted by valine. -This causes severe changes to the structure of hemoglobin.
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27
Q

What is the sequence of amino acids in a protein called?

A

The primary structure.

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28
Q

What does the primary structure of a protein define?

A

All aspects of the structure and function of a protein.

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29
Q

What does the secondary structure of a protein involve?

A

The folding of the chains on themselves to form pleated sheets or alpha helixes.

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30
Q

When is the tertiary structure of a protein given rise to?

A

When the polypeptide folds and coils to form a complex three-dimensional shape.

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31
Q

When does a quaternary structure of a protein only occur?

A

In proteins that are made up of two or more polypeptide chains and refers to the way the multiple subunits are held together in a multi-subunit complex.

32
Q

Examples of proteins with quaternary structure

A

Hemoglobin and rubisco.

33
Q

Diagram showing the relationship between a protein’s amino acid sequence and its ultimate form or conformation. (The four levels of protein structure)

A
34
Q

Why is human hemoglobin a good example of a protein with a quaternary structure?

A
  • It has two alpha and two beta chains.

- Together with the heme group, hemoglobin forms a functional structure that can transport four molecules of oxygen.

35
Q

Diagram of human hemoglobin

A
36
Q

Which characteristic of hemoglobin allows it to be considered a protein with a quaternary structure?

A

It consists of four polypeptide chains.

37
Q

What would happen if a single amino acid in a protein consisting of 325 amino acids were changed?

A

The primary structure of the protein would be altered, as well as its tertiary structure.

38
Q

The following diagram shows the structure of lysozyme, a protein consisting of a single polypeptide, found in egg white. What is the name given to this level of protein shape? (Insert diagram)

A

Tertiary

39
Q

Each organism has a complete and unique DNA content, which is called a ___

A

Genome

40
Q

Each organism also has a unique set of proteins that are coded by its genome. This unique set of proteins is called a ___

A

Proteome

41
Q

How is proteome analysis useful in medical research and cancer treatment?

A

To treat certain cancers, the proteome of a patient’s cancer cells is analyzed to determine if particular chemotherapy will be successful.

42
Q

Each species has its own unique set of proteins. However, ____

A
  • Proteomes of individuals within a species can vary.

- Each of us can have a slightly different set of proteins due to differences in the amino acid sequence.

43
Q

How can the proteome of a species be analyzed?

A

Gel electrophoresis can be used to separate protein.

44
Q

Diagram of gel electrophoresis of proteins. Each band on a gel plate represents a different protein.

A
45
Q

When comparing the proteome of a yeast cell with that of a human cell, the latter is more complex because ___

A

The human genome codes for more proteins than the genome of yeast.

46
Q

What can proteins be divided into groups based on?

A
  • Their chemical structure and functions.
  • One of the most common divisions of proteins is based on their solubility in water.
  • There are globular and fibrous proteins.
47
Q

Diagram of a fibrous protein (collagen)

A
48
Q

Diagram of a globular protein (hemoglobin)

A
49
Q

Give an example of a fibrous protein.

A

Collagen

50
Q

Give an example of a globular protein.

A

Hemoglobin

51
Q

Globular proteins.

A
  • Globular proteins, as the name implies, are globe-like or spherical.
  • They tend to play active roles in the cell’s metabolism.
  • They consist of complex polypeptide chains that can be linked to other chains to form large complex proteins.
  • An example of this is hemoglobin, which has two alpha and two beta chains.
  • They are usually soluble in water because their hydrophobic R groups are folded into the core of the molecule, away from the surrounding water molecules.
52
Q

Fibrous proteins

A
  • Fibrous proteins are more like a fiber - long and thread-like.
  • Usually, fibrous proteins are made of long polypeptide chains where the hydrophobic R groups are exposed, making the molecule insoluble.
  • They are often found in structural parts of organisms, such as tendons and skin (e.g. collagen and keratin).
53
Q

Give examples of some of the functions of proteins.

A

They are involved in almost every metabolic reaction as receptors, transport channels, pumps, and enzymes.

54
Q

What type of protein is rubisco?

A

Globular

55
Q

What is the function of rubisco?

A

An enzyme involved in the fixation of CO 2 in chloroplasts.

56
Q

What type of protein is insulin?

A

Globular

57
Q

What is the function of insulin?

A

A hormone produced by the beta cells of the pancreas, which is involved in glucose uptake from the blood.

58
Q

What type of protein is immunoglobulin?

A

Globular

59
Q

What is the function of immunoglobulin?

A

These are large Y-shaped proteins, also called antibodies, involved in fighting infections by specifically recognizing and binding to antigen molecules.

60
Q

What type of protein is rhodopsin?

A

Globular

61
Q

What is the function of rhodopsin?

A

It is a protein linked to the pigment found on the membrane of rod (photoreceptor) cells of the retina, where it allows very low light intensities to be detected.

62
Q

What type of protein is collagen?

A

Fibrous

63
Q

What is the function of collagen?

A
  • A structural protein, found in muscles, tendons, and ligaments, where it gives tensile strength.
  • It also occurs in skin and bones, where it prevents tearing and fractures, respectively.
64
Q

What type of protein is spider silk?

A

Fibrous

65
Q

What is the function of spider silk?

A
  • A fibrous protein produced by spiders for their webs to be able to suspend themselves to catch prey.
  • It can be extended and is very resistant to breaking.
66
Q

State the name of the protein that catalyzes the fixation of CO2 in chloroplasts.

A

Rubisco

67
Q

What is denaturation?

A
  • A process in which proteins lose their secondary and tertiary structures (in some cases also quaternary).
  • The hydrogen bonds formed between R-groups of amino acids and amino groups of different amino acids are disrupted.
  • Active sites lose their shape.
  • As a result, the whole enzyme loses its enzymatic properties.
68
Q

What are the two main ways in which proteins can be denatured?

A
  • One is by exposing the protein to higher temperatures, and the other is by changing the pH of a surrounding solution.
  • Proteins have an optimum temperature and pH at which they function best.
  • Any deviation from these values influences the functionality of the proteins.
69
Q

Explain how temperature can denature a protein.

A
  • When proteins lose their conformation, the interaction between certain amino acids will be changed, so that the quaternary and tertiary structures, and in some extreme conditions the secondary structures, are irreversibly changed.
  • This results in the denatured proteins losing their form and their function.
  • It should be noted that peptide bonds holding adjacent amino acids do not break during the denaturation process.
  • Therefore, the primary structure of the protein is not disrupted.
70
Q

Why are very high fevers dangerous for humans?

A

-At temperatures above 40 °C, some proteins start to denature and enzymes no longer function properly.

-If a patient suffers from these high temperatures for
too long, the result can be death.

  • Not all proteins are so easily denatured by raised temperatures.
  • Certain enzymes that break down RNA and prion proteins are extremely stable and require long periods of high temperature (above 100 °C) before they denature.
71
Q

Explain how pH can denature a protein.

A
  • The pH of a solution can affect the functionality of a protein.
  • Strong alkaline or acidic solutions can break the bonds between the non-adjacent amino acids or between the polypeptide chains of quaternary proteins.
  • The result is the same as with heat: the protein denatures and loses functionality.
72
Q

Diagram of the denaturation of a normal protein.

A
73
Q

What happens to the structure of a protein when it’s denatured?

A

The secondary, tertiary, and in some cases, the quaternary structures of the protein are irreversibly changed.

74
Q

The sequence of amino acids in a polypeptide is determined by the sequence of ___

A

DNA nucleotides in a gene

75
Q

What is a polypeptide?

A

A single chain of amino acids

76
Q

Explain how heat can cause a protein to denature

A
  • Heat causes the atoms within the protein to vibrate
  • If the vibrations are great enough, intermolecular interactions between non-adjacent amino acids (those involved in protein folding) break
  • This usually results in a permanent loss of shape
77
Q

Explain how changes in pH can cause a protein to denature

A
  • Each protein has a pH range in which it has its normal three-dimensional shape
  • Changes away from this pH range cause intermolecular interactions between non-adjacent amino acids (those involved in protein folding) to break
  • Denaturation caused by mild changes to pH can be reversible

IB HL Biology (68 decks)

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