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BIOLOGY STAGE 2 RATGANG > TOPIC 1.3 STRUCTURE AND FUCNTION OF PROTEINS [completed] > Flashcards

TOPIC 1.3 STRUCTURE AND FUCNTION OF PROTEINS [completed] Flashcards

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1
Q

What makes up a protein?

A

they are all polymers of only 20 different amino acids, in a specific order.

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2
Q

what are the three groups amino acids are classified into?

A

Essential amino acids
Nonessential amino acids
Conditional amino acids

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3
Q

What are essential amino acids?

A

Essential amino acids cannot be made by the body. As a result, they must come from food.

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4
Q

what are non-essential amino acids?

A

Nonessential means that our bodies produce an amino acid, even if we do not get it from the food we eat.

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5
Q

what are conditional amino acids?

A

Conditional amino acids are usually not essential, except in times of illness and stress.

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6
Q

what is an amino acid composed of?

A

amino group
variable side chain
carboxylic acid
[refer to slide 11, 1.3 for diagram]

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7
Q

what happens when amino acids are linked together?

A

Amino acids are linked by peptide bonds to form polypeptide chains

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8
Q

how are amino acids linked together?

A

The α-carboxyl group of one amino acid to α-amino group another amino acid

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9
Q

what is the reaction that takes place when amino acids combine together?

A

The amino and carboxyl groups on a pair of amino acids undergo a condensation reaction forming a covalent bond.

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10
Q

what is the significance of a side chain in amino acids?

A

side chain (R-group) can vary between amino acids.

> this has a significant impact on the shape and structure of the overall protein molecule.

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11
Q

what is the structure of an amino acid?

A

a carboxylic acid group and an amine group that are each attached to a carbon atom called the α carbon.

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12
Q

what are the two types of amino acids?

A

Hydrophobic and Hydrophilic

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13
Q

What is a hydrophilic amino acid?

A

Amino Acids with polar side chains that can be soluble in water are hydrophilic.

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14
Q

what are hydrophobic amino acids?

A

Hydrophobic Amino acids avoid water, and are non soluble in water.

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15
Q

what is cysteine? [amino acid]

A

Cysteine is amino acid that has a chemically reactive side chain that can form bonds with another cysteine.

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16
Q

why do proteins fold?

A

specific three-dimensional shapes allow proteins to perform biological functions.

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17
Q

how do proteins fold?

A

The sequence and interactions between the side chains of these different amino acids allow proteins to fold into complex shapes.

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18
Q

why is the shapes of proteins important?

A

The shape of a protein is very important because it determines its function of a protein

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19
Q

what are the structures of proteins?

A

Primary
Secondary
Tertiary
Quaternary

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20
Q

how is the primary sequence determined?

A

This sequence is determined by the nucleotide sequence of the gene that encodes the protein.

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21
Q

how do secondary interactions form?

A

In addition to the bonds that link the amino acids in a protein together, several other weaker interactions determine how a protein will fold.

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22
Q

what is a primary structure?

A

The specific amino acid sequence of a protein is its primary structure.

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23
Q

what is a beta pleated sheet?

A

hydrogen bonds occur across two chains, linking the amino acids in one chain to those in the other. Often many parallel chains are linked, forming a beta-pleated sheet.

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24
Q

what is an alpha helix?

A

hydrogen bonds form along a single chain, linking one amino acid to another farther down the chain, causing the chain to coil up to a shape called an alpha-helix.

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25
Q

what are the two types of hydrogen bonding in the secondary structure?

A

they for either an alpha helix or a beta pleated sheet.

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26
Q

what is a secondary structure?

A

contains regions of amino acid chains that are stabilized by hydrogen bonds from the polypeptide backbone.

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27
Q

how does a protein become a tertiary shape?

A

A protein is usually forced into its tertiary shape by hydrophobic exclusion from water.
Proteins which have a folded shape such as hormones are called globular proteins.

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28
Q

how does a tertiary structure remain stable?

A

The tertiary structure exists as the protein bends and twists to achieve maximum stability.

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29
Q

what does the 3D tertiary structure display?

A

The 3D shape of the protein displays the grooves and clefts that act as active sites in enzymes and receptor-binding sites in hormones.

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30
Q

what is a tertiary structure?

A

The tertiary structure refers to the 3-D structure or shape of the polypeptide caused by the way the poly peptide chain is folded.

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31
Q

how does a protein become a tertiary shape?

A

protein is usually forced into its tertiary shape by hydrophobic exclusion from water.
Proteins which have a folded shape such as hormones are called globular proteins.

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32
Q

how does a quaternary structure occur?

A

two or more polypeptide chains associate to form a functional protein, the individual chains are referred to as subunits of the protein.

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33
Q

what is a quaternary structure?

A

a protein is the association of several protein chains or subunits into a closely packed arrangement. Each of the subunits has its own primary, secondary, and tertiary structure.

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34
Q

what is the process of secondary protein folding

A
  • Hydrogen bonding between different amino acids.
  • Disulfide bridges between two cysteine side chains.
  • Ionic bonds can form`
  • Van der Waals attractions
  • Polar portions gathering on the outside to gather with water while non-polar remain inside.
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35
Q

how does a protein become a tertiary shape?

A

A protein is usually forced into its tertiary shape by hydrophobic exclusion from water.
Proteins which have a folded shape such as hormones are called globular proteins.

36
Q

what is an example of a quaternary structure?

A

Haemoglobin, for example, is a protein composed of two alpha-chain subunits and two beta-chain subunits.

37
Q

what is the effect of the changes in the identity of amino acids?

A

there are profound effects, such as sickle cell anaemia.

38
Q

how does sickle cell anaemia occur?

A

Sickle cell anaemia occurs when there is a mutation that alters the identify of a single amino acid at the corner of the beta units of the haemoglobin molecule

39
Q

what does sickle cell anaemia do to the haemoglobin?

A

This causes a ‘sticky’ patch which causes one haemoglobin molecule to stick to another.

40
Q

what is a genome?

A

Each genome contains the information need to allow the organism to reproduce and pass on genetic information to new generations

41
Q

what are the four types of biomolecules?

A

lipids
nucleic acid
proteins
carbohydrates

42
Q

what are lipids?

A

Lipids are macromolecules made of fatty acid monomers

43
Q

what are the main functions of lipids?

A
  • Lipids provide structural support for cells
  • Store energy
  • Lipids are involved in cell signaling
  • Lipids are non-polar and do not interact with water
44
Q

what are nucleic acids?

A

Nucleic acidsare macromolecules that store genetic information and enable protein production.

45
Q

what are nucleic acids composed of?

A

These molecules are composed of long strands of nucleotides. Nucleotides are composed of a nitrogenous base, a five-carbon sugar, and a phosphate group.

46
Q

what biomolecules are RNA and DNA?

A

Nucleic Acids

47
Q

what are carbohydrates?

A

Carbohydrates the most abundant and widespread organic substances in nature, and they are essential of all living things.

48
Q

what are some examples of carbohydrates?

A

sugars, starches, saccharides, and polysaccharides

49
Q

What does the name carbohydrate mean?

A

Carbohydrate” means a “hydrate of carbon.”

50
Q

what is the composition of carbohydrates?

A

Sugar Backbone of Nucleic Acids - Deoxyribose in DNA and Ribose in RNA

51
Q

what type of molecule is a protein?

A

proteins are macromolecules

52
Q

what does it mean when proteins have a dynamic structure?

A
  • They are continually undergoing changes
  • Binding to receptors on the cell membrane
  • Forming complexes with other molecules
  • Being synthesized and broken down
53
Q

what are Proteins and nucleic acids composed of?

A

are composed of a collection of atoms bonded together in specific arrangements.

54
Q

what are the two ways protein structures are represented?

A

Wire Frame Diagrams
Backbone and Ribbon Diagrams

55
Q

what are wire frame diagrams?

A

a line is drawn for each of the covalent bonds formed between the atoms.
small balls and sticks are used to make the three-dimensional shape easier to understand.

56
Q

what are backbone diagrams?

A

These images highlight the way a protein chain folds.
draw a tube that connects the positions of each amino acid.

57
Q

what are ribbon diagrams?

A

Ribbon diagrams add two special representations: a spring-shaped ribbon for alpha helices and a flat arrow that shows beta strands.

58
Q

what are the main functions of proteins?

A

Structure
Hormones
Immunity
Transport
Sensation
Movement
Enzymes

59
Q

what is cellular communication?

A

Cells have proteins calledreceptorsthat bind to signalling molecules and initiate a physiological response.

60
Q

Different receptors are specific for different molecules, what is an example of this?

A

Dopamine receptors bind dopamine, insulin binds insulin receptors, nerve growth factor receptors bind nerve growth factor, and so on.

61
Q

what do receptors respond to?

A

Receptors can also respond directly to light or pressure, which makes cells sensitive to events in the atmosphere.

62
Q

what are receptor proteins?

A

A molecule inside or on the surface of a cell that binds to a specific substance and causes a specific effect in the cell.

63
Q

how do cells know which signals to respond to?

A

through receptor proteins within the cell. When a signal molecule approaches a receptor protein of the right shape, the two can bind.

64
Q

what does the binding between the signal molecule and receptor protein do?

A

This binding induces a change in the receptor protein’s shape ultimately producing a response in the cell.

65
Q

what type of protein is a receptor protein?

A

Receptors are generally transmembrane proteins

66
Q

what do transmembrane proteins [receptor proteins] do?

A

bind to signalling molecules outside the cell and subsequently transmit the signal through a sequence of molecular switches to internal signalling pathways.

67
Q

what are hormones?

A

Hormones are chemical messengers that are secreted directly into the blood, which carries them to organs and tissues of the body to exert their functions.

68
Q

what occurs between hormones and receptor proteins?

A

Hormones bind to receptors to initiate a cellular response

69
Q

how are hormones able to bind to cell receptors?

A

Many hormones are proteins, and it is the differences in their structure that allow them to bind to specific cell membrane receptors and bring about their action.

70
Q

what are the three major classes of Membrane receptors?

A

G-protein-coupled receptors,
ion channel receptors,
Enzyme-linked receptors.

71
Q

what are some processes hormones are involved in?

A

Development and growth
- Metabolism of food items
- Sexual function and reproductive growth and health
- Cognitive function and mood
- Maintenance of body temperature and thirst

72
Q

what are the steps of hormone signalling within the human body?

A

Synthesis of a hormone
- Storage of the hormone in a gland, then secretion into the bloodstream
- Transport via the blood to certain types of cells called target cells
- Binding to a complimentary receptor protein in the cell membrane of the target cell
- Relaying a message to the nucleus inside the cell which leads to a cellular response or triggering a change in the shape of channel into the cell

73
Q

what are antibodies?

A

Antibodiesare specialized, Y-shapedproteinsthat bind like a lock-and-key to the body’s foreign invaders — whether they are viruses, bacteria or other non-self molecule.

74
Q

what are antigens?

A

Antigens are molecules, usually foreign or ‘non-self’ that provoke a specific immune response.

75
Q

where are antigens found?

A

They can be found embedded in the surface of viruses or cells e.g. bacteria.

76
Q

what do white blood cells do?

A

White blood cells called Lympocytes (B Cells) respond to the presence of antigens by producing proteins called antibodies.

77
Q

what do antibodies do?

A

Antibodies act by binding to specific antigens in a complementary manner, leading to their deactivation or neutralization.

78
Q

how can antobodies and antigens bind?

A

It is the particular 3-D structure of the protein molecule (which occurs as a result of it’s primary, secondary, tertiary and quaternary structure) that enables it to bind with, and inactivate the antigen.

79
Q

what are regulatory proteins?

A

Any protein that influences the regions of a DNA molecule that are transcribed by RNA polymerase during the process of transcription.

80
Q

what do regulatory proteins do?

A

Regulatory proteins identify specific sequences on the DNA double helix, without unwinding it.

81
Q

What are activators?

A

The binding of other proteins, called activators, to DNA near genes assists the binding of RNA polymerase and therefore promotes transcription.
[they are regulatory proteins btw]

82
Q

what is a proteome?

A

a proteome is used to describe all of the proteins found in a cell or organism at a specific time.

83
Q

what is proteomics?

A

The term proteomics refers to the study of proteins, including the abundance, variations and modifications to proteins.

84
Q

what are biomarkers?

A

Biomarkers are molecules, such as proteins found in blood and often give indications of abnormal processes or disease.

85
Q

why is it not entirely correct to refer to biomarkers as the ‘blueprint’ ?

A

It is often stated that genes are the ‘blueprint’ of the cell, but the proteins they code for are the molecules of structure and function in cells and organisms

BIOLOGY STAGE 2 RATGANG (4 decks)

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