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ESA 1 - Medical Cell Biology & Genetics > Session 4.3a - Lecture 1 - Protein Structure > Flashcards

Session 4.3a - Lecture 1 - Protein Structure Flashcards

Slides 1-11

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1
Q

ILO

A
  • What do proteins do
  • Structural aspects
  • Think about how some of these things fit together and work
  • E.g. enzymes
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2
Q

Do NOT need to know all the molecular detail of the DNA repair pathways

A

Steve Foster lectures

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3
Q

What was the take home message from SF lectures?

A

There are many different types of DNA repair mechanisms

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4
Q

Why do we need many different types of DNA repair mechanisms?

A

Because DNA repair is very important; if things go wrong with DNA we need to put them right

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5
Q

What can occur if DNA is damaged and not repaired?

A

If there are changes, that will affect DNA and therefore the function of the cell, so it is critically important to have DNA repair mechanisms

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6
Q

Why do we need to know about DNA repair mechanisms?

A

We need to UNDERSTAND the importance of their role, as if DNA is not fixed then the function of the cell is changed

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7
Q

What is non-homologous end joining (NHEJ)?

A

NHEJ is joining DNA when there’s a double stranded break.

Need to know BASICS but NOT all the proteins involved

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8
Q

Why can NHEJ go wrong?

A

Although NHEJ is a neat process that repairs dsbreaks quite nicely, it is NOT very selective. This means that the process can be prone to errors.

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9
Q

What can occur if NHEJ goes wrong?

A

Translocation events can occur.

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10
Q

What are the levels to proteins?

A

Primary
Secondary
Tertiary and
Quaternary structure

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11
Q

What are proteins made up from?

A

Amino acids

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12
Q

How do proteins differ?

A

Although they are all made up from amino acids joined together, these tend to FOLD UP in different ways

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13
Q

What is the primary structure of a protein?

A

Just the amino acids joined together

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14
Q

What is the secondary structure of a protein?

A

The localised folding of the amino acid sequence

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15
Q

What is the tertiary structure of a protein?

A

When the protein is folded up as a whole

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16
Q

What is the quaternary structure of a protein?

A

When more than one subunit comes together to form a protein

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17
Q

Fig. 2

Label the image

A

Left - proteins crystals used to get 3D structure of proteins

Primary structure
Secondary structure
Tertiary structure
Quaternary structure

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18
Q

What is the relationship between protein structure and function?

A

Proteins fold up in different ways (due to their amino acid sequence) which relates to their function

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19
Q

Why do we need to know about proteins, why are they important?

A

Proteins play crucial roles in virtually all biochemical processes - they do virtually everything in your cell that is of any consequence.

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20
Q

What is the difference between DNA and protein?

A

DNA carries all the information but it’s the proteins that do things.

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21
Q

What are the functions of proteins that are important in medicine?

A
  • Catalysts
  • Transporters
  • Structural support
  • Machines
  • Immune protection
  • Ion channels
  • Receptors
  • Ligands in cell signalling
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22
Q

What is an example of proteins as catalysts?

A

Enzymes

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23
Q

What are enzymes an example of?

A

Catalysts

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24
Q

What is virtually every enzyme?

A

A protein (there might be other things associated with it but virtually all enzymes are proteins).

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25
Q

Give 2 examples of things proteins can transport

A

Oxygen and iron

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26
Q

Other than oxygen and iron around the body, where else can proteins transport things?

A

Things across cell membranes

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27
Q

What is the support in the body?

A

All support in body is really protein-based

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28
Q

What is an example of structural support in the body from proteins?

A

Collagens in skin and bone

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29
Q

What are the proteins found in bone, skin etc. that function as structural support?

A
  • Collagen

- Other scaffolding proteins

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30
Q

How do proteins act as molecular machines?

A

In muscular contraction and motion

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31
Q

What are the protein elements involved in muscles?

A

Actin and myosin

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32
Q

Where are actin and myosin found in muscles?

A

In sarcomeres

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33
Q

What is a sarcomere

A

The basic unit of striated muscle tissue.

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34
Q

How do proteins function for immune protection?

A

Immunoglobulins

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35
Q

What type of immunity is due to proteins?

A

Virtually all adaptive immunity down to role of proteins

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36
Q

What is the role of immunoglobulins?

A

Recognise any antigen effectively that comes into your body

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37
Q

What is the significance of proteins being immunoglobulins?

A

They need to recognise any antigen that comes into your body, which means there must be a huge repertoire of Igs! This can be produced by proteins because there are numerous different ways a protein can fold.

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38
Q

How are proteins important for cell communication?

A

They can form ion channels, receptors and ligands in cell signalling

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39
Q

What is the common function of ion channels, receptors and ligands?

A

Cell communication

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40
Q

What is the function of an ion channel?

A

For example, to set off electrical impulses in neuronal cells

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41
Q

What are receptors used for?

A

For hormones, neurotransmitters etc.

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42
Q

Give an example of a function of a receptor

A

Takes signals from outside the cell and passes to inside the cell - important for how you get hormonal regulation, for example.

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43
Q

Give an example of proteins as ligands in cell signalling

A

Growth factors

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44
Q

How are proteins and ligands interconnected?

A

Many proteins themselves will act as ligands - e.g. growth factors are protein-based.

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45
Q

What are the key features of proteins?

A
  • Proteins are polypeptides
  • The amino acid sequence of a protein is encoded by a gene
  • The polypeptide chain folds into a complex and highly specific three-dimensional structure, determined by the sequence of amino acids
  • The folding of proteins depends on the chemical and
    physical properties of the amino acids
  • The amino acid sequence of a protein is encoded by a gene
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46
Q

What are proteins?

A

Polypeptides - they are macromolecules made up of amino acids

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47
Q

What are polypeptides?

A

Chains of amino acids, aka proteins.

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48
Q

What is a macromolecule?

A

A big molecule

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49
Q

What is the simple unit of a protein?

A

An amino acid

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50
Q

What is the relation between amino acid and protein?

A

The amino acid is the simple repeating unit in a protein

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51
Q

What forms a protein?

A

Amino acids joined covalently to give the sequence of the protein (like beads on a strong)

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52
Q

How are amino acids joined together in proteins?

A

By strong covalent bonds known as peptide bonds.

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53
Q

What type of bond is a peptide bond?

A

Covalent (strong)

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54
Q

Fig. 4 (left)

Label this image

A
  • Monomers

- A linear polymer

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55
Q

What is another word for macromolecule?

A

Polymer

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56
Q

If a protein is a polymer, what is the monomer?

A

Amino acid

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57
Q

If an amino acid is a monomer, what is the polymer?

A

Protein

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58
Q

If a protein is a polymer, what is an amino acid?

A

Monomer

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59
Q

If an amino acid is a monomer, what is a protein?

A

Polymer

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60
Q

Fig. 4 (right)

What does this picture represent?

A

A protein sequence of amino acid, represented via a letter code (like genome sequences).

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61
Q

How are amino acids represented in a code by molecular biologists?

A

There is a 20-letter code (don’t need to learn)

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62
Q

How is the amino acid sequence of a protein encoded for?

A

By a gene

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63
Q

What does a gene do in relation to proteins?

A

Encodes an amino acid sequence of a protein

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64
Q

What determines the amino acid sequence of a protein?

A

The nucleotide sequence of a gene

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65
Q

What does the nucleotide sequence of a gene determine?

A

The amino acid sequence of a protein

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66
Q

The amino acid sequence of a protein is encoded by a gene. What does this link?

A

This is critically important because it links your GENOME (nucleotide sequence) to your PROTEOME (protein sequence).

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67
Q

Define genome and proteome?

A

GENOME = nucleotide sequence

PROTEOME = protein sequence

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68
Q

Why is it important clinically to understand that DNA (genome) is linked to the protein (proteome)?

A

If you get a mutation in a GENE, you can affect the PROTEIN.

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69
Q

What is wrong with the beads on a string model of proteins?

A

Proteins don’t really adopt that conformation - in some cases they do - but in most cases they fold up into a fine 3D structure

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70
Q

What determines the 3D structure of proteins?

A

The specific amino acid sequence that make up that particular protein

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71
Q

What does the amino acid sequence dictate?

A

The 3D structure of proteins

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72
Q

What is it about amino acids that affects the individuality of proteins?

A

The chemical and physical properties of those particular amino acid “residues” that make up a protein actually contribute to the 3D sequence of the protein.

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73
Q

What is the relation between the chemical and physical properties of an amino acid that make up a protein?

A

The properties of those particular amino acid “residues” (as we call them) that make up a protein actually contribute to the 3D sequence of the protein.

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74
Q

What is important about 3D structure?

A

3D structure often determines what a protein does.

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75
Q

Describe how amino acids are related to protein function?

A

The make up of a protein (its specific amino acid sequence) controls overall 3D shape and 3D shape defines its role.

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76
Q

What encodes the amino acid sequence of a protein?

A

A gene

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77
Q

What does a gene encode in proteins?

A

The amino acid sequence

78
Q

How are nucleotides connected to genes?

A

The nucleotide sequence of a gene determines the amino acid sequence of a protein

79
Q

How is expression of a protein dictated?

A

Unidirectionally (from DNA to protein)

80
Q

How do we get from DNA to proteins?

A
  • Gene contains our nucleotide sequence that encodes for a protein
  • This gets converted to RNA by the process of TRANSCRIPTION
  • We make the final protein by TRANSLATING that mRNA sequence
81
Q

Fig. 6

Draw/fill in this simple diagram to explain DNA to protein formation.

A 
DNA Replication
--Transcription-->
RNA
--Translation-->
Proteins
82
Q

What are the basic building blocks of proteins?

A

Amino acids are the building blocks of proteins

83
Q

What do amino acids consist of?

A

A central carbon atom (the a-carbon) covalently bonded to:

  • an amino group (-NH2)
  • a carboxyl group (-COOH)
  • a hydrogen atom (-H)
  • a distinctive R group (side chain)
84
Q

What is the central carbon of an amino acid called?

A

The a-carbon

85
Q

What is the a-carbon of an amino acid?

A

The central carbon

86
Q

How is the central carbon of an amino acid connected to the other groups?

A

By covalent bonds

87
Q

What is the amino group?

A

-NH2

88
Q

What is -NH2 called?

A

An amino group

89
Q

What is the carboxyl group?

A

-COOH (remember, it is not actually a carbon bonded to an oxygen to a hydrogen: got a slightly different structure)

90
Q

What is -COOH called?

A

Carboxyl group

91
Q

What does H stand for?

A

Hydrogen atom

92
Q

What is the R group?

A

A distinctive side chain

93
Q

What is the side chain of an amino acid?

A

The distinctive R group

94
Q

Draw the general structure of an amino acid.

A

Ca

  • NH2
  • COOH
  • R
  • H
95
Q

Fig. 7

Caption this image

A

General structure of an amino acid

96
Q

What is the significance of the alpha carbon in terms of structure?

A

Because there are 4 DIFFERENT groups around this carbon then these often have stereoisomers.

97
Q

Why can amino acids be stereoisomers?

A

Because there are 4 different groups around the central a-carbon

98
Q

A central carbon with 4 different groups attached to it is called what?

A

A stereoisomer

99
Q

What significance is there in amino acids being stereoisomers?

A

There are isomeric forms of amino acids in most cases.

100
Q

Isoleucine is normally found in a powder.

What would the structure be of isoleucine taken from a powder in a bottle?

A

It would have the generalised structure - i.e. NOT IONISED

101
Q

Isoleucine is normally found in a powder.

What would happen to the structure of an amino acid if we put it into water, i.e. make a solution out of it?

A

It would become ionised (no longer the general structure of an amino acid)

102
Q

What is the significance of the presence of both an amino and carboxyl group on an amino acid?

A

This gives us ionisation states of amino acids

103
Q

Fig. 8

Caption the images

A

Unionised form of amino acid (left)

Ionised form of amino acid (right)

104
Q

Draw the unionised and ionised form of amino acids?

A

Ca-R-H on both

Unionised - NH2, COOH

Ionised - NH3+, COO-

105
Q

What can ionise on an amino acid?

A

Both the carboxyl group (-COOH) and the amino group (-NH2) can ionise, and potentially the side chain

106
Q

What do we mean by ionise (in relation to amino acids)?

A

Simply, they will form ions

107
Q

What form does an amino acid take in solution?

A

The ionised form

108
Q

Example ESA1 question

Draw an amino acid in solution.

A

Draw the IONISED form
- make sure you draw the ionised form!

NH3+, COO-

109
Q

What happens to the amino and carboxyl group of amino acids in solution?

A

Protonated amino group NH3+

Deprotonated carboxyl group COO-

110
Q

Why do we get the ionised structure in solution?

A

The carboxyl group acts as an acid and the amino group acts as a base.

111
Q

Which group of the amino acid acts like an acid?

A

The carboxyl side chain (carboxylic acid)

112
Q

What are acids?

A

Proton donors

113
Q

What do we call groups that can donate a proton?

A

Acids

114
Q

Acidic side chains donate their proton to do what?

A

Become ionised

115
Q

How do acidic side chains become ionised?

A

By donating a proton

116
Q

What is the dissociation equation for carboxylic acid?

A

COOH COO- + H+

117
Q

What form will carboxylic take at physiologic pH?

A

COO-

It will always, or mostly be, in COO- form.

118
Q

What does the amino group of an amino acid act as?

A

A base

119
Q

What acts as a base in the amino acid?

A

The amino group

120
Q

How do bases function chemically?

A

They attract protons

121
Q

What do we call groups that attract protons?

A

Bases

122
Q

What can become protonated on an amino acid?

A

The NH2 group/the base

123
Q

What is the consequence of the NH2 group attracting a proton?

A

It becomes positively charged

124
Q

What is the dissociation equation for amino groups?

A

NH2 + H+ NH3+

125
Q

What is the significance of the equilibrium in this equation?

NH2 + H+ NH3+

A

NH3+ can act as an acid and become NH2

126
Q

Why is it important to note that acid and base equations are equilibrium equations?

A

One side of the equation acts as an acid and the other side acts as a base.

127
Q

What do we call a compound that is doubly charged with 0 net charge?

A

A zwitterion

128
Q

What is a zwitterion?

A

A molecule or ion having separate positively and negatively charged groups with an overall net charge of 0

129
Q

Why are amino acids called zwitterions?

A

In solution, they have separate positively (NH3+) and negatively charged groups (COO-) [The side chain has not been included].

130
Q

How do we classify amino acids?

A

Classified according to the chemical properties of the R (side chains) groups.

131
Q

Why do we classify AA according to their side chain/R group?

A

The amino and carboxyl group of proteins (with the exception of the ones at the end) are covalently bonded to adjacent amino acids creating a peptide bond, thus being unavailable for reaction.

It is therefore the amino acid side chain that is available for chemical reaction and causes the chemical properties of a protein.

132
Q

Fig. 9

What is this structure?

A

A very small protein, or peptide

133
Q

What do we call a very small protein?

A

Peptide

134
Q

What is a peptide?

A

A very small protein

135
Q

What do we find at the N-terminal end of a protein?

A

A free amino group

136
Q

Where is a free amino group found on a protein?

A

At the N- or amino-terminal end

137
Q

Fig. 9

Label the first two amino acids.

A

Serine (CH2OH)

Glycine (H)

138
Q

Fig. 9

Identify a peptide bond

A

Yellow

139
Q

Fig. 9

What do the yellow and red represent?

A

Red - side chains

Yellow - peptide bonds

140
Q

How are peptide bonds formed?

A

Between carboxyl group of one amino acid and amino group of another

141
Q

What is found between the carboxyl group of one amino acid and an amino group of another?

A

Peptide bond

142
Q

What does a peptide bond do and what does this mean chemically?

A

Bind two amino acids together, meaning they lose their amino and carboxyl groups

143
Q

How often do peptide bonds occur in amino acids?

A

Between all amino acid residues in this peptide

144
Q

Where is there a free carboxyl group in an protein?

A

At the C- or Carboxyl-terminus end

145
Q

What do you find at the C- or Carboxyl-terminus end of a protein?

A

A carboxyl group

146
Q

What are the ends of a protein called and what do you find there?

A

N- or amino-terminal end
NH3+/NH2

C- or carboxyl-terminal end
COO-/COOH

147
Q

What causes the chemical properties of a protein?

A

The side chains of the individual amino acids each makes up.

148
Q

Fig. 9

Label the diagram as fully as possible

A

Amino-terminal end (NH3+)

Carboxyl-terminal end (COO-)

Yellow = peptide bond

Red = side chains

Black C = central carbon

Amino acid = circle around central carbon atom and edges between C-N

Amino acid sequence = serine, glycine, tyrosine, alanine, leucine

149
Q

Draw a peptide from N- to C- terminus containing serine, glycine, tyrosine, alanine and leucine.

A 
Amino-terminal end NH3+-
C-H-CH2OH-C=O-N-H-
C-H-H-C=O-N-H-
C-H-CH2-benzene-OH-C=O-N-H-
C-H-CH3-C=O-N-H-
C-H-CH2-CH-CH3-CH3-C=O-N-H-
-COO- Carboxyl-terminal end
150
Q

How many aNH3+ are there?

A

Only 1

151
Q

How many aCOO- are there?

A

Only 1

152
Q

Where is the aNH3+?

A

At the N-terminal end

153
Q

Where is the aCOO-?

A

At the C-terminal end

154
Q

What is at the N-terminal end?

A

aNH3+

155
Q

What is at the C-terminal end?

A

aCOO-

156
Q

What is determined by the R groups?

A

Acid-base behaviour

157
Q

How is acid-base behaviour determined in proteins?

A

By the R groups

158
Q

What is an amino acid residue?

A

An amino acid residue is what remains of an amino acid after it has been joined by a peptide bond to form a protein

159
Q

When do we think about amino acids, as opposed to amino acid residues?

A

AA - When they’re in solution

AAR - in a protein

160
Q

What do we find in the constituents of a protein?

A

Amino acid RESIDUES

161
Q

Where are amino acid RESIDUES found?

A

In the constituents of a protein

162
Q

Fig. 10

Label these images and name the amino acid

A

Amino acid
Amino acid residue

Alanine

163
Q

Draw alanine as an amino acid and an amino acid residue

A

Amino acid:
C-[COO-]-H-[NH3+]-CH3

Amino acid residue:
C-[C=O]–H-[N-H]–CH3

164
Q

What are the functional properties of an amino acid residue?

A

Lost its amino and carboxyl group so only have a side chain

165
Q

How should we refer to amino acids:-

Amino acid or amino acid residue?

A

We should always term them amino acid residues when we’re talking about how they are in proteins; the carboxyl and amino groups are joined together by a peptide bond

166
Q

What do these represent in amino acids?

Hydrophobic, hydrophilic, polar, non-polar, acidic, basic, neutral, aliphatic, aromatic etc.?

A

Classified according to the chemical and physical properties of the R groups

167
Q

How can amino acids be classified?

A

Chemical properties

  • Hydrophobic
  • Hydrophilic
  • Polar
  • Non-polar
  • Acidic
  • Basic
  • Neutral

Physical properties

  • Aliphatic
  • Aromatic
168
Q

How can amino acids be classified according to their chemical properties?

A
  • Hydrophobic
  • Hydrophilic
  • Polar
  • Non-polar
  • Acidic
  • Basic
  • Neutral
169
Q

How can amino acids be classified according to their physical properties?

A
  • Aliphatic

- Aromatic

170
Q

What do hydrophobic and hydrophilic mean?

A

Hydrophobic = water-hating

Hydrophilic = water-loving

171
Q

What are the words to define water-hating and water-loving?

A

Hydrophobic = water-hating

Hydrophilic = water-loving

172
Q

If a molecule has a partial charge it is considered _____

A

Polar

173
Q

If a molecule does not have a partial charge it is considered _____

A

Non-polar

174
Q

A polar molecule has a _______ ______

A

PARTIAL charge

175
Q

A non-polar molecule _____ ___ have a _______ ______

A

Does not have a partial charge

176
Q

Polar is effectively the same as _________ in terms of classification

A

Hydrophilic

177
Q

Non-polar is effectively the same as _________ in terms of classification

A

Hydrophobic

178
Q

Hydrophilic is effectively the same as _________ in terms of classification

A

Polar

179
Q

Hydrophobic is effectively the same as _________ in terms of classification

A

Non-polar

180
Q

We can define whether an amino acid is polar or not into further categories

A

Acidic
Basic
Neutral

181
Q

What is a neutral amino acid?

A

No overall charge

182
Q

What is an amino acid with no overall charge?

A

Neutral

183
Q

Neutral amino acids can still be polar - true or false?

Why?

A

True

They can have groups that can become charged but at physiological pH they are not, because they are weak acids/bases

184
Q

What charges do acidic or basic amino acids have on them?

A

Acidic = -ve charge

Basic = +ve charge

185
Q

Negative and positively charged amino acids can be classified into ___?

A

Acidic = -ve charge

Basic = +ve charge

186
Q

Why do we want to know how to classify amino acids?

A

Classifying by their chemical properties (and physical properties) enables us to see how the final protein works.

187
Q

Why do we classify amino acids based on shape?

A

There are many different shapes/sizes/structures of amino acids (these ultimately can affect their chemical properties)

188
Q

Define aromatic

A

Has a ring-like structure

189
Q

Define aliphatic

A

Long chain of carbons and hydrogens

190
Q

What chemical term can be used to describe a molecule that has a ring-like structure?

A

Aromatic

191
Q

What chemical term can be used to describe a molecule that is composed of a long chain of carbons and hydrogens

A

Aliphatic

ESA 1 - Medical Cell Biology & Genetics (21 decks)

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