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ME2019 PART 1 > Proteins 1 > Flashcards

Proteins 1 Flashcards

1
Q

What are the major steps of protein synthesis?

A

DNA to RNA (transcription)

RNA to protein (translation)

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2
Q

What is transcription?

A

The first step of gene expression where a particular section of DNA is copied onto RNA

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3
Q

What is translation?

A

The process where ribosomes synthesis proteins

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4
Q

What does a diagram of DNA look like?

A
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5
Q

What kind of bonds link the two bases of two DNA backbones?

A

Hydrogen bonds

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6
Q

What is the backbone of DNA called?

A

Deoxyribose-phosphate backbone

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7
Q

What are the four bases present in DNA?

A

Adenine (A)

Cytosine (C)

Thysine (T)

Guanine (G)

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8
Q

What is the base pairing of DNA?

A

Adenine pairs with thymine

Cytosine pairs with guanine

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9
Q

What is the double helix?

A

The double stranded molecule that DNA exists as

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10
Q

What does the general structure of an amino acid look like?

A
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11
Q

What are the sections of an amino acid?

A

Amino group

Side chain

Carboylic acid group

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12
Q

Does each amino acid have a unique side chain?

A

Yes

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13
Q

What is physiological pH?

A

7.4

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14
Q

What happens to an amino acid at physiological pH?

A

The carboxyl group dissosiates forming a negatively charged carboxylate ion (-COO^-) and the amino group is protonated (-NH3^-)

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15
Q

What does dissociate mean?

A

Molecule splits

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16
Q

What does protonated mean?

A

Transfer a proton to a molecule

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17
Q

What does the dissociation of amino acids at physiological pH allow them to do?

A

Amino acids join together with a peptide bond with the loss of 1 molecule of water

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18
Q

What does the reaction of two amino acids joining together look like?

A
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19
Q

Where does translation occur?

A

In the ribosome

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20
Q

What determines the properties of an amino acid/protein?

A

The side chain

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21
Q

What are different side chain properties

A

Aliphatic (organic compounds where carbon atoms form open rings, not aromatic rings)

Aromatic

Sulphur containing

Basic

Acidic

Uncharged polar

Other (such as proline)

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22
Q

What do non polar side chains not do?

A

Bind or give of protons

Participate in hydrogen or ionic bonds

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23
Q

Non polar side chains can be thought of as being hydrophobic, what interactions do they promote?

A

In aqueous solution (polar environment) they cluster in the interior to give 3D structure

In hydrophobic environments they are on the outside interacting with the lipid environment

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24
Q

What does hydrophobic mean?

A

Repels water, tends to have no charge

25
Q

What does hydrophilic mean?

A

Attracted to water, dissolves in water

26
Q

What are the properties of uncharged polar chains?

A

Have a net charge of 0

Contain partial charges that can form bonds

27
Q

What are the properties of sulphur containing side chains?

A

Contains a sulfhydroxyl group (-SH) which is often important in the active site of enzymes

28
Q

What are the properties of acidic side chains?

A

Side chains are fully ionised, containing a negatively charged carboxylate group (-COO-)

Negatively charged at physiological pH

Are orignially proton donors (before they are ionised)

29
Q

What does an amino acid with an acidic side chain look like?

A
30
Q

What are the properties of basic side chains?

A

Originally accept protons (before ionised)

Positively charged at physiological pH

Are fully ionised, containing a positively charged amino group (-NH3+)

31
Q

How many kinds of amino acids are coded by DNA?

A

20

32
Q

What are the four protein structures?

A

Primary

Secondary

Tertiary

Quarternary

33
Q

What is the primary structure of a protein?

A

The sequence of amino acids in a polypeptide chain

34
Q

What is the primary structure the source of?

A

Versitility and function due to there being 20 different occupants for each position an an enormous range of sequences

35
Q

What is the secondary structure of a protein?

A

The spatial arrangement of amino acid residues that are near each other in the linear sequence

36
Q

What are the three forms of secondary structures?

A

Alpha helix

Beta sheet

Beta bends

37
Q

What is the alpha helix structure?

A

A coiled structure held in place by hydrogen bonds between every N-H group and the O of the C=O group in the next turn of the helix

38
Q

What is the beta sheet structure?

A

Composed of two or more peptide chains which are almost fully extended, the hydrogen bond is perpendicular to the polypeptide backbone

39
Q

What is the tertiary structure of a protein?

A

Spatial arrangment of amino acid recidues that are far apart in a linear sequence

40
Q

What forces hold the tertiary structure in place?

A

van der Waals

Ionic interactions

Hydrogen bonds

Disulphide bridges

Hydrophobic interactions

41
Q

What are van der Waals?

A

Non specific weak attraction between atoms 0.3-0.4nm apart

They are individually weak but collectively strong

42
Q

What are ionic interactions?

A

Occurs between two oppositely charged side chains

These are strong

43
Q

What are hydrogen bonds?

A

Occur when H is bonded to O, N or F and lone pair of electrons are present

Similar to van der Waal but are stronger and more permanent

They are 1/20 the strenth of covalent bonds

44
Q

What are examples of molecules that form hydrogen bonds?

A

Water and ammonia

45
Q

What is a disulphide bridge?

A

Strong covalent bond between two cysteine residues

Can occur within and between a polypeptide

46
Q

What are hydrophobic interactions?

A

Intra-polypeptide interactions occuring in an environment with proteins which water is excluded

47
Q

Where are hydrophilic and hydrophobic side chains found within a protein?

A

Hydrophillic side chains are found on the outside interacting with the environment (making the molecule soluble)

Hydrophobic side chains are found on the inside interacting with each other (giving 3D structure)

48
Q

What is the quarternary structure of a protein?

A

Spatial arrangement of individual polypeptide chains in a multi sub unit protein

49
Q

How are the subunits in the quarternary structure held together?

A

Non covalent interactions, they may function independently or in collaboration

50
Q

What is denaturing?

A

Disruption and possible loss of both the secondary and tertiary structures

Leads to the loss of 3D structure and function

51
Q

Are denaturing reactions enough to break the peptide bonds of the primary structure?

A

No

52
Q

What is renaturation

A

Gaining of a proteins 3D shape and function after denaturation

It is rarely possible as the effects of denaturation are often permanent

53
Q

What are some causes of denaturation?

A

Acids

Heat

Solvents (ethanol, methanol)

Cross linking reagents (formaldehydes)

Chaotropic agent (urea)

Disulphide bond reducers

54
Q

What are some effects of denaturation?

A

Decreased solubility

Altered water binding capacity

Loss of biological activity

Improved digestability

55
Q

What is protein digestion?

A

Cleavage of the peptide bonds within the primary structure

56
Q

What are types of protein digestions?

A

Peptidases (cleavage of peptide bonds)

Endopeptidases (cleave of internal bonds)

Exopeptidases (cleavage of one amino acid at a time)

Carboxypeptidases (cleaves at the -COOH terminal)

Aminopeptidases (cleavage at the -NH2 terminal)

57
Q

What is protein structure dependent on?

A

DNA sequence coding for amino acids

Interactions of amino acids

structure determines function

58
Q

What happens when proteins are denatured?

A

Structure and function are lost

ME2019 PART 1 (55 decks)

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