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AH biology > U1-KA2 - PROTEINS- 2)protein Structure > Flashcards

U1-KA2 - PROTEINS- 2)protein Structure Flashcards

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1
Q

What are amino acids

A

Amino acids are the building blocks of proteins ; amino acid sequence determines protein structure

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2
Q

What is a monomer

A
  • a monomer is a molecule that may bind chemically to other molecules to form a polymer
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3
Q

Proteins are ________ of amino acid ________

A

Proteins are polymers of amino acid monomers

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4
Q

How are the amino acids in a protein linked

A
  • the amino acids in a Protein are linked by peptide bonds to form polypeptides
  • peptide bonds are covalent and very strong , they are difficult to beak
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5
Q

Peptide bonds are ________ and very strong. They are _________ to break

A

Peptide bonds are covalent and very strong , they are difficult to break .

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6
Q

Amino acids have the same basic structure , what does it consist of

A

All amino acids have a central carbon with four groups attached( an amine (NH2), a carboxylic acid group (COOH) , a hydrogen and a variable R group

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7
Q

How are amino acids classed

A

Amino acids are classed according to their properties

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8
Q

When are amino acid monomers linked together

A

Amino acid monomers are linked together during translation at ribosome

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9
Q

How are amino acids linked together

A
  • Amino acids linked together at ribosome during translation
  • an enzyme causes a condensation reaction between two adjacent amino acids
  • a water molecule is removed by joining the OH a of the COOH of one amino acid to a hydrogen from the NH2 from the other amino acid
  • the bond that links amino acids is peptide bond
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10
Q

What is N terminus and C terminus

A
  • the chain has an NH2 group at the N terminus and a COOH group at the C terminus
  • the order in which the amino acids are synthesised into a polypeptide chain from N terminus to C terminus is called the primary structure
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11
Q

Classification :

  • how are amino acids actually classified
  • how many groups are there of amino acids
  • what are these groups
A
  • amino acids are classified according to there R groups
  • there are 4 classes
  • the classes are : acidic (negatively charged) , basic( positively charged)
    , polar and hydrophobic (non polar)
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12
Q

How do R groups vary

A

The R groups of amino acid vary in size , shape , charge , hydrogen bonding capacity and chemical reactivity

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13
Q
  • how is there such a wide range of functions carried out by proteins
A

The wide range of functions carried out by proteins results from the diversity of R groups.

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14
Q

Why are interactions between R groups so important

A
  • interactions between R groups are very important in determining the overall shape of proteins , and the R can influence the position of protein molecules in a cell.
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15
Q

Basic (positively charged)

  • what other group defines the Molecule
  • charge
  • hydrogen bonds? Hydrophobic or hydrophilic
  • ionic bonds ?
A
  • side chain contains a second NH2 (amine)
  • additional amino group gives net positive charge : The NH2 group gains a proton to become positively charged
  • the R groups form hydrogen bonds if they are on the surface of the protein or with other amino acids if they are within the molecule
  • therefore are hydrophilic : :attracted to water
  • can form ionic bonds
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16
Q

Acidic (negatively charged)

A
  • contains second COOH group (carboxyl group )
  • the COOH group donates a proton to become negatively charged
  • R groups form hydrogen bonds with water if they are on the surface of the protein or with other amino acids if they are within the molecule
  • hydrophilic
  • can form ionic bonds
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17
Q

Polar (neutral )
- what is electronegativity

  • how do polar bonds occur
  • hydrogen bonds ?
  • Hydrophilic or hydrophobic
  • common groups in polar molecules
A
  • electronegativity is the measure of the attraction of an atom for the electrons in a bond
  • polar bonds occur due when an atom has high electronegativity and one has low - the one with higher electronegativity has a greater share of electrons
  • this results In the atom having a slight negative charge compared to the other atom which has a slight positive charge
  • these side chains are also hydrophilic as they form weak hydrogen bonds with water molecules
  • Polar r groups usually at surface of soluble protein
  • polar amino acids generally have nitrogen /sulphur / oxygen groups
    Etc (OH) group (-SH) group or (NH2)
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18
Q

Hydrophobic / non polar

A
  • hydrophobic side chains only have hydrogen and carbon atoms ie hydrocarbon
  • these R groups carry no charge / cluster together away from the surface of the protein molecule in a hydrophobic pocket so they do not interact readily with water molecules (do no form hydrogen bonds)
19
Q

How is the structure of a protein determined

A

The structure of a protein is determined by the sequence of amino acids

20
Q

How is the sequence of amino acids determined

A

The sequence of amino acids is determined by the order of bases on the DNA and subsequently the mature mRNA molecule

21
Q

Explain what “levels” of of protein structure means

A
  • so, as we already know a protein is a linear sequence of amino acids linked together by peptide bonds
  • under appropriate conditions proteins spontaneously fold into a specific three dimensional shape
  • this unique shape will form a functional protein
  • ALL proteins will have 3 levels of structure : primary, secondary ,tertiary.
22
Q
  • how many levels of protein structure are there

- how many do ALL a proteins have

A
  • There are 4 possible levels : primary , secondary , tertiary and quaternary
  • all proteins have 3 : primary,secondary , tertiary
23
Q

What is the primary structure

-how does this contribute to function of protein

A
  • the primary structure is the sequence in which the amino acids are synthesised into the polypeptide
  • the amino acid sequence determines the proteins structure and hence the function of the proteins
  • the amino acids along the length of the polypeptide chain interact with one another
24
Q

What is the secondary structure

- how is it stabilised

A
  • some amino acids form hydrogen bonds which results in the secondary protein structure
  • the secondary structure of a protein is stabilised by hydrogen bonds between atoms of the same chain
25
Q

How / between what do the hydrogen bonds in the secondary structure form

A

The hydrogen of the N-H has a weak positive charge , so it is electrically attracted to the weak negative charge on the oxygen of the C - - O of another peptide bond

26
Q

What are the 3 types of secondary structure

A
  • a helix
  • b pleated sheet (beta sheet)
  • turns
27
Q

The a helix

A
  • a spiral with the R group sticking outwards
28
Q

Beta sheet

A
  • the B pleated sheet has parts of the polypeptide chain running alongside each other to form a corrugated sheet , with the R groups sitting above and below
29
Q

B pleated sheet

Antiparallel and parallel?

A
  • the B pleated sheet are usually antiparallel (chains in opposite directs with respect to the N-C polarity) but they can also be parallel B pleated sheets (chains that run same direction with respect to N-C polarity. )
  • the sheets are parallel or antiparallel depending on their N and C termini ( look In scholar book)
30
Q

Turns

  • what are they
  • what do they do
  • what stabilises the interaction
  • where do they lie, and what does it mean they can do
A
  • turns are parts of polypeptide : parts of a polypeptide may also revere the direction of the chain making a turn
  • turns usually join different secondary structures together or allow changes in the direction of the polypeptide causing folding or creat compact molecule
  • hydrogen bonds again stabilise this interaction
  • turns often lie on the surface of the proteins and so participate in interactions between proteins and other molecules
31
Q

What is tertiary structure

- what does it consist of

A
  • the tertiary structure is the final overall folded shape of the whole polypeptide
  • consists of : this three dimensional conformation contains regions of secondary structure , which are stabilised in position by the interactions between R groups of amino acids
32
Q

How are the R groups in different secondary structures close enough to react to form tertiary structure

A
  • the R groups may have been far apart in the primary structure but the folding at the secondary level brings some R groups close enough to react
33
Q

What are possible interactions between R groups

A
  • hydrophobic interactions
  • ionic bonds
  • London dispersion forces
  • hydrogen bonds
  • disulphide bridges
34
Q

Hydrophobic interactions

  • occur between which molecules
  • why do they fold
A
  • occur between non polar R groups along the length of the polypeptide
  • folding or these regions occurs, so that they form a central hydrophobic core forming hydrophobic pockets : this separates non polar hydrophobic R groups from water while the polar hydrophilic R groups are expressed on the outside of the structure free to interact with water
35
Q

Ionic bonds

  • occur between what molecules
  • pH effect on ionic bonds
  • give examples of ionised groups
A
  • charge depends attraction occluding between oppositely charged polar R groups
  • these groups are strongly charged and strongly attract to each other
  • pH effects ionic bonding and can result in the denaturation of the protein at extremes of pH as the H+ and OH- ions in solution interact with the charge across the ionic bond
  • COOH and NH2 groups ionise to become COO- and NH3+. These groups are strongly attracted to each other as they are strongly charged
36
Q

London dispersion forces

  • what are they
  • occur between which molecules
A
  • weak temporary attractions between atoms caused by localised movements of their electrons
  • between non polar R groups
37
Q

Hydrogen bonds

  • what are they
  • occur between which molecules
A
  • hydrogen bonding is a weak polar interaction based in differences in electrical charge
  • usually occurs between polar side chains
  • often between hydrogen and electronegative elements such as Nitrogen , oxygen
38
Q

Disulphide bridge

  • what is it
  • occurs between what molecules
  • how does it occur
  • where can they occur
A
  • covalent bond - between R groups containing sulphur
  • hydrogen is removed from each -SH R group to join with a free oxygen and the e atoms join with a very strong bond
  • these can occur within a single polypeptide (tertiary structure) or between adjacent polypeptides (subunits , quaternary structure)
39
Q

How are interactions in tertiary structure affected by

  • temperature
  • pH (which groups are affected by pH)
A
  • increasing temperature disrupts the interactions that hold the protein in shape : the protein begins to unfold eventually becoming denatured
  • changes on acidic and basic R groups are affected by pH : as pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost , which gradually changes the confrontation of the protein until it becomes denatured
40
Q

What is quaternary structure

  • how does it exist
  • what brings about the structure
A

Quaternary structure exists in proteins with tow or more connect polypeptide subunits.

  • the subunits are linked to each other by bonds or interactions between certain R groups of the different subunits.
  • quaternary structure describes the spatial arrangement of these subunits
41
Q

Example of protein with quaternary structure

A

Eg - collagen is made of three polypeptide subunits. Some proteins such as lysosome or myoglobin have only one polypeptide chain so tertiary structure is the final level of there structure.

42
Q

What is a prosthetic group

- give an example

A
  • in addition to the four levels of protein structure , some proteins can also have a prosthetic group
  • this is a non protein group which is tightly bound to the polypeptide unit and is essential for the proteins function
  • for example , myoglobin in muscles has a complex haem group which helps to draw oxygen into the muscle cells from the blood.
43
Q

Talk about the role of amino acid R groups - in determining the location of proteins within cells

A
  • the membrane consist of a phospholipid bi layer and the phospholipids have hydrophilic heads and hydrophobic tails, and the bi layer has some embedded proteins , and other proteins on the surface
  • polar R groups are found on the surface of soluble proteins - soluble proteins are in the cytoplasm
  • hydrophobic / non polar r groups cluster away from the surface , at the centre of the protein in a hydrophobic pocket
  • membrane proteins are integral / peripheral
  • integral proteins are embedded , as they have hydrophobic R groups which interact with hydrophobic region (tails) of the membrane
  • peripheral proteins are loosely associated with the membrane , they have hydrophilic R groups reacting with hydrophilic heads of phospholipids

AH biology (23 decks)

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