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proteins Flashcards

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Organic Chemistry 101 flashcards
1
Q

,proteins are organic molecules (contain carbon) made up of:

A

long chains of amino acids

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2
Q

name the constituents of amino acids

A

-carbon
-hydrogen
-oxygen
-nitrogen
- sulphur or could contain phosphorus

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3
Q

what important structures do proteins have in the body

A

metabolic roles- enzyme substrate reactions
transport roles- such as haemoglobin (transports oxygen in the blood from lungs to tissues for respiration)
structural roles- connecting muscles to bones

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4
Q

structures of amino acids

A

amino acids are the builiding blocks used to make proteins- they are monomers

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5
Q

how many out of 500 amino acids are used to make proteins

A

only 20 out of 500 amino acids are used to make proteins

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6
Q

all amino acids have the same basic structure but different…

A

chemical R group

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7
Q

what is the basic structure of an amino acid

A

they have a central carbon atom bonded to a carboxyl group and a amino group -NH2, a hydrogen atom and a chemical R group.
each of the 20 naturally occurring amino acids have a different chemical R group

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8
Q

what three things can R groups vary in

A

-size
-polarity
-charge

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9
Q

simple definition of amino acids

A

monomer units used to make proteins

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10
Q

forming peptide bonds
how is a dipeptide formed

A

two amino acids are joined together via condensation reaction to form a dipeptide

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11
Q

what kind of reaction is used to break down a dipeptide into two amino acids

A

-hydrolysis reaction
two hydrogen atoms and an oxygen atom are added to the dipeptide to break it up into two amino acids

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12
Q

how does the condensation reaction occur to form the dipeptide

A

the condensation reaction occurs between the carboxyl group -COOH and the amino group NH2 on adjacent amino acids. overall a molecule of water is released as one oxygen atom and two hydrogen atoms are removed form the amino acids. this creates a peptide bond which joins two amino acids together to form a dipeptide.

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13
Q

how does the hydrolysis reaction to break the dipeptide into two amino acids occur

A

a hydrolysis reaction requires water as one oxygen and two hydrogen atoms are added to the dipeptide. this breaks the peptide bond forming two amino acids/

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14
Q

definition of a peptide bond

A

the covalent bond formed when two amino acids are joined together by a condensation reaction

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15
Q

how are polypeptides formed

A

many amino acids can be joined together in a series of condensation reactions to form a polypeptide. polypeptides can also be broken down into amino acids by a series of hydrolysis reaction.

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16
Q

how is a protein formed

A

a protein is formed when one or more polypeptide fold into a specific shape that allows it to perform a specific function.

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17
Q

definition of polypeptide

A

a polymer made of amino acids joined together by peptide bonds

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18
Q

primary structure of proteins
definition

A

the sequence of amino acids in a polypeptide chain

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19
Q

when a polypetide chain is made what determines the primary structure of the protein

A

when a polypeptide chain is made, the order of the amino acids determines the primary stucture of the protein.

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20
Q

secondary structure of a protein

A

the polypeptide chains can curl or fold into alpha helices or beat pleated sheets due to the formation of hydrogen bonds

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21
Q

the coiling or folding of polypeptide chains arises due to the structure of amino acids-

A

they all contain an amino group -NH2 and a carboxyl group -COOH when bonded in a chain

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22
Q

the hydrogen in the NH- group is slightly positive and the oxygen in the -COOH carboxyl group is slightly negative what does this result in

A

this results in hydrogen bonds forming between the amino acids

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23
Q

what holds the secondary structures of a helices and beta pleated sheets together

A

the many hundreds of hydrogen bonds between the amino acids.

24
Q

in an a helix:

A

the polypeptide chain coils and hydrogen bonds between the amino acids keeps the coil stable

25
Q

in b pleated sheets:

A

The chains form zig zags and fold over themselves and the hydrogen bonds stablises this structure.

26
Q

secondary structure definition

A
  • the curling or folding of polypeptide chains into a helices and b pleated sheets due to the formation of hydrogen bonds
27
Q

definition of tertiary structure

A

the overall specific 3d shape of a protein which is determined by interactions between R groups and properties of R groups.

28
Q

definition of quarternary structure

A

the specific 3d shape of a protein determined by the multiple polypeptide chains and or prosthetic groups bonded together.

29
Q

how does the primary structure determine a proteins shape.

A

the primary structure of a protein determines its shape by determining the secondary, tertiary and quartenary structure.

30
Q

although secondary structure is stablised by hydrogen bonds additional types of bonds also hold tertiary, quartenary structures together:

A
  • ionic bonds
    -disulphide links
    -hydrophyllic and hydrophobic interactions
31
Q

types of additional bonds that hold tertiary and quartenary structures together

A

hydrogen bonds- form between polar R groups
the hydrogen in the amino group is slightly positive and the oxygen in the carboxyl group is slighlty negative, this causes hydrogen bonds to form between the amino acids.
ionic bonds- these form between positively and negatively charged R groups
disulphide links- these form between sulphur atoms in R groups

32
Q

the specific 3d structure of a protein is also determined by the hydrophillic and hydrophobic R groups

A

Amino acids with hydrophobic R groups tend to be found in the centre of the protein away from the water
amino acids with hydrophyllic R groups tend to be found on the outside of the protein close to the water.

33
Q

the primary stucture determines the secondary, tertiary and quartenary structures which give the proteins their unique shapes. however the bonds that maintain structure can be broken down by changes in:

A

PH and temperature this results in change of shape preventing the protein from being able to carry out its function, the protein is said to be denatured.

34
Q

Globular proteins have a few specific features
list the features of globular proteins

A

-roughly spherical
-hydrophobic r groups on the inside and hydrophyllic r groups in the inside so they are soluble in water
have very specific shapes which allow them to perform specific functions

35
Q

definition of a globular protein

A

A protein with spherical shape that is soluble in water and typically have metabollic roles.

36
Q

name three globular proteins

A

-haemoglobin (metabollic role)
-insulin (hormonal role)
-pepsin (transport/ hormonal role)

37
Q

haemoglobin is a globular protein that is found in red blood cells and transports oxygen in the blood from lungs to tissues for respiration
what type of structure does haemoglobin have and why?

A

haemoglobin has a quartenary structure because it contains 4 polypeptide chains

38
Q

why is haemoglobin a conjugated protein

A

-because haemglobin contains haem groups. which are prostethic groups ( non peptide groups). each prostethic group is attached to a polypeptide chain

39
Q

what is the meaning of a conjugated protein

A

a conjugated protein is a protein that functions in interaction with other non polypeptide chemical groups attatched by covalent bonding or weak interactions.

40
Q

what ions do the four prosthetic groups (the haem groups) contain

A

iron ions
fe 2+ they do not contain any amino acids

41
Q

each haemoglobin molecule carries how many molecules of oxygen

A

one oxygen molecule binds to each haem group and there are four haem groups each attached to one of the four polypeptide chains, allowing each haemoglobin molecule to carry four molecules of oxygen

42
Q

insulin - hormone made and secreted by the pancreas controls blood glucose concentration
function of insulin?

A

to maintain blood glucose concentration

43
Q

structure of insulin

A

composed by 2 polypeptide chains chain A starts with an alpha helix and chain B ends with with a beta pleated sheet. both are folded into tertiary structures which are joined by disulphide bonds.

44
Q

in insulin, what kind of bonds are the two poly peptide chains joined together by

A

disulphide links

45
Q

what does the shape of insulin allow it to do

A

the shape of insulin allows it to specifically bind to receptors on cell membranes to help lower blood glucose concentration

46
Q

what allows insulin to be soluble.

A

insulin contains hydrophyllic r groups on the outside making it soluble in water.
this allows insulin to dissolve in the blood and be transported around the body.

47
Q

pepsin is also a type of globular protein
what is the function of pepsin

A

the function of pepsin is to catalyse the digestion of proteins in the stomach.

48
Q

what is the structure of pepsin

A

formed by a single polypeptide chain, folded into a symmetrical tertiary structure.

49
Q

why do many enzymes get denatured at a low PH

A

many enzymes can denature at a low PH because they contain amino acids with basic R groups. Basic R groups accept protons (hydrogen ions) and become positively charged. this can affect the ionic bonds and hydrogen bonds in the protein, this can denature the protein and alter its function

50
Q

how does pepsin work in a low ph

A

pepsin contains fewer basic R groups but more acidic R groups so the tertiary structure is less affected by low PH.

51
Q

what kind of bonds help keep the tertiary structure of pepsin stable

A

hydrogen bonds and disulphide links

52
Q

definition of fibrous proteins

A

fibrous proteins are strong long insoluble proteins that have mainly structural roles.

53
Q

what similar properties do fibrous proteins have with each other

A

-they contain long polypeptide chains with repeating sequences of amino acids.
the amino acids have non polar R groups so the proteins are insoluble in water.
the polypeptide chains are able to form fibres which make proteins stronger.

54
Q

collagen forms very strong fibres, so is used to provide strength to many parts of the body
give examples

A

-collagen can be used to make bone
-collagen forms cartilage and connective tissue
-collagen used to make tendons which connect muscle to bone allowing skeleton to move
-collagen is found in artery walls to withstand high blood pressure (to prevent vessels from bursting)

55
Q

keratin is another example of a fibrous protein, its hard and strong and therefore used to form body parts such as fingernails, hooves and horns.
what is the primary structure of keratin

A

primary structure of keratin contains high amounts of cysteine which is an amino acid containing sulphur. this results in disulphide links forming between the two polypeptide chains. the disulphide links is what makes the molecule extremely strong.

56
Q

elastin is the final example of a fibrous protein
it has elastic properties so that it can stretch and recoil
elastin is stretchy due to the coiling of the elastin molecules and the cross links that keep them together.

A

elastin is stretchy because of the coiling of elastin molcules and the cross links that keep them together.

57
Q

give examples of places where elastin is found

A

elastin is found in the lungs to help them inflate and deflate during ventilation
elastin is found in our bladder to help it expand to hold urine
elastin is found in blood vessel walls where it helps maintain blood pressure by recoiling or stretching.

Biological Molecules (8 decks)

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