protein structure and function Flashcards
protein structure I protein structure II protein function and enzymology
1
Q
what are the 4 most important classes of large molecule
A
- carbohydrates
- lipids
- proteins
- nucleic acids
2
Q
what are the 3 main types of macromolecule
A
- carbohydrates
- proteins
- nucleic acids
3
Q
what is a polymer
A
a long molecules consisting of many similar or identical building blocks called monomers linked by covalent bonds
4
Q
what facilitates the formation of polymers from monomers in cells
A
enzymes
5
Q
what is a common reaction in the formation of polymers
A
dehydration reaction (condensation polymerisation) - monomers are covalently bound to each other with the loss of a water molecule
6
Q
by what reaction do polymers disassemble into monomers
A
hydrolysis - the bonds between monomers in a polymer are broken by the addition of water molecules
7
Q
are lipids polymers
A
no - but hydrolysis and condensation are still involved in their synthesis and breakdown
8
Q
how many essential amino acids are there
A
20
9
Q
what are carbohydrates
A
they include sugars and polymers of sugars
10
Q
what are the simplest carbohydrates
A
monosaccharides - single sugars
followed by disaccharides - double sugars (2 monosaccharides)
followed by polysaccharides (carbohydrates - they are made of many sugars)
11
Q
what is the most common monosaccharide
A
glucose
12
Q
what are the 2 different types of sugar depending on the position of the carbonyl group
A
aldehyde sugar - aldose
ketone sugar - ketose
13
Q
what are hexoses, trioses and pentoses
A
hexoses - sugars with 6 carbons
trioses - sugars with 3 carbons
pentoses - sugars with 5 carbons
14
Q
although often drawn as linear structures what shape do sugars form in aqueous solution under physiological conditions
A
they form rings because it is the most stable form
15
Q
what are 2 important roles of sugars
A
they are used for cellular work (respiration) and for synthesis of other types of small organic molecules (such as amino acids and fatty acids)
16
Q
what kind of bond forms between two monosaccharides in a disaccharide
A
glycosidic linkage - a type of covalent bond
17
Q
what are the monomers of maltose
A
2 glucose molecules (they are joined by a 1-4 glycosidic bond)
18
Q
what are the monomers of sucrose
A
a glucose molecule and a fructose molecule
19
Q
in what form do plants transport carbohydrate from leaves to roots and other non photosynthetic organs
A
in the form of sucrose
20
Q
what are the monomers of lactose
A
a glucose molecule and a galactose molecule
21
Q
disaccharides must be broke down into …………. for use as energy by organisms
A
monosaccharides
22
Q
which enzyme breaks down lactose and explain how this relates to lactose intolerance
A
lactase
those intolerant to lactose lack lactase and the sugar is instead broken down by intestinal bacteria causing gas and cramping
23
Q
where do plants store starch and what is it made of
A
they store it in plastids (plastids include chloroplasts)
it is made of glucose monomers
24
Q
why does starch represent stored energy
A
because glucose is a major cellular fuel
25
what are the major sources of starch in the human diet
the fruits of wheat, maize, rice and other grasses
26
most glucose monomers are joined by what kind of linkages
1-4 linkages
27
what is the simplest form of starch
amylose (unbranched)
28
what is a more complex form of starch
amylopectin (branched) - it has 1-6 linkages at branch points
29
what is glycogen
a polymer of glucose that is more extensively branched than amylopectin
30
where do vertebrates store glycogen
liver and muscle cells
31
what are the 2 classes of polypeptides
structural and storage
32
give an example of a structural polypeptide
cellulose - a polymer of glucose with 1-4 glycosidic linkages
33
what is the difference between the glucose linkages in starch and cellulose
there are 2 slightly different ring structures for glucose - alpha (hydroxyl pointing down) and beta (hydroxyl pointing up)
cellulose has beta glucose whereas starch only has alpha
34
what is the shape of starch molecules
highly helical
35
what is the shape of cellulose
straight - never branched
36
in plant cell walls parallel cellulose molecules held together by hydrogen bonds are grouped into units called ……………..
microfibrils -- cable like - very strong
37
enzymes that hydrolyse the alpha linkages of starch are able to/not able to hydrolyse the beta linkages of cellulose
not able to because the molecules are different shapes and enzymes are highly specific to shape
38
can we digest cellulose
no - but it aids digestion by stimulating mucus secretion
39
which organisms can digest cellulose
cows - they have microbes (prokaryotes and protists) that break it down into sugars
40
what is chitin
a carbohydrate used by arthropods to build their exoskeletons
41
what is an exoskeleton
a hard case that surrounds soft parts of an a animal
it is made up of chitin embedded in a layer of proteins I
it becomes hardened when proteins are linked together or encrusted with calcium
42
what kind of linkages does chitin contain and how is it different to cellulose
beta linkages like cellulose but it has a nitrogen containing linkage whereas cellulose doesn't
43
why are lipids not considered macromolecules
they are not big enough
44
what is the common trait of all lipids
they mix very poorly with water
45
why are lipids non polar
even through they have some hydrophilic bonds they are mostly made up of long nonpolar hydrocarbon chains
46
what types of lipids are most important to biology
fats, phospholipids and steroids
47
what are fats made from
glycerol and fatty acids
48
what is glycerol
a triol - each of its 3 carbons has a hydroxyl group attached
49
what is a fatty acid
it has a long carbon skeleton
| at one end of the skeleton is a carboxyl group giving it the acid name
50
how are fats made
3 fatty acid molecules join to glycerol by ester linkages
| the resulting fat is often called a triglycerol/triglyceride
51
what is a saturated fatty acid
one with no double bonds in the carbon chain so the maximum number of hydrogens are able to bind
52
what is an unsaturated fatty acid
one with one or more double bonds in the carbon chain
53
most double bonds in fatty acids are cis/trans
cis - this creates a kink in the hydrocarbon chain
54
saturated/unsaturated fats can pack together closely
saturated
55
unsaturated fats are usually ………… at room temperature
liquid (usually referred to as oils)
56
saturated fats are usually ………… at room temperature
solid
57
what are hydrogenated vegetable oils
found in marge - unsaturated fats have been synthetically saturated by addition of hydrogen, allowing them to solidify
58
what types of fats can contribute to the development of atherosclerosis (a cardiovascular disease)
saturated fats
59
trans fats contribute to ……….. disease
coronary
60
what is the major function of fats
energy storage
61
why are phospholipids essential for cells
because they are a major component in membranes
62
what is the structure of a phospholipid
2 fatty acids attached to glycerol
the 3rd hydroxyl of glycerol is attached to a phosphate group - usually another small polar molecule is linked to this phosphate e.g. choline
63
the phosphate head of a phospholipid is hydrophobic/hydrophilic while the tail is hydrophobic/hydrophilic
hydrophilic
| hydrophobic
64
when phospholipids are added to water they assemble into what
phospholipid bilayer - they are also arranged like this on the surface of a cell making up the membrane
65
what are steroids
lipids characterized by a carbon skeleton consisting of 4 fused rings
66
what is cholesterol
a type of steroid that is crucial in animals in their membranes and as precursors for other steroids
it is synthesised in the liver
67
what are most enzymes made of
proteins
68
how can enzymes regulate metabolism
by acting as catalysts
69
what is the bond between amino acids in a polypeptide called
peptide bonds
70
how many polypeptides make up proteins
one or more
71
what is the alpha carbon of an amino acid
the carbon in the centre
72
give different functions of proteins
```
enzymes
defence
storage
transport
hormones
receptors
contractile and motor proteins
structural
```
73
what are the 3 different types of sidechain
hydrophobic (nonpolar)
hydrophilic (polar)
electrically charged (polar)
74
list the 9 hydrophobic amino acids
```
gly - glycine
ala - alanine
val - valine
leu - leucine
ile - isoleucine
met - methionine
phe - phenylalanine
trp - tryptophan
pro - proline
```
75
list the 6 hydrophilic neutral amino acids
```
ser - serine
thr - threonine
cys - cysteine
tyr - tyrosine
asn - asparagine
gln - glutamine
```
76
list the 2 acidic amino acids
asp - aspartic acid
| glu - glutamic acid
77
list the 3 basic amino acids
lys - lysine
arg - arginine
his - histidine
78
what is the polypeptide backbone
the repeated sequence of atoms
79
what determines the chemical nature of a polypeptide
its shape which is ultimately determined by its sequence of amino acids - more specifically the sequence of side chains
80
why type of proteins are spherical
globular
81
what type of proteins are shaped like long fibres
fibrous proteins
82
the function of a protein usually depends on its ability to ..…………. and bind to another molecule
recognise e.g. antibodies binding to antigens
83
what molecules mimic endorphins which bind to the brain to relieve pain or give euphoria
morphine, heroin and other opiate drugs
84
what are the 4 different structural levels in proteins
primary
secondary
tertiary
quaternary
85
what is the primary structure of a protein
the sequence of its amino acids - this dictates the secondary and tertiary structures due to the chemical nature of the backbone and sidechains
86
what is the secondary structure of a protein
regions stabilized by hydrogen bonds between atoms of the polypeptide backbone (not sidechains)
the 2 secondary structures are:
- alpha-helix - coil held together by H bonds between every 4th amino acid - dominate globular proteins - the side chains are on the outside of the helical rod
- beta-sheet - 2 or more segments of polypeptide chain lying side by side connected by H bonds - these dominate fibrous proteins - can be twisted into a cylinder - can be parallel or anntiparallel
87
what is the tertiary structure of a protein
the 3D shape stabilized by interactions between side chains
interactions include:
- hydrophobic interactions (hydrophobic sidechains cluster in the centre and interact via van der waals)
- interactions between acid and base side chains (ionic)
- interactions between hydrophilic sidechains (hydrogen bonding)
- disulphide bridges (S-S) between cysteine monomers sulfhydryl groups (-SH)
88
what is the quaternary structure of a protein
association of 2 or more polypeptides (only some proteins)
| the polypeptides can be the same or different
89
describe the structure of haemoglobin
2 alpha and 2 beta subunits that all consist primarily of alpha helices
each subunit has a non polypeptide component called heme which contains an iron atom that binds oxygen
90
what causes sickle cell anaemia
the substitution of an amino acid in the primary structure of haemoglobin
91
what is the shape of a normal red blood cell
disk shaped - biconcave
92
what shape are blood cells in patients with sickle cell anaemia
sickle shape - abnormal haemoglobin molecules tend to aggregate into chains - these can clog vessels and impede flow
93
apart from the different levels of protein structure what else can influence protein shape and function
the physical and chemical conditions in the proteins environment
94
what is denaturation
when weak chemical interactions and bonds within a protein are destroyed causing the protein to unravel and lose its native shape
this can be due to many environmental factors including pH, salt conc, temperature etc
95
name some diseases caused by accumulation of misfolded proteins
Alzheimer's
Parkinson's
mad cow disease
96
what method is most commonly used to determine the 3D structure of a protein
x-ray crystallography which depends on diffraction of an x-ray beam by the atoms of a crystalized molecule
NMR can also be used to help find out the structure
97
why is the structure of some proteins difficult to determine
some proteins don't have a distinct 3D structure until they interact with a target protein or other molecule
these are called intrinsically disordered proteins
98
what programmes an amino acid
a gene
99
what do genes consist of
DNA
100
what are the monomers of nucleic acids called
nucleotides
101
what are the 2 types of nucleic acid
DNA and RNA
102
what is gene expression
the process of DNA directing RNA synthesis and through RNA controlling protein synthesis
103
what is the site of protein synthesis
ribosomes
104
mRNA conveys genetic instructions for protein synthesis from the nucleus to the …………. in the cytoplasm
ribosome
105
what is the general form of a nucleic acid
5 carbon sugar (pentose)
nitrogenous base (nitrogen containing)
1 to 3 phosphate groups (begins with 3 but 2 are lost in the polymerisation process)
106
what is a nucleoside
the portion of a nucleotide that has no phosphate groups (base plus sugar)
107
what is the structure of the nitrogenous base
has 1 or 2 rings that contain nitrogen atoms
| the 2 families of nitrogenous bas are pyrimidines and purines
108
describe the structure of a pyrimidine
1 six membered ring of carbon and nitrogen atoms
| pyrimidine family members include thymine, cytosine and uracil
109
describe the structure of purine
a larger 6 membered ring fused with a 5 membered ring
| purine family members include guanine and adenine
110
thymine is only found in DNA/RNA
| uracil is only found in DNA/RNA
thymine - DNA
| uracil - RNA
111
what is the DNA sugar called
deoxyribose sugar - lacks an oxygen atom on the second carbon of the ring compared to ribose sugar
112
what is the sugar called in RNA
ribose sugar
113
what end of the nucleotide is the phosphate attached to
5'
114
what kind of reaction links nucleotides together
dehydration
115
adjacent nucleotides are linked by a .................... linkage which consists of a phosphate group that links the sugars of the 2 nucleotides
phosphodiester
116
the repeating pattern of sugar and phosphate is called what
the sugar phosphate backbone
117
what is attached the 3' end of a polynucleotide
hydroxyl group
118
in what direction is a polynucleotide built
5' to 3'
119
what describes the direction of polynucleotide strands in a double helix of DNA
they are antiparallel - one runs 5' to 3' and the other runs 3' to 5'
120
what type of bond forms between bases
hydrogen
121
are RNA molecules single stranded or double stranded
single
122
what does tRNA do
brings amino acids to the ribosome during polypeptide synthesis
123
differences between DNA and RNA
DNA double helix but RNA has variable shape
DNA is double stranded whereas RNA is single stranded
RNA contains the base Uracil and DNA doesn't
DNA contains the base Thymine whereas RNA doesn't
124
what is a genome
the full complement of an organisms DNA
125
what is bioinformatics
the use of computer software and other computational tools to handle and analyses large data sets
126
genomics
the comparison of different genomes or parts of them
127
what is proteomics
analysis of large sets of proteins including their sequences
128
what is Ehlers-Danloss syndrome caused by
defects in collagen synthesis
129
all amino acids found in proteins are of which form D or L
L
130
what do chaperones do
they help proteins fold up properly if they don't fold spontaneously
131
what is a domain
an independently stable part of a polypeptide, usually with a specific function(they often correspond to an exon)
132
what is the structure of antibodies
contain 2 heavy and 2 light chains joined by disulphide bridges; both types of chain have variable and constant regions. Antigen specificity is conferred by the variable regions.
133
what part of the antigen does the antibody recognise
the epitope
134
at high altitude levels of …………. rises and enhances oxygen unloading from haemoglobin
BPG
135
what is a globin
related proteins with very similar structures but different functions.
