protein structure and function Flashcards
protein structure I protein structure II protein function and enzymology
what are the 4 most important classes of large molecule
- carbohydrates
- lipids
- proteins
- nucleic acids
what are the 3 main types of macromolecule
- carbohydrates
- proteins
- nucleic acids
what is a polymer
a long molecules consisting of many similar or identical building blocks called monomers linked by covalent bonds
what facilitates the formation of polymers from monomers in cells
enzymes
what is a common reaction in the formation of polymers
dehydration reaction (condensation polymerisation) - monomers are covalently bound to each other with the loss of a water molecule
by what reaction do polymers disassemble into monomers
hydrolysis - the bonds between monomers in a polymer are broken by the addition of water molecules
are lipids polymers
no - but hydrolysis and condensation are still involved in their synthesis and breakdown
how many essential amino acids are there
20
what are carbohydrates
they include sugars and polymers of sugars
what are the simplest carbohydrates
monosaccharides - single sugars
followed by disaccharides - double sugars (2 monosaccharides)
followed by polysaccharides (carbohydrates - they are made of many sugars)
what is the most common monosaccharide
glucose
what are the 2 different types of sugar depending on the position of the carbonyl group
aldehyde sugar - aldose
ketone sugar - ketose
what are hexoses, trioses and pentoses
hexoses - sugars with 6 carbons
trioses - sugars with 3 carbons
pentoses - sugars with 5 carbons
although often drawn as linear structures what shape do sugars form in aqueous solution under physiological conditions
they form rings because it is the most stable form
what are 2 important roles of sugars
they are used for cellular work (respiration) and for synthesis of other types of small organic molecules (such as amino acids and fatty acids)
what kind of bond forms between two monosaccharides in a disaccharide
glycosidic linkage - a type of covalent bond
what are the monomers of maltose
2 glucose molecules (they are joined by a 1-4 glycosidic bond)
what are the monomers of sucrose
a glucose molecule and a fructose molecule
in what form do plants transport carbohydrate from leaves to roots and other non photosynthetic organs
in the form of sucrose
what are the monomers of lactose
a glucose molecule and a galactose molecule
disaccharides must be broke down into …………. for use as energy by organisms
monosaccharides
which enzyme breaks down lactose and explain how this relates to lactose intolerance
lactase
those intolerant to lactose lack lactase and the sugar is instead broken down by intestinal bacteria causing gas and cramping
where do plants store starch and what is it made of
they store it in plastids (plastids include chloroplasts)
it is made of glucose monomers
why does starch represent stored energy
because glucose is a major cellular fuel
what are the major sources of starch in the human diet
the fruits of wheat, maize, rice and other grasses
most glucose monomers are joined by what kind of linkages
1-4 linkages
what is the simplest form of starch
amylose (unbranched)
what is a more complex form of starch
amylopectin (branched) - it has 1-6 linkages at branch points
what is glycogen
a polymer of glucose that is more extensively branched than amylopectin
where do vertebrates store glycogen
liver and muscle cells
what are the 2 classes of polypeptides
structural and storage
give an example of a structural polypeptide
cellulose - a polymer of glucose with 1-4 glycosidic linkages
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
what is the shape of starch molecules
highly helical
what is the shape of cellulose
straight - never branched
in plant cell walls parallel cellulose molecules held together by hydrogen bonds are grouped into units called ……………..
microfibrils – cable like - very strong
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
can we digest cellulose
no - but it aids digestion by stimulating mucus secretion
which organisms can digest cellulose
cows - they have microbes (prokaryotes and protists) that break it down into sugars
what is chitin
a carbohydrate used by arthropods to build their exoskeletons
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
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
why are lipids not considered macromolecules
they are not big enough
what is the common trait of all lipids
they mix very poorly with water
why are lipids non polar
even through they have some hydrophilic bonds they are mostly made up of long nonpolar hydrocarbon chains
what types of lipids are most important to biology
fats, phospholipids and steroids
what are fats made from
glycerol and fatty acids
what is glycerol
a triol - each of its 3 carbons has a hydroxyl group attached
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
how are fats made
3 fatty acid molecules join to glycerol by ester linkages
the resulting fat is often called a triglycerol/triglyceride
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
what is an unsaturated fatty acid
one with one or more double bonds in the carbon chain
most double bonds in fatty acids are cis/trans
cis - this creates a kink in the hydrocarbon chain
saturated/unsaturated fats can pack together closely
saturated
unsaturated fats are usually ………… at room temperature
liquid (usually referred to as oils)
saturated fats are usually ………… at room temperature
solid
what are hydrogenated vegetable oils
found in marge - unsaturated fats have been synthetically saturated by addition of hydrogen, allowing them to solidify
what types of fats can contribute to the development of atherosclerosis (a cardiovascular disease)
saturated fats
trans fats contribute to ……….. disease
coronary
what is the major function of fats
energy storage
why are phospholipids essential for cells
because they are a major component in membranes
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
the phosphate head of a phospholipid is hydrophobic/hydrophilic while the tail is hydrophobic/hydrophilic
hydrophilic
hydrophobic
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
what are steroids
lipids characterized by a carbon skeleton consisting of 4 fused rings
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
what are most enzymes made of
proteins
how can enzymes regulate metabolism
by acting as catalysts
what is the bond between amino acids in a polypeptide called
peptide bonds
how many polypeptides make up proteins
one or more
what is the alpha carbon of an amino acid
the carbon in the centre
give different functions of proteins
enzymes defence storage transport hormones receptors contractile and motor proteins structural
what are the 3 different types of sidechain
hydrophobic (nonpolar)
hydrophilic (polar)
electrically charged (polar)
list the 9 hydrophobic amino acids
gly - glycine ala - alanine val - valine leu - leucine ile - isoleucine met - methionine phe - phenylalanine trp - tryptophan pro - proline
list the 6 hydrophilic neutral amino acids
ser - serine thr - threonine cys - cysteine tyr - tyrosine asn - asparagine gln - glutamine
list the 2 acidic amino acids
asp - aspartic acid
glu - glutamic acid
list the 3 basic amino acids
lys - lysine
arg - arginine
his - histidine
what is the polypeptide backbone
the repeated sequence of atoms
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
why type of proteins are spherical
globular
what type of proteins are shaped like long fibres
fibrous proteins
the function of a protein usually depends on its ability to ..…………. and bind to another molecule
recognise e.g. antibodies binding to antigens
what molecules mimic endorphins which bind to the brain to relieve pain or give euphoria
morphine, heroin and other opiate drugs
what are the 4 different structural levels in proteins
primary
secondary
tertiary
quaternary
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
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
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)
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
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
what causes sickle cell anaemia
the substitution of an amino acid in the primary structure of haemoglobin
what is the shape of a normal red blood cell
disk shaped - biconcave
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
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
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
name some diseases caused by accumulation of misfolded proteins
Alzheimer’s
Parkinson’s
mad cow disease
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
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
what programmes an amino acid
a gene
what do genes consist of
DNA
what are the monomers of nucleic acids called
nucleotides
what are the 2 types of nucleic acid
DNA and RNA
what is gene expression
the process of DNA directing RNA synthesis and through RNA controlling protein synthesis
what is the site of protein synthesis
ribosomes
mRNA conveys genetic instructions for protein synthesis from the nucleus to the …………. in the cytoplasm
ribosome
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)
what is a nucleoside
the portion of a nucleotide that has no phosphate groups (base plus sugar)
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
describe the structure of a pyrimidine
1 six membered ring of carbon and nitrogen atoms
pyrimidine family members include thymine, cytosine and uracil
describe the structure of purine
a larger 6 membered ring fused with a 5 membered ring
purine family members include guanine and adenine
thymine is only found in DNA/RNA
uracil is only found in DNA/RNA
thymine - DNA
uracil - RNA
what is the DNA sugar called
deoxyribose sugar - lacks an oxygen atom on the second carbon of the ring compared to ribose sugar
what is the sugar called in RNA
ribose sugar
what end of the nucleotide is the phosphate attached to
5’
what kind of reaction links nucleotides together
dehydration
adjacent nucleotides are linked by a ……………….. linkage which consists of a phosphate group that links the sugars of the 2 nucleotides
phosphodiester
the repeating pattern of sugar and phosphate is called what
the sugar phosphate backbone
what is attached the 3’ end of a polynucleotide
hydroxyl group
in what direction is a polynucleotide built
5’ to 3’
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’
what type of bond forms between bases
hydrogen
are RNA molecules single stranded or double stranded
single
what does tRNA do
brings amino acids to the ribosome during polypeptide synthesis
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
what is a genome
the full complement of an organisms DNA
what is bioinformatics
the use of computer software and other computational tools to handle and analyses large data sets
genomics
the comparison of different genomes or parts of them
what is proteomics
analysis of large sets of proteins including their sequences
what is Ehlers-Danloss syndrome caused by
defects in collagen synthesis
all amino acids found in proteins are of which form D or L
L
what do chaperones do
they help proteins fold up properly if they don’t fold spontaneously
what is a domain
an independently stable part of a polypeptide, usually with a specific function(they often correspond to an exon)
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.
what part of the antigen does the antibody recognise
the epitope
at high altitude levels of …………. rises and enhances oxygen unloading from haemoglobin
BPG
what is a globin
related proteins with very similar structures but different functions.
