Lecture 5 Part 1. Biochemistry Flashcards
What are the functions of proteins
- Enzyme Catalysts ie endonuclease = speed up reactions - pull 2 molecules together, put them in the right orientation that will make reaction more likely to occur
- Transport and Storage ie Heamoglobin
- Co-ordinate Movement ie cytoskeletal actin… tubulin
- Mechanical Support ie collagen
- Immune Protection ie Immunoglobins - tag microbes
- Signaling and Receptors ie toll like receptors
- Ion Channels/pores ie Integral proteins in plasma membrane
What does an amino acid contain - structure
- A central C
- amino group (NH2)
- carboxyl group (COOH)
- H atom
- R group
What varies and determines type of amino acid
R group
How many standard amino acids are there
20
What does R group determine
Differences between amino acids and the chemical nature of it
Different electrochemical properties of amino acid
What are the different chemical properties of amino acids
- Acidic – Glutamate/Aspartate
- Basic - Serine, Tyrosine
- Non-Polar – Alanine, Valine,
- Polar
Proline
- The R group covalently binds to the NH2+ group of the central Carbon ‘folding back’ the amino acid
- Can function to induce kinks into alpha helices, since it is unable to adopt a normal helical conformation
How is proline different to other amino acids
Conformational rigidity
What does rigidity of proline help
Stabilize folded proteins
Where is proline often found
In very tight turns in protein structures, where the polypeptide chain must change direction
What is it unable to do
Adopt a normal helical conformation
What are proteins
Linear sequences of amino acids held together by peptide bonds
What forms when proteins join
Dipeptide
What does either end of dipeptide have that allows further bonding
Has an amino and carboxyl group free
What would further peptide bonding create
oligopeptide (<25 aa) or polypeptide (>25aa).
What happens during a condensation reaction
When 2 molecules join together with the formation of a new chemical bond, forming a water molecule
What is formed during condensation reaction
H20
How do R groups stick out in sequence
Do not stick out from the same backbone in the same orientation as each other.
R groups opposite side on 2 amino acids - one r group sticks out on one side, other R group sticks out other side
What determines protein shape
Amino acid sequence
Where are polar amino acids located
Outside of the protein in an aqueous environment
Where are non polar amino acids located
Inside
What does polypeptide chain fold into
A shape which is stabilized by several non-covalent interactions.
What are the 4 types of bonds and what do they do
- Ionic bond
- Hydrogen bond
- van der Waals interactions
- Covalent bonds
Stabilise new 3D structure
What bond doesnt form between R groups at different points along protein sequence
Covalent bonds
What stabilises new 3D structure
Non - covalent interactions
Disulphide bond
- Stabilising cross link between Sulphur and Sulphur (covalent bond)
- S-S bond between cysteine residues
What is confirmation
Folding pattern of a protein
What can polypeptide chains fold into
Regular structure ( 3D) - stabilise itself with interactions
What two patters predominate in proteins and why
- α-helix
- β-‘pleated’ sheet
- Because they efficiently fill space
What are the secondary protein structures
- α-helix
- β-‘pleated’ sheet
α-helix
- Rod like structure or coil)
single polypeptide chain - Tightly coiled backbone forms the inner part of the rod and the R groups extend outward
- Stabilised by hydrogen bonds between NH to CO groups of the main chain.
- Roughly 4 amino acids to every 1 turn of chain
β-‘pleated’ sheet
- Extended polypeptide chains that fold back over each other - more H bonding
- Formed by linking two or more β-strands - adjacent - parallel or anti parallel
What are the levels of organisation of protein structure
- Primary
- Secondary
- Tertiary
- Quaternary
What is primary structure
Sequence of amino acids
What is secondary structure
α helix and β sheet formation with folding as a result of hydrogen bonding between peptides
What is tertiary structure
3D conformation – folding of the polypeptide chain – disulphide bonds form between the R groups of the α helices and β sheets
What is Quaternary structure
Complex of several polypeptide chains
Example of Quaternary structure
Haemoglobin
What are carbohydrates
- Compounds containing C , H , O
- Carbo = carbon
hydrate = water, which contains hydrogen and oxygen - Essentially hydrated Carbon (C + H2O)
What elements do carbs contain
C , H , O
What is role of carbohydrates
Make up most organic matter on Earth:
- Polysaccharides serve as compact energy storage molecules (glycogen or starch) - breaks down = glucose = energy Or structural elements in plant cell walls (cellulose) - humans cant use - cant break down in body
- Monomeric sugars act as intermediates in metabolism (glucose and other molecules in the glycolytic pathway
- Phosphorylated sugars form the structural framework of DNA and RNA (ribose)
- Glycoproteins and glycolipids are found on cell surfaces – cell recognition - glycocalyx
What are monosaccharides
Composed of one simple sugar like glucose and fructose
What are disaccharides
Composed of two monosaccharides
What are oligosacchharides
Composed of a small number of monosaccharides
few sugars < 15
What are polysaccharides
Polymeric carbohydrate molecule composed of long chains of monosaccharides
Monosaccharides
- The building bocks of carbohydrates:
- Simplest form of carbohydrates
- Usually colourless, water-soluble, crystalline solids
- General formula (CH20)n n ≥ 3
- Contain 3-6 carbon atoms - form backbone of molecule
C3= trioses
C5= pentoses
C6= hexoses
What do monosaccharides contain
An aldehyde group (called aldose)
Or ketone group (called ketose)
Ring structure formation:
In aqueous solution, the aldehyde or ketone group of a sugar molecule tends to react with a hydroxyl group of same molecule, thereby closing molecule into a ring
How are sugar derivatives formed
The hydroxyl group (OH) can be replaced with other groups
Examples of sugar derivatives
- Phosphorylated sugars (i.e glucose-6-phosphate)
are used in glycolysis. - Sugars can also form a covalent bonds with nitrogenous bases - change amount of energy released
- The hydroxyl group could be replaced by an amine group (NH2). These are common components of glycoproteins.
What are disaccharides
2 monosaccharides join via a condensation reaction
What’s the covalent bond in a disaccharide
Glycosidic bond
O - glycosidic bond
C1 binds to Oxygen
N - glycosidic bond
C1 binds to Nitrogen
S - glycosidic bond
C1 binds to Sulphur
C - glycosidic bond
C1 binds to Carbon
What are the common saccharides
Sucrose - glucose and fructose
Lactose - glucose and galactose
Maltose - glucose and glucsoe
What are oligosaccharides
Polymer containing a small number of component monosaccharides (<15)
Functions of oligosaccharides
commonly found on the plasma membrane of animal cells where they play a role in cell-cell recognition - glycocalyx
Is branching possible for oligosaccharides
Yes
What can you make with oligosaccharides
Either make O-glycosidic bonds or N-glycosodic bounds with amino acid R groups or to lipids to make glycoporteins or glycolipids
Which oligosaccharides may be linear or branched chains
covalently linked to proteins or to membrane lipids
branched - reacting through hydroxyl groups
What do oligosaccharies of glycoproteins and glycolipids often include
Modified sugars
e.g. acetlyglucosamine
What monosaccharides do oligosaccharies of glycoproteins and glycolipids often include
glucose
galactose
mannose
fructose
What happens in O glycosidic linked oligosaccharide
link to a protein via a glycosidic bond between a sugar residue and an hydroxyl group (OH) on serine or threonine amino acids
What happens in N glycosidic linked oligosaccharide
complex and branched
What do N - linked glycoproteins all contain
Common core of 3 mannose sugars attached to protein - make these branched
Whats attached to common core of N linked glycoproteins
Variety of sugars
O - linked glycoproteins
Either single chain or branched
What’s glycocalyx
Outer layer – bound polysaccharides on the cell surface and superficial layer of unbound proteoglycans and glycoproteins
What are the functions of glycocalyx
Cell recognition
Cell adhesion
Protection
Permeability barrier
Whats the difference between glycoproteins and proteoglycans
- Proteoglycans represent a subclass of glycoproteins
- Both composed of protein and carbohydrate
- In a glycoprotein the complexity and length of the oligosaccharide is limited to <15 sugars
- In a proteoglycan the structure is more complicated and much larger
- Proteoglycans form ground substance of connective tissues
Proteoglycans role
- Proteoglycans play an important role in connective tissues (ground substance ie cartilage, vitreous), extracellular matrix - wound healing
- Proportion of collagen and proteoglycans varies between different connective tissues
- Proteoglycans create hydrated spaces around cells and withstand compression
- Regulate fluid and can bind cations (Zinc, Iron, Copper) to form electrochemical gradients + wound healing
What do proteoglycans play an important role in
Connective tissue
Proteoglycan structure: glycosaminoglycans (GAGS)- what are they
Repeating disaccharide units
Held together by another carbon and hydrogen chain = make up ground susbtance - density of ground susbtance based on ratio of collagen fibres and hydrogen
Structure of GAGS
Extend perpendicular from the core protein to form a proteoglycan – bottlebrush structure
GAGS sticking on outside, protein chain in middle
Examples of proteoglycans
Hyaluronic acid – vitreous
Dermatan sulphate- skin
Chondroitin sulphate- cartilage
Keratan sulphate –basement membrane/cornea stroma
What are polysaccharides
Polymeric carbohydrate molecule composed of long chains of monosaccharide units
What are polysaccharides bound together by
Glycosidic linkages
How do polysaccharides break down into constituent monosaccharides or oligosaccharides
Hydrolysis
Structure of polysaccharides
Linear or highly branched
Types of polysaccharides
Storage or Structural
What are lipids
Naturally occurring molecules
Role of lipids
- Components of membranes (phospholipids and sphingolipids, cholesterol)
- Several proteins are covalently modified by fatty acids
- Act as energy stores (triacylglycerols) and fuel molecules
- Fatty acid derivatives serve as hormones (i.e steroids) and intracellular second messangers
What are the types of lipids
Fatty acids Triglycerides Phospholipids Steroids Glycolipids
Structure of fatty acid
Carboxylic acids with long hydrocarbon chain ‘tails’
Carboxyl group attached to a long hydrocarbon chain and a methyl group: CH3(CH)nCOOH
Saturated
No double bonds between carbons in hydrocarbon tail
Straight
Unsaturated
One or more double bonds = shape into fatty acids
Bends or kinks in tail
What are triglycerides
3 fatty acids joined together through ester linkage to Glycerol (carbohydrate).
Role of triglycerides
Energy store
Where are fatty acids stored
Adipocytes as triglyceride (lipid inclusions in cells)
How is fatty acid released from triglyceride
Its hydrolysed
Where are adipocytes mostly found
In the abdominal cavity and subcutaneous tissue
Property of adipocyte
Metabolically very active; stored triglyceride is constantly hydrolyzed and resynthesised
What is a phospholipid
Contains 2 fatty acids bound through ester linkage to glycerol, but where the third fatty acid would bind in a triglyceride, you have a link to phosphoric acid . The phosphate is also bound to a polar head group (alcohol)
What are phospholipids major constituents of
Cell membranes
Where are steroid hormones derived from
Cholestrol except retinoic acid
Role of cholestrol
Major component of cell membranes – imparts fluidity and maintains the integrity of the membrane
How does cholestrol travel around in body
in lipoproteins
Cholestrol in membrane
- Cholesterol hydroxyl group aligns with the polar head phosphate group of the phospholipid
- Steroid ring interacts with the hydrocarbon chain closest to the polar head group of the phospholipid
- Cholesterol immobilises the first few CH2 groups of the hydrocarbon chain closest to the polar head groups – less deformable bilayer
- Decreases lipid fluidity by preventing motion of hydrocarbon chains
- Enhances permeability-barrier properties of the bilayer
What are glycolipids
- Complex lipid that contains a sugar.
- They are structural lipids
- Sugar and fatty acid - between phospholipids
What is the sugar in glycolipids
Glucose or galactose
Structure of glycolipids
Composed of a hydrophobic region
(the two long hydrocarbon chains) and polar region, which in this lipid consists of one or more sugar residues
(No phosphate).
What are Lipoproteins
Core of triglycerides and/or cholesterol and a surface monolayer of phospholipid, unesterified cholesterol and proteins
Role of lipoproteins
Transport of lipids and cholesterol in the blood
How do lipoproteins differ
In the ratio of protein to lipids - classified according to their density:
HDL - High density lipoprotein
Highest in density due to high protein:lipid ratio, carry 20% plasma cholesterol
LDL - Low density lipoprotein
Highest in cholesterol as % of weight, carry 60% plasma cholesterol
VLDL - Very Low density lipoprotein
Carry triglycerides
What is amino acid
Monomer of protein
How do amino acids have different physical properties
Affects physical space of it and how other amino acids can fit around it e.g size
What is a kink
point in the helix where there is a sharp change in the direction of the helix axis
A sharp twist or curve in something that is otherwise straight
What is peptide bond
Covalent bond between C in COOH and N in NH2
Is amino acid chain functional on its own and why
No
It hasn’t developed specialised regions to do specific functions
How is R group hydrophobic
Doesn’t like aqueous environment - polypeptide chain in water in cells - hide, rest of chain twist around it = hydrophobic region hidden inside protein
How is each R group specific
Specific interaction with another R group = specific shape and function
What environment does ring structure form
Aqueous
What happens in N - glycosidic bond
Sugar reacting with nitrogenous ring = hydroxyl ring displaced
What is proteoglycan
Type of protein carb mix - secreted into extracellular place = form part of ground susbtance of connective tissues
