Structure And Function Of Proteins Flashcards
What do proteins do?
- brief explanation
They come in many shapes and sizes that have a variety of functions such as catalysis, defence, transport, motion, regulation and storage
Enzyme catalysis
- class, example and example of use
Class: enzymes
Examples: glucosidase, proteases, polymerises and kinases
Example of use: cleave polysaccharides, protein breakdown, synth nuclei acids and phospho prots
Defense
- class, example and example of use
Class: Ig, toxins, antigens
Example: MHC, antibodies and snake venom
Use: mark non-self for elim, block nerve function and self recog
Transport
- class, example and use
Circulating transporters: haem/myoglobin and cytochromes
Movement of O2 and CO2 in muscles and blood and movement of electrons
Membrane transporters: Na/K pump, proton pump and glucose transporter
Membrane potential, chemiosmosis and gluc transport
Support
- class, example and use
Fibres:
Collagen, keratin and fibrin
Forms cartilage, forms hair and nails and form blood clots
Motion:
- class, example and use
Muscles:
Actin and myosin
Contract muscle fibres
Regulation:
- class, example and use
Osmotic proteins: - serum albumin - maintains osmotic conc of blood Gene regulators: - Iac repressor - regs transcrip Hormones: - insulin, vasopressin, oxytocin - control blood gluc, water retention and reg uterine contract and milk prod
Storage:
- class, example and use
Ion-binding:
- ferritin, casein, calmodulin
- store iron in spleen, store ions in milk and binds Ca
Ways to classify proteins
Size: port or pep
Class: fibrous or globular
Role: structural or functional
Location: intra/extracellular, soluble and membranal
Structural proteins
Such as actin/intermediate filaments of cytoskeleton
Intracellular vs extracellular
Intra: targeted to a specific organelle
Extra: lumen of RER
Integral vs peripheral
Integral proteins are within the membrane
Peripheral proteins are beneath the membrane
What are proteins made of?
Monomers such as amino acids
Polymers such as polypeptides
Cellular structure such as intermediate/actin filaments
The central dogma of molecular biology
DNA to RNA to polypeptide to functional protein (involving folding into 3D structure with chemical modification)
How can such a variety of shapes and functions arise from a string of amino acids?
Structure gives shape to key parts of amino acids, in specific position to aid in their function
- to interact/bind with non-prot molecules or other proteins
- taking part in chem reactions such as catalysis
Traditional enzyme characteristics
Enzyme contains an active site that is specific to the substrate, when it bind it become the enzyme-substrate complex (active site molded by 1/2/3 structure)
How many different amino acids exist
20 different types: NON AROMATIC -non polar: alanine, glycine (valine, isoleucine and leucine) -polar uncharged: serine, asparagine, glutamine (threonine) -charged: glutamic acid, arginine, aspartic acid (lysine) AROMATIC -non polar: (phenylalanine, tryptophan) -polar uncharged: (tyrosine) -charges: (histidine) SPECIAL FUNCTION -non polar: (proline, methionine) -polar uncharged: (cysteine)
The amino acid structure
N-C-C
Forming a polypeptide
2 amino acid come together forming a dipeptide via creating a peptide bind, releasing water
Formed during translation
Polypeptide has an amino end (NH3) and carboxyl end (COOH)
Primary structure
One letter code, a culmination of many amino acids in a line such as S=Serine
Protein translation
The protein will start to fold whilst it is still being translated
First stage of folding
Nearby amino acids start to form regions of stable structure such as alpha-helix or beta-sheets
Amino acids form bonds that create the specific structures
Examples: bacterial porin (all beta) and ferritin (all alpha)
Alpha helix importance
Especially important in the structure of integrate membrane proteins
How does the polypeptide chain rapidly fold into a compact shape
This is done via hydrophobic exclusions, that pushes the hydrophobic amino acids into the middle of the protein and the hydrophilic amino acids into the outer protein, this starts to form the tertiary structure
Tertiary structure bonds
Hydrogen bonds (O-H) weak Disulphide bonds (S-S) strong, between 2 cysteines Ionic bonds (+ve with -ve) strong van see Waals (electron clouds) weak maximise contact of atoms Hydrophobic exclusions (phobic inside and phillic outside) This turns into the quaternary structure
Quaternary structure
A dimer
A tetramer 2 alpha and 2 beta globins such as haemoglobin
Globular and fibrous
Protein structure is hierarchical
Primary: structure is the protein sequence; the order of the amino acids from the N-term to the C-term
Secondary: structure describes the local structure of stresses of protein: alpha-helixes or beta-sheets
Tertiary: structure describes the relative positioning in the 3 dimensions of the secondary elements of a single molecule
Quaternary: structure describes proteins that contain more than one chain
Protein degradation
Proteins can degrade via denaturation leading to a denature protein by breaking the secondary structure losing the 3D shape
Anfinsen experiment
Native ribonuclease contains disulphides bonds these are then reduced forming reduced ribonuclease, with the addition of heat the protein will lose its structure, this can also be reversed by cooling and oxidising the disulphide bonds back to their original formation
Chaperone protein
- function
They allow the repairing of midfielder protein forming the correctly folded protein
Chaperone protein: GroE
Degrad of proteins
Aging: degrad over time as they are chemically altered
Half-life: variable between proteins
Size of proteins
Describes in kDa or amino acid length
Is it a protein or a peptide
A peptide tends to be used for very small proteins (>50 aas)
Fibrous or Globular
Usually describes as structural or functional
Functional proteins: instigate biochem change
Structural proteins: inside the cell such as the cytoskeleton or cell mem
Location of proteins
- intracell vs extracell
Have key difference on their biochem
Extra cell prots: have to function without an energy supply, are extra tough and have disulphide bonds (structural support) mainly glycoproteins
Intra cell prots: have to be located to a specific organelle
Soluble or membrane
Free proteins or those attaches to membrane by some mean
Membrane-bound are strongly bound and difficult to isolate and study
Protein denaturation
By high temperature, changes in pH and certain chemicals
Amino acid monomer structure
Amino group, carboxyl group and alpha carbon with side chain
Peptide bonds
Broken down by proteases, high temperature and pH
Entropy for hydrophobic exclusions
Consequence of water molecules wanting to remove themselves from the vicinity of the hydrophobic amino acids and the latter being forced into the close contact with each other
Primary structure dictates 3D structure
One consequence of denaturation is that the protein becomes insoluble (individual proteins can’t be insoluble) individual mis-folded protein molecules bind to each other on a process called aggregation forming an insoluble lump of protein
Lysosomes
Proteins are taken to them to be degraded by proteases broken down into amino acid monomers
Prosthetic groups
Conjugated to proteins, inorganic such as Fe, Zn and Ca
Organic such as pyridoxal phosphate
Porphyrin ring: the haem group of haemoglobin, contains Fe
Motifs and Domains
Immunoglobulins: Fab domain, Fc domain and the antigen-binding site
Domains can be structural or functional
Motifs such as helix-turn-helix and beta-alpha-beta, a combination of motifs are called folds
Hydrolysis is peptide bond
Produces amino acids
Does not need energy input
Proteases speed the process up
Endoproteases can cleave polypeptide chain (from end of the chain)
Dietary supply:
- amino acids
Begins in stomach via pepsin
Completed in intestine (trypsin, chymotrypsin in duo)
Degrad of tissue protein:
- amino acid source
Normal turnover rate of proteins
2 methods: ubiquitin-proteasome pathway; abnorm prots on the cell cytosine (26S protease complex), gagged by ubiquitin, and ATP-depend step
Lysosomal pathway; long-lived proteins in the lysosomes
Degraded by proteases called cathepsins (broad spec and ATP-independ)
Enter lysosomes by endocytosis, and autophagy.
Fate of amino acids
Synth of prots: DNA, RNA and ribosomes
Synth other compounds: purines, pyrimidines and NuTs
Remainder: provide energy/energy stores, no amino acid storage and they mainly stay in the liver or muscles
Excess protein
Protein’s amino group is removed to form ammonia, and is converted to urea leaving the carbon skeleton (alpha-ketoacid)
Urea cycle:
- stages
Transamination: amino acid + alpha ketoglitarate reversibly forms glutamate + alpha-keto acid
Require co-factor of pyridoxal phosphate (derived from vit B6)
AST and ALT
Aspartate transaminase: forms aspartate from glutamate (liver)
Alanine transaminase: many amino acids and muscle prots are transaminated to alanine for transport to the liver, then is further converted to glutamate
Nitrogen disposal:
- routes of disposal
Oxi deamination: prod NH4
- direct removal of the amino group to form ammonia, catalysed by glutamate dehydrogenase (GluDH)
Glutamate —> alpha ketoglutarate
Ammonia enters the urea cycle, and a-ketonwill be transaminated
Transamination to aspartate:
- formation of aspartate form glutamate
- aspartate enters urea cycle and a-Leto same as above
Nitrogen disposal:
- urea characteristics
- urea cycle
Small, uncharged and highly water soluble (easily diffuse) and little energy requirement
1. Urea + arginine + water = ornithine + urea
2. ornithine + carbamoyl phosphate from the mito matrix (ammonia prod in mito)
3. Citrulline + aspartate + 2ATP = Argininosucciate
4. Argininosucciate loses fumarate prods arginine
Overall reaction: aspartate + NH4 + CO2 + H2O + 4ATP reversibly forming urea + fumarate + 4ADP
Fate of urea
Transferred in blood to kidneys, can regen oxaloacetate via Malays in the cytosine using AST reaction (Malate dehydrogenase reaction), generating a net 1.5 ATP
Amino acid synthesis:
- process
- Starts with a C skeleton from central metabolism
- Use transamination reaction to add amino group
- Further step to final amino acid structure
Essential amino acids
Lysine, methionine, threonine, valine, leucine, leucine, isoleucine, phenylalanine, tryptophan and histidine
Purine and pyrimidines
Purine: adenine and guanine
Pyrimidines: cytosine, uracil and thymine
Amino acids are precious ones for important biomolecules
Histidine to histamine
Tyrosine forming hormones such as thyroxine, adrenaline, melanin and dopamine
Tryptophan: serotonin
Arginine: nitric acid
Serine: phospholipids
Glycine: creative, bile salts and porphyrins
Amino acids feed into the TCA cycle
Added into each step of the cycle
Metabolically classifies into 2 classes:
- glucogenic and ketogenic
Glucogenic: TCA cycle intermediate are gen and used for ATP or converted to glucose
Ketogenic: acetyl CoA gen to be converted to ATP or triglycerides for storage in adipose tissue (ketone bodies fuel)
Energy metabolism in muscle cells:
- overview
- excess protein
- high exercise
Excess protein:
- excess not stored, broken down for ATP generation or storages as glycogen or triglycerides (formation to amino acids via ALT)
- muscle cells take up branches chain amino acids from the blood and use carbon skeleton for fuel/storage (BCAA aminotransferase)
High intensity exercise:
- rate of cycling between ATP to ADP
- using creatine P used to replenish ATP
