Cell Biology- Protein Synthesis
Beta bends are normally composed of...
4 amino acids, one of which is often proline (this causes a kink in the polypeptide chain)
Degeneracy (genetic code)
Degeneracy: also called redundancy = a given amino acid may have more than one triplet coding for it (Arg is coded by six different codons)
Function of Enzymes and peptide hormones
Direct and regulate metabolism
E site
E site: occupied by the empty tRNA as it isabout to exit the ribosome
missense mutation
Missense mutation: The codon containing the changed base may code for a different amino acid (UCA → Ser; CCA → Pro)
What types of bonds make up the primary structure?
peptide bonds- between C-atom of carboxyl group of 1 AA and N-atom of amino group of another AA
Are globular proteins soluble in water?
yes! its readily soluble.
Where are ribosomes found?
"free" in the cytosol or in close association with the endoplasmic reticulum(rER)
AA's with uncharged polar side chains have a __ net charge at physiologic pH. a. Zero b. Positive C. Negative
0
STEPS IN PROTEIN SYNTHESIS
1. Activation 2. Initiation 3. Elongation 4. Termination 5. Folding and posttranslational modifications
Name some types of structure of proteins
1. Fibrous proteins 2. Globular proteins 3. Intermediate proteins
Name some examples of Composition Proteins
1. Simple proteins 2. Glycoproteins 3. Nucleoproteins 4. Chromoproteins 5. Lipoproteins 6. Flavoproteins 7. Metalloproteins
Name some examples of functional proteins
1. Structural proteins 2. Enzymes 3. Hormones 4. Respiratory pigments 5. Transport proteins 6. Contractile proteins 7. Storage proteins 8. Immunoglobulins 9. Toxins
Selenocysteine
21st proteinogenic AA, not coded directly by genetic code
Peptides are different from proteins as they have ___ or fewer amino acids
50
A site
A site: binds an incoming aminoacyl-tRNAaccording to the codon occupying the site
Activation of protein synthesis (mention what happens and where it occurs)
AAs are activated by special aminoacyl-tRNA synthetases in the cytosol, AA attached to tRNA
What happens to all the excess AA's? (amino acid catabolism) (Nitrogen metabolism)
All amino acids in excess of biosynthetic needs are rapidly degraded (transamination following oxidative deamination in liver and kidney) → into ammonia (NH3) and corresponding α-keto acids, the carbon skeletons of AA In the second phase of amino acid catabolism, the carbon skeletons of the α-keto acids are converted to common intermediates of energy-producing metabolic pathways, which can be metabolized to CO2 and H2O, glucose, fatty acids, or ketone bodies by the central pathways of metabolism (gluconeogenesis, glycolysis, TCA cycle)
Where do peptides bond?
Amino acids are linked by peptide bonds between theα-carboxyl group of one amino acid and the α-amino group of another
When there is a lot of misfolded proteins, what sort of diseases can happen? (fyi)
Amyloid diseases (FYI) • Abnormal conformation of fibrillary protein assemblies of β-pleated sheets called amyloids • Implicated in degenerative diseases such as Alzheimer, Parkinson, and Huntington Prion diseases (FYI) - Infectious protein is an altered version of a normal prion protein, it forms insoluble aggregates of fibrils - E.g. Creutzfeldt-Jakob disease in humans, scrapie in sheep, bovine spongiform encephalopathy in cattle ('Mad Cow' disease)
Proteins as Enzymes
Biological catalysts, reduce activation energy of reactants and speed up reactions Most of them are globular, conjugated proteins, Examples: DNA Polymerase, Lipase
contractile proteins function
Can contract muscles with the expense of energy from ATP Examples: Actin, Myosin
WHAT SORTS OF DISEASES COULD HAPPEN IF THERE WAS A CHANGE IN CRITICAL AMINO ACIDS IN A PROTEIN?
Changes in amino acids (→ mutations in the DNA)can lead to a non-functional protein or to a misfolded one • Examples: sickle cell anemia, Alzheimer disease,transport defects, enzyme deficiencies
Regard conjugated proteins, what classifies the different types?
Classification based on the nature of the prosthetic groups (p.g.): a) Phosphoproteins: p.g. is phosphoric acid (e.g. Casein/milk, Vitellin/egg) b) Glycoproteins: p.g. is carbohydrate (most membrane proteins) c) Nucleoproteins: p.g. is nucleic acid (proteins in chromosomes, ribosomes) d) Chromoproteins: p.g. is pigment or chrome (Haemoglobin, Phytochrome) e) Lipoproteins: p.g. is lipid (some membrane proteins, chylomicrons) f) Flavoproteins: p.g. is FAD- Flavin Adenine Dinucleotide (proteins of electron transportsystem) g) Metalloproteins: p.g. is metal ions (Nitrate Reductase)
Proteins as Respiratory pigments, give an example
Coloured, conjugated proteins with a pigment (chrome) as their p.g. Examples: Haemoglobin, Myoglobin
conjugated proteins structure
Complex, contain one or more non-amino acid components usually globular These non protein parts are called prosthetic groups, essential for biological function
Structural proteins are in
Components of connective tissue, bone, tendons, skin, feathers, nail, hair, horn Mostly fibrous proteins, insoluble in water, Examples: Collagen, Keratin, Elastin
Simple proteins composition
Composed of only amino acids, relatively simple structure Examples: Myosin, Collagen, Keratin, Insulin
1. Describe the flow of information according to the central dogma of molecular biology.
DNA → RNA → Protein Transcription → Splicing →Translation
What types of bonds stabilize the tertiary structure?
Disulfide bonds Hydrophobic interactions Hydrogen bonds Ionic interactions
Protein translation
Each tRNA has an attachment site for a specific amino acid at its 3'-end and an anticodon that pairs with a specific codon on the mRNA (adapter combining amino acids with codons)
Causes of mutations (name 3)
Errors during replication of DNA: esp. during meiosis, when cells divide to produce gametes Damage to DNA: via Radiation, Carcinogens and other toxins, Viruses and bacteria Errors during repair! Mutations can cause negative or positive changes, and are important for evolution, but also cause pathology
The polypeptide backbone does assume a random three-dimensional structure. T/F
False, It generally forms regular arrangements of amino acids located near each other in linear sequence (secondary structures)
Function of Immunoglobulins
Fight infectious bacteria and viruses
Function of Structural proteins (collagen, keratins)
Form tissues and bones, acting like steel cables in reinforced concrete
what?
Here's a meme break, you got this!
Describe the overall formula of an alpha helix. (Be sure to also mention how many AA's per turn , type of bond, the shape of the structure)
Hydrogen bonds between carboxy- and amino groups of amino acids (distance of4 AA) → spiral structure(example keratin)
Are fibrous proteins soluble in water?
Insoluble in water
When folding proteins, what sort of interactions determine how long the pp (polypeptide) chain folds and the shape (3D shape)?
Interactions between the side chains of amino acids determine how a long polypeptide chain folds into the three dimensional shape of the functional protein
Intermediate proteins structure
Intermediate shape more or less linear
Where does post-translational modification occur on the AA?
It can occur on the amino acid side chains, or at the C- or N- termini
Cysteine, why is the amino acid special and different from the other AA's?
It has an SH bond that is slightly polarized BUT BUT BUT its a non-polarized molecule
In post-translational modifications of proteins involves what sort of modifications?
It involves the formation of covalent and generally enzymatic modifications of proteins following protein biosynthesis
Why are peptide bonds resistant to conditions that denature proteins such as heating and high concentrations of urea?
It is a strong covalent bond
Describe the structure of fibrous proteins
Linear in shape The secondary structure is functionally most important Usually do not have a (complex) tertiary structure Tough and strong Long parallel polypeptide chains cross-linked at regular intervals
Why does denaturing a protein not denature the primary polypeptide structure?
NO hydrolysis of peptide bonds, primary structure (generally) remains intact
Are polypeptides ever branched? Y/N
No! Its long, continuous, and unbranched
7. What are the four general groups of amino acids, what determines the biochemical behavior of an amino acid?
Nonpolar side chains Uncharged Polar side chains Polar Acidic side chains Polar Basic side chains The side chains are what determine the function of the AA
Nonsense mutation
Nonsense mutation: The codon containing the changed base may become a termination codon (UCA → Ser; UAA → Stop and the protein will be truncated)
How are non-standard amino acids (the non basic 20 AA) synthesized?
Nonstandard amino acids are synthesized by chemical modifications of standard amino acids
How does the body get proteins? (3 ways)
Obtained from the diet (9 AA are essential) Synthesized de novo Released through the degradation of body protein
Where does protein folding occur and how long does it take?
Occurs in the cell in seconds to minutes
P site
P site: is occupied by peptidyl-tRNA whichcarries the chain of amino acids that hasalready been synthesized
What sort of functions do the fibrous proteins do for the cell?
Perform structural functions in the cell
Function of Contractile proteins in muscle (actin and myosin)
Permit movement
22. Name some differences between prokaryotes and eukaryotes with regard to transcription and translation
Prokaryotes → 50S and 30S subunits = 70S R
Proline, why is the amino acid special and different from the other AA's?
Proline differs from other nonpolar amino acids in that its side chain and alpha-amino nitrogen form a rigid, five-membered ring structure It has a secondary (rather than primary) amino group (imino group)
What is a good way to break peptide bonds? (with out enzymes)
Prolonged exposure to strong acid or base at elevated temperature is necessary to break these bonds nonenzymatically
Which structures get denatured during protein denaturation?
Protein denaturation results in the unfolding and disorganization of a protein's secondary and tertiary structures
Hormones give some examples
Proteinaceous hormones such as Insulin, Glucagon, Gastrin, Cholecystokinin/CCK
Ribosomes consist of two subunits. What are they?
Ribosomes consist of two subunits (60Sand 40S in eukaryotes = 80S Ribosome,50/30 S = 70S Ribosome in prokaryotes)
Hydroxylation of tryptophan yields...
Serotonin
21. What is sickle cell anemia, what is its cause, and some effects for sufferers?
Sickle cell anemia is caused by a single nucleotide substitution in the gene for beta-globin missense mutation changes Glufor Val at position 6 The symptoms are characterized by episodes of pain, chronic hemolytic anemia, infections
Name the 3 types of mutations
Silent mutation Missense mutation Nonsense mutation
5. Explain the basic, general shape of an amino acid
So! There is not really a "basic general shape" mentioned. I think she wants us to know the general formula of amino acids and that it is linear an amino group an alpha carbon a side chain and a carboxyl group
globular proteins structure
Spherical/globular shape Polypeptide chain tightly folded into spherical shapes Tertiary structure is functionally most important Physically softer
alpha helix- describe structure
Spiral structure, a tightly packed, coiled polypeptide chain core Side chains of component amino acids extend outward to avoid interfering sterically with each other
What stabilizes the alpha helix structure? (be really specific)
Stabilized by extensive hydrogen bonding between the peptide-bond carbonyloxygens and amide hydrogens
Steps of Elonggation (protein synthesis)
Step 1: Binding of the aminoacyl-tRNA to the A-site of the ribosome Step 2: Generation of the peptide bond in P-site Step 3: Movement of the ribosome along the mRNA then translocates the tRNA from A-site to P-site, ‚empty' tRNA dissociate from E-site
storage proteins function
Store metal ions and... amino acids? found in seeds and pulses, egg and milk Examples: Ferritin (iron), Casein, Ovoalbumin, Gluten
Do subunits work together or independently of each other? (Not a Yes or No answer)
Subunits may function independently of each other, or may work cooperatively, such as in hemoglobin Hemoglobin, binding of oxygen to one subunit increases the affinity of other subunits for oxygen
What makes tertiary structure proteins different from secondary ones?
Tertiary is both the folding of the domains and the final arrangement of the domains in the polypeptide. Secondary forms regular arrangements of amino acids located near each other in linear sequence
Silent mutation
The codon containing the changed base may code for the same amino acid (UCA → Ser; UCU → Ser)
POST-TRANSCRIPTIONAL MODIFICATIONS
The process in eukaryotic cells where primary transcript RNA is converted to mature RNA It is ESSENTIAL for the correct translation of eukaryote genomes
What 3 steps are in the post transcriptional modifications?
The process involves three major steps: 1. Addition of a 5' cap 2. Addition of a 3' polyadenylation tail 3. Splicing (removal of introns (non-coding sequences) and joining of exons (coding sequences important for translation)
What makes an AA unique from other AA?
The side chain (R) R groups can be polar, nonpolar, negatively and positively charged
Why are non-polar AA's side chains considered to be "oily" or "lipid like"?
The side chains promote hydrophobic interactions!
What will happen to a protein when its in an aqueous solution?
The side chains tend to cluster together in the interior protein (hydrophobic effect)
What is the "unique" geometry of proline used for? What is the downfall to this?
The unique geometry of proline aids with the formation of the fibrous structure of i.e. collagen, but interrupts the α-helices in globular proteins
Function of Transport proteins (albumins, hemoglobin)
Transport essential molecules through the bloodstream
What is the fate of newly synthesized proteins? (name 5)
Transport into the Endoplasmic Reticulum→ cisternae Protein folding Transport from the ER to the Golgi apparatus (in vesicles) Glycosylation of newly synthesized proteins takes place in the Golgi apparatus Transport to other organelles
Transport proteins function
Transport materials in cells and form channels, Example: Serum Albumin
2. List the different functions of membrane proteins (I don't think she expects you to know all of these, just at least be able to recognize the limitations of the protein membranes)
Transport proteins Channels Enzymes Signal proteins Hormone receptors Structure proteins Second messengers
Most α-amino acids are found in proteins (proteinogenic) but two of them are not. Which ones are they and how are they synthesized?
Triiodothyronine and thyroxine → thyroid hormones, synthesized from tyrosine slightly changed around AA
Can denatured proteins be renatured?
Under ideal conditions, denaturation may be reversible, so the protein refolds once the denaturing agent is removed Mostly proteins, once denatured, remain permanently disordered (insoluble, precipitate)
1. Regard the Central dogma, what does it mean for proteins?
We get proteins through translation! Proteins are made from information of our genes.
Proteins are the product of our genes. Y/N?
Yes! Think Central dogma!
What determines the role of amino acids in the protein?
a distinctive side chain (R-group)bonded to the α-carbon, this side chain determines the role of the amino acid in the protein
Specificity (genetic code and regard aa)
a particular codon always codes for the same amino acid
@ Physiologic pH the side chains (of AA's with POLAR ACIDIC side chains) are ____ and ____. a. fully ionized, and neutrally charged b. fully ionized, positively charged c. fully de-ionized, negatively charged d. fully ionized, and positively charged e. fully ionized, negatively charged
a. fully ionized, negatively charged
Phosphorylation
addition of a phosphoryl group
Elongation of protein synthesis (also mention what sort of energy is required)
addition of amino acids to the carboxyl end of the growing peptide chain. The ribosome moves from 5'-end to the 3'-end of the mRNA, GTP is required.
What is the most common protein structure?
alpha helix
Are amino acids stored in the body?
amino acids are not stored by the body, no protein exists just for storage of amino acids
What all makes up an amino acid?
an amino group, an acid (carboxyl group), and a distinctive side chain (R-group)bonded to the α-carbon
QUATERNARY STRUCTURE
an arrangement of many polypeptide subunits
2 types of beta sheets
antiparallel and parallel
What are rER-ribosomes responsible for?
are responsible for SYNTHESIZING PROTEINS that are to be EXPORTED from the cell or to be placed in cell membranes (plasma, ER, lysosome membranes)
Initiation of protein synthesis (Mention what happens and where it occurs)
assembly of components of the translation system before peptide bond formation occurs, the formation of ribosome complex (SSU, LSU, mRNA)
Glycosylation
attachment of a glycan (carbohydrate, polysaccharide)
@ Physiologic pH the side chains (of AA's with POLAR BASIC side chains) are ____ and ____. a. fully ionized, and neutrally charged b. fully ionized, positively charged c. fully de-ionized, negatively charged d. fully ionized, and positively charged e. fully ionized, negatively charged (Dr. Freeman says questions like these will definitely be in the exam!)
b. fully ionized, positively charged
which type of beta sheet protein structure are common in nature?
both
Methylation of lysine yields...
carnitine
Polymeric
composed of many repeating monomers (ex: proteins)
Most enzymes are___ proteins
conjugated and or globular
What is the shortest peptide possible?
dipeptides
What happens to free ammonia?
excreted in urine, but most is used in synthesis of urea (CO(NH2)2)→ Urea cycle
Keratins
fibrous protein component of hair and skin, rigidity determined by number of disulfide bonds between constituent polypeptide chains
What sort of things can globular proteins form?
form enzymes, antibodies, and some hormones Examples: Insulin, Haemoglobin, Albumin, DNA Polymerase, and RNA Polymerase
How are Peptide (amide) bonds formed?
formed when carboxyl of one amino acid reacts with the amino group of another
what are domains, in regards to protein?
fundamental functional and three-dimensional structural unitsof polypeptides
Describe Myoglobin structure
globular, flexible molecule, but also highly α-helical
What bonds helps build the pleated structure (beta protein)?
h bonds
What sort of things can denature a protein?
heat, organic solvents, strong acids or bases, detergents, heavy metal ions such as lead
Decarboxylation of histidine yields...
histamine
What types of bonds stabilize the secondary structure?
hydrogen bonds, weak bonds
What stabilizes the quaternary structure protein?
hydrogen-bonds and also by hydrophobic and hydrophilic interactions between AA-R-groups
Under what conditions do condensation reactions occur?
is not a spontaneous reaction, but depends on ATP-dependent activation by attachment of AA to a tRNA (by an enzyme) leaves water!
Universality (genetic code)
it is conserved from very early stages of evolution
What is the common structure shared by all proteins?
linear polymers of amino acid
where does protein metabolism occur?
liver
Acetylation and methylation of serotonin yields...
melatonin
Is protein folding a spontaneous process? (not a yes or no answer, will need to explain answer)
not generally a spontaneous process, but it requires facilitation from a specialized group of proteins: 'Molecular chaperones' or 'Heat shock proteins (Hsp)
Organelles involved in protein synthesis
nucleus, ribosomes, & Golgi apparatus
Termination of protein synthesis (mention when it occurs and how much energy is needed for translation)
occurs when one of the three termination codons moves into the A site, at least 4 high-energy phosphate equivalents (from ATP and GTP) are needed for each peptide bond to guarantee fidelity of translation
Throwback to Block 1: How many amino acids are in oligo peptides and in poly peptides?
oligo: 2-20 AA poly: 21-50 AA
Where is Oxytocin produced?
peptide hormone produced in the hypothalamus (uterine contractions and milk secretion)
Glucagon
peptide hormone, produced by α-cells of the pancreas
CCK (cholecystokinin)
peptide hormone, stimulates pancreas and liver secretion
Gastrin
peptide hormone, stomach hormone that stimulates the secretion of gastric glands
Folding and posttranslational modifications
polypeptides fold into active, 3-dimensional forms; many are processed further
Glycosylation is a... post-translational mod post-transcriptional mod
post transcriptional mod
Phosphorylation is a ... post-translational mod post-transcriptional mod
post transcriptional mod
Atrial Natriuretic Peptide (ANP)
produced in the heart (atria), essential for regulation of blood volume and pressure
antidiuretic hormone (ADH) What is it and where is it produced?
produced in the hypothalamus and essential for the maintenance of water balance (ur- urine related)
AA's with polar acidic side chains are ___ donors. a. electron donors b. Proton donors c. Blood donors d. R group donors
proton donors
AA's with polar basic side chains accept___. a. protons b. electrons
protons
Beta bends, what do they do?
reverse the direction of a polypeptide chain, helping it form a compact, globular shape this makes it crucial for protein structure and function
What sort of solubility does intermediate protein have in the water?
soluble in water eg. blood clotting proteins
What does cytosolic ribosomes do?
synthesize cytosolic proteins or those intended for the nucleus, mitochondria or peroxisomes
Proteinogenic
the ability of certain (20) amino acids to be integrated into proteins
Nonoverlapping and commaless (genetic code)
the code is read from a fixed starting point as a continuous sequence of bases without any punctuation between codons
Creatine
tripeptide involved in energy production in muscle and cardiac cells
Melanin
tripeptide, a pigment occurring in several tissues, synthesized from tyrosine via DOPA
How many polypeptides/polypeptide chains does it take to make a pleated structure?
two or more separate polypeptide chains or segments of polypeptides
3. Describe the basic structure of a protein
unbranched long chains of polypeptides
What normally happens to misfolded proteins?
usually tagged and degraded in the cell
Chaperones
• Chaperones are heat-stable proteins • Also called 'heat shock proteins'(Hsp) • High activity at high temperatures • Chaperones are ATPases
What do the 4 types of bonds do for the tertiary structure? (Note: this is a particularly difficult question)
• Hydrogen bonds between the R-groups of the individual AA • Ionic bonds → bond between oppositely charged ions (anions - and cations +) (stronger than H-bond) • Disulfide bridges → S-S-bond between 2 thiol groups (S-containing groups) in AA-R-groups (strongbond) • Hydrophobic interactions → between hydrophobic (nonpolar) AA-side groups (can be strong)
Review: Golgi apparatus, where is it and what is it's function?
• In cytoplasm of eukaryotes • Place of modification of proteins after synthesis • Packages and stores proteins
alternative splicing (what is it and is is post translational or post transcriptional?)
• Specific signal sequences in the mRNA are recognized by an enzyme called "small nuclear ribonucleoprotein particle" (snRNP) and removed from the transcript • Post-transcriptional modification
Describe the steps of the folding cycle. (there are 5 steps)
• The folding cycle requires ATP • The chaperone is bound to ADP • ADP/Chaperone-complex has a high affinity for unfolded proteins • After binding ADP is released • After protein folding and ATP binding the complex dissociates and the correctly folded protein is released
POST-TRANSLATIONAL MODIFICATIONS OF PROTEINS, NAME THE FUNCTION
• This process describes modifications of many eukaryotic proteins to form mature proteins, helps to regulate enzyme activity, promotes folding, and aids with stabilizing proteins • It can extend the 20 standard AA by modifying their functional groups or by adding new ones, such as phosphate groups