ALL ABOUT PROTEINS (CH 4)

Question 1

What class of biomolecules define the structural and functional identity of the cell?

Answer 1

Proteins

Question 2

What is the chemical composition of bacterial cell?

Answer 2

70% water, 30% chemicals (proteins make up half of the chemicals)

Question 3

What are the most important functional (diverse) molecules in the cell?

Answer 3

Proteins!

Question 4

Describe the Cytosol. How does it aid in function of organelles?

Answer 4

highly organized, and mobile gel substance. packed with ribosomes, make soluble, cytosolic proteins movement for organelles and biomolecules controlled by cytoskeletal proteins.

Question 5

List the functions of the protein. Provide examples.

Answer 5

1. Enzymes- catalyze formation/breakage of covalent bonds. Ex: polymerase- copy DNA
2. Structural proteins- provide mechanical support to cells and tissues. Ex: collagen/elastin form fibers in tendons or ligaments; tubulin make microtubules for PM
3. Transport proteins- carry small molecules or ions
   Ex: serum albumin carry lipids, Hb carries O2,
   4.Motor proteins- generate movement in cells/tissues.
   Ex: myosin provides motive force
4. Storage proteins- store amino acids or ions
   Ex: iron stored in liver through binding ferritin; ovalbumin in egg white, source of aa for bird embryo
5. Signal proteins: carry extracellular signals from cell to cell ex: hormones like insulin-control glucose levels in blood.
   7.Receptor proteins- detect signals and transmit to cell response machinery. Ex: rhodopsin in retina detects light
6. Transcription Regulators: bind to DNA to switch genes on or off. Ex: lac repressor in bacteria silences genes for enzymes that degrade sugar lactose.
   9 Special-purpose proteins- variable functions
   Ex: antifreeze proteins of fish protect blood against freezing, fluorescent proteins from jelly fish emit green light.

Question 6

describe the structure of proteins:

Answer 6

cellular molecular machines: Polymers made up of amino acid residues that contain both carboxyl group and Amino groups. Proteins also have side chain (R) group that help identify each unique aa.

Question 7

How many amino acids are there. describe the side chain of an amino acid when pH is 7.

Answer 7

20 amino acids. at pH 7, amino group gains proton (NH3+) and Carboxyl group loses H+ (COO-).

Question 8

Are proteins made of L or D amino acid residues? How does structure look like? Why?

Answer 8

Proteins have L amino acid- residues because this isomer is metabolically active and processed by enzymes. (d aa residue not active) . L aa residue: NH3+ on left side, carboxyl on right, R and H group.

Question 9

What kind of bonds link amino acids? what is unique about the bond formation? what is the Mesomeric effect?

Answer 9

Amino acids linked by covalent PEPTIDE BONDS (formed by condensation). Peptide bonds have resonance which limits rotation between carbonyl carbon and nitrogen. Mesomeric effect: positions carbonyl carbon opposite to amino group Hydrogen orientation. (-) and (+) charges in opp orientation

Question 10

what defines the unique, functional properties of proteins? more specifically?

Answer 10

the amino acid residues define unique protein properties. More specifically the AMINO ACID SIDE CHAINS.

Question 11

What 2 ways can amino acids be abbreviated. Provide examples.

Answer 11

Amino acids can be abbreviated by 3 letters or 1 letter. ex: Alanine has ALA or A abbreviation.

Question 12

list the basic, acidic, polar (uncharged) and nonpolar groups of amino acids. Name the strongest basic group. Any unique properties?

Answer 12

Basic Side chains- carry positive charge, ex: Lysine (K), Histidine (H)and Arginine (R). strongest basic side chain is Arginine (+ charge stable by resonance), weakest is histidine (partial + charge)

Acidic Side chains - Negatively charged (COO-)
Ex: glutamic acid (E) and Aspartic acid (D) difference between aa is length of chain. glutamic longer.

Uncharged polar side chains- ability to form H-bonds between water molecules and each other.
EX: Asparagine (N), glutamine (Q), serine (S), threonine (T), tyrosine (Y); N and Q- have amide (uncharged)
Serine and Threonine have polar OH groups; Tyrosine has BOTH polar and aromatic group. S, Y, T can absorb UV light since aa can act as substrate and detect proteins.

Nonpolar side chains- vary by length
Ex: Alanine (A), Valine (V), Leucine (L), Isoleucine (I), Proline (P), Phenylalanine (F), Methionine (M), Glycine (G), Tryptophan (W), Cysteine (C). In proline, side chain makes covalent bond with own amino group, ring has limited rotation. Glycine is aa without functional radical group (only has H). 2 cysteine side chains can form disulfide bond in proteins, flexible side chains useful for chromophore, oxidative phosphorylation.

Question 13

Describe the central dogma of proteins. What occurs during translation? How and where is translation conducted?

Answer 13

flow of genetic information form DNA to RNA to Proteins. Translation- synthesis of proteins in all cells, starting with N-terminus. During translation, linear code of DNA AND RNA are converted into sequence of amino acid residues in polypeptides. Translation conducted by large nucleoprotein complexes called ribosomes. Ribosomes have two subunits (L and S) that assemble into functional ribosome on MRNA template before translation starts, and dissociates after translation ends.

Question 14

Where are ribosomal subunits assembled? what occurs in the cytosol?

Answer 14

ribosomal subunits are assembled in the nucleus. ribosomal assembly are in nucleoli. after exporting ribosomes in cytosol, the proteins are synthesized in cytosol.

Question 15

Differentiate between proteins and peptide. What is the largest protein? smallest peptide?

Answer 15

peptides- small polypeptide chains that are less than 50 aa long. Example of peptides include homopeptide (short chain of same repeating aa, Ala-Ala-Ala-Ala-Ala). peptides are not proteins because proteins has functional meaning. proteins have separate unstructured polypeptide function that is acquired upon folding and maturation (involve cutting and chemical modifications)- post translational modification.
The largest protein is Titin (30,000 aa) used in muscle cells. The smallest peptide is THYROTROPIN-Releasing Hormone (TRH) (neurohormone that consists of 3 aa- Glutamic acid, Histidine and proline)

Question 16

What occurs between the nonpolar and polar side chains in protein folding vs unfolded proteins?

Answer 16

In unfolded proteins, the non polar and polar side chains attach to polypeptide backbone in linear form. As proteins starts to fold, polar side chains form hydrogen bonds to water on outside of chain. Meanwhile the nonpolar (hydrophobic) side chains are packed inside the interior of chain to form hydrophobic core region (avoid surfac with water).

Question 17

What are the four types of models used to describe protein confirmation?

Answer 17

1. Backbone model- show orientation and position of polypeptide backbone
2. Ribbon model- show Beta sheets, alpha helix, give idea of space in proteins
3. Wire model- shows all side chains, distance between them.
4. Space-filling model- see entire surface of protein, partial spheres (contents jumbled together)

Question 18

What are three ways H-bonds can form in proteins?

Answer 18

1. H-bond between peptide bond and side chain (backbone-side chain)
2. H-bond between 2 peptide bonds (backbone-backbone)
3. H-bond between 2 side chains (side chain-side chain)

Question 19

What are the four types of noncovalent bonds that are present in folded proteins?

Answer 19

1. Electrostatic attractions (ionic bonds or salt bridges) between charged aa side chains
2. H-bonds between carbonyl and imido (NH) groups of peptide bond atoms and aa side chains
3. Hydrophobic interactions between nonpolar aa side chains
   4 Van der waals interactions.

Question 20

what are Van der Waal interactions?

Answer 20

weak forces generated when atoms are close enough so that electron cloud of one atom attract nucleus of another atom. Ex: long fatty acid residues have VDW to keep chains together (PM Stability), graphite sheets

Question 21

What are zinc fingers?

Answer 21

special protein folds stabilized by electrostatic interactions. zinc has positive charge, and stabilized protein by wrapping 2 cysteine and 2 histidine residues around itself tightly (form 2 beta sheets, alpha helix), interact with e-density nitrogen and sulfur atoms. used in DNA binding

Question 22

How do proteins form active sites?

Answer 22

from proper, precise folding of proteins and distant amino acid residues form binding site (Cyclic AMP derivative processed in active site, noncovalent interactions occur also).

Question 23

What mediates the catalytic activities of enzymes or protein binding activities? Provide examples.

Answer 23

Cofactors- which can be Ion metals or compounds derived from vitamins. Ex: ATP, Iron, Retinol (chromophore bound to opsin, visualize light), heme (cofactor for HB)

Question 24

What defines the ability of polypeptides to fold in functional proteins? How can proteins be denatured. Can it be refolded?

Answer 24

Amino acid sequences. protein (that’s purified) may denature after being isolated from cell and exposed to UREA (O=c-Nh2-Nh2 ;high concentration)
Yes, once remove urea, protein slowly refolds into original confirmation (shows protein folding happens on its own)

Question 25

How do covalent bonds stabilize protein folds?

Answer 25

covalent bonds in the form of DISULFIDE BONDS (2 cysteines interact) can stabilize proteins fold and allow for small flexibility or certain orientation of polypeptides.

Question 26

Describe the structure of antibodies and how they are stabilized.

Answer 26

Antibodies- Y-shaped proteins made of many polypeptides, 2 light chains, 2 heavy chains.
stabilized and connected by disulfide bonds. Have antigen binding site and loops that bind antigen.

Question 27

Describe the structure of collagen and elastin. differentiate how elastin looks when relaxed vs stretched.

Answer 27

Collagen- extensive network of collagen fibrils (each made of 3 interlocked polypeptide chains held together by H-bonds)
Elastin- composed of extensive network of coiled polypeptides linked by disulfide bonds.
when relaxed- elastin seen in coils; when stretched elastin is cross-link by S-S bonds.
elastin allows flexibility, stretchable and stability of proteins.

Question 28

What are the folding pattern in proteins?

Answer 28

variety of shapes and sizes of proteins, all have common folding pattern (alpha helix, beta sheets, loops, turns)

Question 29

what are the technological methods to determining protein structures?

Answer 29

Cryo-Electron Microscopy- most common; for large macromolecules, dynamic proteins; freeze proteins in ice
X-ray crystallography- revolutionized study, resolve proteins; form crystal, diffract e-
NMR spectroscopy- nuclear magnetic resonance-compute 3d structures, protein exposed to magnets,

Question 30

What are alpha helix and Beta sheet conformations. Is the backbone of polypeptides hydrophobic or hydrophilic?

Answer 30

Alpha helix- R or L handed with peptide bonds inside, and side chains extending outward, Helices stabilized by H-bonds between backbone NH group and backbone C=O group 4th down from chain.
Beta sheet- 2 or more segments of polypeptide line up next to each other forming strand held by H-bonds. B- sheets can be parallel (Strands in same direction) or antiparallel (strands in opposite directions)
HYDROPHILLIC backbone

Question 31

What kind of secondary structures form transmembrane protein domains? How?

Answer 31

Alpha helixes form transmembrane protein domains- made of 2 phospholipids and hydrophobic aa side chain. hydrophobic interactions are promoted by hydrophilic environment; disrupted in non-polar environment since polar molecules can only exclude themselves away from nonpolar molecules in polar environment.

Question 32

what are coiled coil domains?

Answer 32

Extremely stable structure- 2 alpha helixes wrap around each other and are mediated by hydrophobic aa residues that align each other, while hydrophilic aa residues from h-bonds with water molecules and move outwards.

Question 33

What are protein families? provide example? similarities?

Answer 33

Protein families have similar folding patterns, similar functions, similar protein sequence. ex: elastase (break down fats, carbs and proteins in pancreas) and chymotrypsin ( break down proteins into amino acids in small intestine). Both proteins cleave at C-terminus of hydrophobic aa and break down things.

Question 34

Describe quaternary protein structures? what are homodimers? Heterodimers? Oligomers?

Answer 34

Quaternary structure- spatial arrangement of subunits (polypeptide chains). Dimers- made from 2 subunits with single identical binding site on each monomer. Homodimers- 2 identical proteins
Heterodimers- complex from 2 different proteins. Oligomers- consist of more than 1 dimers (ex: trimers, tetramers) with 2 nonidentical binding sites.

Question 35

What are multimeric protein structures? Examples?

Answer 35

proteins that contain 2 or more subunits and noncovalently bonded. subunits with one binding site- form dimers. multiple binding sites form helix, or rings. Ex: microtubules or actin filaments.
many oligomeric proteins occur in form of fibrils/filaments that are made of long chains of separate globular proteins.

Question 36

What are the benefits of scaffold proteins? How?

Answer 36

Scaffold proteins facilitate assembly of functional oligomers (docking site). They help bind signaling proteins in place and bring them closer to each other for interaction to relay messages between cell mem and nucleus.

Question 37

What are spider silk protein fibrils? What are they composed of and how do they contribute to structure?

Answer 37

spider silk fibrils- proteins consisting of beta sheets tightly aligned along each other, with repetitive hydrophobic aa residues (Glycine and Alanine). The glycine (no radical group, allowing flexibility) provides elasticity in protein. Alanine residues are held by H-bonds and forms crystalline areas in protein and gives it strength.

Question 38

What stabilized spider web?

Answer 38

Mobile beta sheets that can stretch the spider silk. when protein is stretched, crystal ions become more aligned and stronger. Flexibility/strength of proteins due to forming intermittent B- sheets.

Question 39

How do protein abnormalities form?

Answer 39

abnormalities form with problems with protein folding, beta sheets stacking up to form amyloid structures.

Question 40

What are prions? What can they do and how can it affect cells?

Answer 40

Prions- abnormal, pathogenic agents that can transmit their misfolded protein shape onto normal variants of the same processes. one molecule of prion able to covert all functional molecules in cell into abnormal ones, forming pathological aggregates (fibrils) and causing cell death.

Question 41

How do proteins become prions? Describe the type of prion diseases.

Answer 41

proteins can become prions due to spontaneous conversion, covalent modification and mutation. prion diseases very dangerous for non-dividing cells like neurons.
example of prion diseases:
Kuru- rare fatal brain disorder, infectious prion in brain tissue (New Guinea)
Mad cow disease- neurological disorder of cattle
Creutzfeldt Jakob disease- fatal human neurodegenerative condition. mutation in PRNP gene beta sheets clump together, brain shrinks, sponge-like. (norm: alpha-helical, abnormal: beta sheet clump)

Question 42

What is the major hallmark of Parkinson’s disease? what causes it?

Answer 42

major hallmark of PD and other neurological disorders- LEWY BODIES
Lewy bodies are made of ALPHA- Synuclein which is a small membrane protein that have mutations and form aggregates (alpha helix turns into fibrils) which are toxic for cell. PD leads to loss of nerve cells that produce dopamine.

Question 43

What is Huntington’s disease? what causes it? Differentiate between normal and abnormal genes.

Answer 43

Huntington’s disease- severe neurological disorder.
Caused by mutations in gene that encodes protein Huntintin (Htt).
Normal huntingtin protein- long stretch of repeated GLUTAMINE residues
Mutations in protein- increase the number of glutamine residues, make protein aggregate (form Htt fibrils)

Question 44

What is the hallmark of Alzheimer’s Disease? what causes it?

Answer 44

Hallmark of Alzheimer’s- Tau protein aggregates
The aggregates appear at later stages of Alzheimer’s disease
Microtubule associated protein- TAU form tangles around brain.

Question 45

Why can’t many proteins fold on their own? what helps the proteins?

Answer 45

majority of misfolded proteins have hydrophobic residues exposed on outside instead of being hidden inside hydrophobic core. exposure of residue to outside (aqueous) causes protein aggregation, trying to minimize contact with water environment. Chaperone proteins help bind and misfolded proteins and correct them to be folded properly, assist in other protein folding

Question 46

What is a common example of chaperone proteins? What happens when there are too many misfolded proteins? what cellular structure is sensitive to HSPs?

Answer 46

Heat shock proteins- help protect the proteins from stressful condition or tissue injuries, they also aid in protein maturation and refolding. require use of ATP hydrolysis (ATP to ADP and Pi) to release unfolded protein into normal one.
if overwhelming number of misfolded proteins, chaperones have small chance of saving cell.
ER- since its where proteins are processed and folded.

Question 47

How do enzymes function as protein catalysts? What are examples of enzymes?

Answer 47

Enzymes have a specific binding site that a substrate will bind to. once substrate binds, it will form enzyme-substrate complex and allow for catalysis of reaction forming enzyme product complex, then product.
ex: hydrolases, nuclease, proteases, ligases, isomerase, polymerase, kinase, phosphatase, oxidoreductase, ATPase. others are trypsin, chymotrypsin, thrombin

Question 48

what factors affect the velocity or speed of enzymatic reactions?

Answer 48

affinity of substrate to enzyme (concentration dependent), stability of ES complex, rate/probability of S to P conversion and speed of Product dissociating from enzyme. Ex: Lysosome hydrolyzing bacterial polysaccharides (breaking it down)

Question 49

List three ways enzymes can promote reactions

Answer 49

1. enzyme can bind to 2 substrates and orient them to create rxn between them
2. bind substrate to enzyme, causes rearrangement of e- in substrate, partial - and + charges (favor reaction)
3. enzyme strains bound to substrate, forcing it towards transition state; favor reaction

Question 50

What is the Michaelis- Menten equation? What are its major components?

Answer 50

describes how the speed of enzymatic process depends on amount of substrate available.
equation: Vo= Vmax x [S]/Km + [S}. each enzyme has characteristic Michaelis-Menten constant (Km) (amount of substrate that permits enzyme to achieve half V max (speed)

Question 51

List the multiple mechanisms that protein activity can be regulated.

Answer 51

1. competitive inhibition
2. Non-competitive (allosteric) modification
   - feedback inhibition (product)
3. Product inhibition
4. Covalent protein modifications
5. Regulatory subunits
6. Polypeptide chain cleavage
7. Environmental conditions

Question 52

what is competitive inhibition? Describe the relationship between Km and Vmax.

Answer 52

Competitive inhibitor competes with substrate to bind to active site. Increasing substrate may outcompete the fixed amount of inhibitor. hence, Km increases, but V max stays the same (not affected)

Question 53

How does Allosteric regulation control enzymes in metabolic processes?

Answer 53

process of effector molecule (such as ADP) binding to a site that is different from active site to induce conformational change and enhance or reduce enzymatic activity. Ex ADP bind enzymes that catalyze oxidation of glucose and control transport/absorption. when ADP is not bound to area, enzyme is 10% active. With ADP bound, enzyme is 100% active.

Question 54

What is non-competitive inhibition? How does it affect Km and Vmax?

Answer 54

process of inhibitor reducing amount of active enzyme molecules. so amount of active enzyme decreases, but not availability of active centers (no change in efficiency of km in other molecules (cannot reach same speed, as those with more active enzyme). Hence, Km stays the same, V max changes.

Question 55

How does feedback inhibition help regulate many metabolic pathways?

Answer 55

When too much product is being made at end of reaction, the end product will inhibit the initial enzyme’s activity (that generates substrate for making more product).

Question 56

What is meant by the term allosteric inhibition?

Answer 56

Using an effector molecule to bind to a site on enzyme that is not active site, and help regulate activity of enzyme.

Question 57

Describe the structure of calmodulin and how it is activated by specific ions. How is the activation of calmodulin beneficial?

Answer 57

Calmodulin - small protein, 4 binding sites, 2 globular domains (amino group, carboxylate (Coo-) group).
protein activated by increasing [ ] of Ca^2+ ions binding to site on calmodulin and can also activate other enzymatic pathways like kinases, and phosphatases. ex of a molecular switch which are important for signal transduction pathways.

Question 58

How do GTP-binding proteins function as molecular switches? Explain the process of the molecular switch.

Answer 58

They are proteins that acts as molecular switches of signal transduction pathways, and transduced signals between neurons in G-coupled receptors. The molecular switch works by: turning on GTPase through binding of GTP.; and turn off protein when binding GDP.

Question 59

Describe the various kinds of covalent protein modifications? How does it change the protein?

Answer 59

the aa side chain of folded proteins are modified by attaching unique groups that will change protein characteristics. Ex: Acetylation(add acetyl to N- terminus of protein or lysine), phosphorylation(add phosphate to S, T, Y aa) methylation (ch3 to K or R aa) , hydroxylation, lipidation, Disulfide bond, glycosylation (add a sugar to N or O in aa), SUMOylation (small ubiquitin modifier), Ubiquitination- add ubiquitin to lysine residue for degradation)

Question 60

Describe the process of Histone acetylation? What happens during Deacetylation? How does this affect genes?

Answer 60

Acetylation- attach acetyl group to lysine residues on histone, which will remove positive charge and allow DNA (negatively charged) to be loosely bound from protein (histone not tightly bound anymore). This allows for gene expression to occur, and transcription factors to bind to hidden parts of chromosome.
Deacetylation_ remove acetyl groups from from histones, allowing histones to become tightly bound around DNA and inactivate genes.

Question 61

How does phosphorylation regulate protein activity (very common) ? Described the enzymes used for this process. What is another common form of phosphorylation that occurs?

Answer 61

Phosphorylation can increase or decrease protein activity. Use kinases to add phosphate group to hydroxyl group of S, T, Y aa. This kinase will turn on switch.
Phosphatase- used to remove phosphate groups from protein, and switches off protein activity.
Autophosphorylation- enzyme can phosphorylate on its own.

Question 62

Describe how pancreatic Zymogens are regulated, including the enzymes involved. what makes this covalent modification unique? Also discuss which enzyme activates trypsinogen.

Answer 62

zymogens are enzyme precursors that are normally inactive and become active once a portion of their polypeptide has been removed. the part of the polypeptide removed is called blocking peptide. PROTEASE- is an enzyme that cleaves off the blocking peptide (degrades polypeptide chains by hydrolyzing peptide bonds). Trypsin cleaves blocking peptide. Cleavage of zymogen is irreversible (as blocking peptide can be reattached to polypeptide chain).

Enterokinase- is a protease that activates TRYPSINOGEN by removing its blocking peptide.

Question 63

What is a protease?

Answer 63

enzyme that hydrolyzes peptide bonds to breakdown polypeptide chains into smaller units.

Question 64

Compare and contrast Condensation and Hydrolysis processes

Answer 64

Condensation- form bond by releasing water molecule.

Hydrolysis- break bond by adding water.

Question 65

Describe the modifications on protein p53 and how it affects its behavior

Answer 65

multiple modification sites on protein p53 (phosphorylation on N- terminal, acetylation, Ubiquitination and phosphorylation on carboxyl terminal). 50 amino acids on protein p 53 which determine protein’s characteristics and behavior.

Question 66

What is the relationship between covalent modification and complexity of proteins?

Answer 66

Covalent modifications of aa side chains will largely increase complexity of protein.