PROTEINS: Study Guide

Question 1

What is the definition of side chain and simple protein

Answer 1

Sidechain: a group of atoms attached to the main part of a molecule and having a ring or chain structure.

Simple Protein: protein that yields only alpha-amino acids or their derivatives by hydrolysis; e.g., albumins, globulins, glutelins, prolamines, albuminoids, histones, protamines.

Question 2

What is the definition of a conformational isomer?

Answer 2

Any of two or more isomers that differ only in stereochemical configuration. They have the same chemical formula but differ in spatial arrangement.

Question 3

What is the difference between Protonation and Deprotonation?

Answer 3

Protonation: The addition of a proton (hydrogen ion) to an atom, molecule or ion, normally to generate a cation.
Deprotonation: is the removal (transfer) of a proton (or hydron, or hydrogen cation), (H+) from a Brønsted–Lowry acid in an acid–base reaction. The species formed is the conjugate base of that acid.

Question 4

What is the difference between acidic and basic AA

Answer 4

Acidic: polar and negatively charged at physiological pH. Both acidic amino acids have a second carboxyl group.

Basic: Basic amino acids are polar amino acids that have a positive charge at the neutral pH.

Question 5

what is the definition of proteinogenic?

Answer 5

amino acids that are incorporated biosynthetically into proteins during translation. The word “proteinogenic” means “protein creating”.

Question 6

what is the definition of a salt bridge?

Answer 6

an interaction between two groups of opposite charge in which at least one pair of heavy atoms is within hydrogen bonding distance. Salt bridges can contribute to protein stability, although the effect depends on the environment

Question 7

what is the definition of an Isoelectric point

Answer 7

the pH at which a particular molecule carries no net electrical charge.

Question 8

what is the definition of a disulfide bond?

Answer 8

also called an S-S bond, or disulfide bridge, is a covalent bond derived from two thiol groups.

Question 9

what is the definition of pKa

Answer 9

Therefore, the pKa is a quantitative measure of how easily or how readily the acid gives up its proton [H+] in solution and thus a measure of the “strength” of the acid. Strong acids have a small pKa, weak acids have a larger pKa.

Question 10

What is the difference between monomorphic and polymorphic

Answer 10

Polymorphism: as related to genomics, refers to the presence of two or more variant forms of a specific DNA sequence that can occur among different individuals or populations. (common variant)

monomorphic: Having but a single form; retaining the same form throughout the various stages of development; of the same or of an essentially similar type of structure;

Question 11

What is the difference between a beta-turn and helix loop

Answer 11

beta turn: generally occur when the protein chain needs to change direction in order to connect two other elements of secondary structure. The most common is the beta turn, in which the change of direction is executed in the space of four residues.

helix loop: s a protein structural motif that characterizes one of the largest families of dimerizing transcription factors.

Question 12

what is the difference between glycoprotein and proteolipid

Answer 12

glycoprotein: proteins containing glycans attached to amino acid side chains. Glycans are oligosaccharide chains; which are saccharide polymers, that can attach to either lipids (glycolipids) or amino acids (glycoproteins).

proteolipid: a protein covalently linked to lipid molecules, which can be fatty acids, isoprenoids or sterols.

Question 13

what is the definition of hydrophobic interaction

Answer 13

the tendency of nonpolar groups or molecules to aggregate in water solution.

Question 14

what is the definition of the native state

Answer 14

the native state of a protein is it’s properly folded and assembled form with operative structure and function. The native state of a protein needs all four levels of biomolecular structure

Question 15

what is the definition of the subunit

Answer 15

a protein subunit or subunit protein is a single protein molecule that assembles (or “coassembles”) with other protein molecules to form a multimeric or oligomeric protein

Question 16

P1: Know the major elements required for life present in all amino acids (AAs).

Answer 16

carbon, oxygen, hydrogen (CHNOPS)

Question 17

P1: Proteins are considered to be “true polymers”. Why?

Answer 17

• large molecules composed of many repeating monomers (interlinked)
  -proteins are polymers comprised of amino acids (monomers)

Question 18

P1:Be able to identify the alpha carbon within the general structure of a free AA.

Answer 18

• general structure: central alpha carbon, primary/ alpha carboxyl group, side chain, primary amine and hydrogen
  -find the amine group connected to the carboxyl- it will be the carbon that they share/ connect with

Question 19

P1:Know the four groups of AA. Which ones have an overall neutral charge? Which ones are hydrophilic?

Answer 19

Group 1: Hydrophobic amino acids
-nonpolar R groups, overall neutral charge at physiological pH
-the group with the most members

Group 2: Polar amino acids
-polar R groups, overall neutral charge
-some can be phosphorylated (serine/tyrosine)
-cysteines (SH) group can form covalent disulfide bonds

Group 3: Positively charged AA
-positive R groups at physiological pH, hydrophilic
-referred to as basic AA (side chains have nitrogen)
-involved in protein ion channels

Group 4: Negatively charged AA
-negative charged R groups, hyrophillic
-referred as acidic amino acids
-involved in ion channels
-has the least members (2/20)

Question 20

P1:Be able to identify peptide bonds within a polypeptide chain.

Answer 20

(slide 19) connects two r groups/ in the middle of them
-often connecting a carbon or nitrogen

Question 21

P1: How do fibrous proteins and globular proteins differ? How are they similar?

Answer 21

-proteins are grouped by shape

-fibrous (simple shape): structural roles (filaments or tubules)/ assist with spatial organization/ serve as anchoring junctions

-globular (complex shape): regulatory or chemical roles/ serve as enzymes or transporters/receptors

Question 22

P1:How does the hydrophobic effect impact protein folding?

Answer 22

-hydrophilic AA: protein exterior
-hydrophobic AA: protein interior (move inwards to avoid water)
-stabilization relies on noncovalent interactions (hydrogen bonds, salt bridges, van der Waals)
-in a nonpolar environment, the opposite composition
-hydrophobic effect drives the folding

Question 23

P1:Define “chiral”. Explain why isomer selection matters for pharmaceuticals.

Answer 23

Chiral: asymmetric in that structure and mirror image not superimposable

-the L isomer of AA is slightly more soluble and is easier to bind/transport
-isomer selection means maximizing drug efficacy
-L isomer active versus d isomer is not or harmful
-isomer selection means to minimize undesirable side effects

Question 24

P1:Know which standard AA is achiral and why.

Answer 24

Glycine is the only AA achiral due to identical hydrogens as the side chains.

Question 25

P1: Define “buffer”. Why are proteins often involved in buffer systems?

Answer 25

Buffer: a solution that resists changes in pH due to an acid-base conjugate pair

importance: small pH changes can have major metabolic implications, organisms tightly control their internal environments
ex. phosphate buffer system

-proteins are involved in buffer systems as can be H+ acceptors or donors, due to the presence of dipolar ions

Question 26

P1:Do all of the standard proteinogenic AA have ionizable side chains? Are AAs with ionizable side chains found in all four groups?

Answer 26

-seven AA have readily ionizable side chains (aspartate, glutamate, histidine, cysteine, tyrosine, lysine, arginine)
-can form ionic bonds and participate in acid-base catalysis (group 2: polar, group 3: Positive, group 4: negative)

Question 27

P1: If given a pH and pKa value, be able to determine a free AA’s ionization state and net charge.

Answer 27

• smaller pKa= stronger acid
  -carboxyl group: pKa 2
  -amine group: pKa 9
  pH> pKa = deprotonated
  pH< pKa = protonated

Question 28

P1: Where does a protein’s net charge come from? Why does pH impact it?

Answer 28

-bc peptide bonds between the carboxyl group of one amino acid and the amine group of another, those groups don’t retain ionization states
-protein charge comes from ionizable side chains and terminal ends

-many biochemical reactions take place only within a narrow pH range

Question 29

P2: Know the four levels of protein structure, and whether each relies mostly on covalent bonds or noncovalent interactions for stability.

Answer 29

1. Primary Structure
   -depends on covalent peptide bonds
2. Secondary structure (alpha helix and beta sheet)
   -a repeating structure formed by rating two single covalent bonds on either side
   -stabilized by hydrogen bonds between carboxyl and amine group
3. Tertiary structure
   -stabilized primarily by noncovalent interactions (including hydrophobic interactions)
4. Quaternary structure
   -stabilized by same chemical bonds as tert structure
   -cross-linking between adjacent subunits may also occur via salt bridges or disulfide bonds

Question 30

P2: Are most peptide bonds in the cis or trans configuration?

Answer 30

in the primary structure, peptide bonds, are usually in the trans configuration
-minimizes steric clashes between neighboring side chains

Question 31

P2: Understand why peptide bonds do not rotate.

Answer 31

primary structure, amino acids are stabilized by uncharged peptide bonds= allowing for tight folding/ packing

-planar bonds with partial double-bond character, so rotation is prohibited (rigid and secure)

Question 32

P2: Be able to identify which amino acid bonds rotate to form secondary structure.

Answer 32

-Carbon atoms in single bonds rotate freely.
-peptide bonds btw AA: DO NOT ROTATE
-covalent bonds within AA: DO ROTATE

Alpha helix: proline, glycine, aspartate and cysteine can be accommodated into a helix
-cause kinks due to size or irregular geometry

Beta sheet: all amino acids can be accommodated, distribution within the sheet will vary

Question 33

P2: How do alpha helices and beta sheets differ? How are they similar?

Answer 33

Alpha helix: rod-like structure/ tightly coiled backbone
-Side chains extend outward in a helical way
- the majority have right-handed screws

Beta sheet: extended, zigzag structure
-side chains extend above or below in alternating pattern
-an anti-parallel arrangement in proteins most stable

-both are stabilized by hydrogen bonds

Question 34

P2: Know which modifications (phosphorylation, glycosylation and fatty acylation) are done to an amino acid’s side chain versus to the polypeptide’s terminal end.

Answer 34

1 . Phosphorylating: the SIDE CHAIN of certain amino acids (alters protein function) - not alpha carbon

2. Glycosylation: adding carbohydrate monomers to the exterior of monomer (glycoprotein)
3. Fatty acylation: adding to the exterior of protein (proteolipids)

Question 35

P2: What level of structure does a denatured protein retain?

Answer 35

retain primary structure: lose secondary, tertiary and quaternary
-enzyme activity reduced or lost as active site compromised

Question 36

P2: Understand “sequence specifies conformation” and its exceptions.

Answer 36

• central principle: the order of AA in a polypeptide chain determines the protein’s 3D shape (the native state structure is most thermodynamically stable)
• for some proteins, the primary structure does not dictate the tertiary structure

-intrinsically unstructured proteins assume a structure based on interaction with other molecules (secondary structure)

-metamorphic proteins have two or more native states that are of equal energy, dual folding proteins (tert structure)

Question 37

P2: Define “prion”. Do prions adhere to “sequence specifies conformation” or not? Why?

Answer 37

-misfolded pathogenic proteins/ infectious as able to transmit misfolding to other proteins of the same type
-highly resistant to proteases

-no, does not follow the central principle because it has very deadly effects. Does not adhere to the protein’s normal native state (the properly folded, assembled and biologically functional protein)

Question 38

P3: Understand how the types of reversible and irreversible inhibitors differ.

Answer 38

Reversible inhibitors less specific; inactivate diverse protein types
Irreversible inhibitors more specific; inactivate specific protein types

Question 39

P3: Be able to identify if end product feedback inhibition is used in regulation in a schematic.

Answer 39

End product interacts with e1 (allosteric) removed from active site. (negative feedback loop)

• Enzyme regulation may involve availability of cofactors and/or effectors
• Inhibited pathway using end product
  And allosteric by feedback inhibition

Question 40

P3: Be able to identify if a reaction is reversible or irreversible in a schematic.

Answer 40

Rapid dissociation of enzyme-inhibitor complex
enzyme-inhibitor complex stabilized by noncovalent interactions
3 common types of reversible inhibition - competitive, uncompetitive, noncompetitive

Question 41

P3: Why are cofactors important?

Answer 41

small non-protein molecules essential for enzyme activity, may be metal ions or derived from vitamins. enzyme “helpers”, not permanently modified by enzyme - different enzymes performing similar chemical reactions can use the same cofactor

Question 42

P3: How do coenzymes and minerals differ?

Answer 42

Metal ion cofactor= mineral
Vitamin dervided cofactor= coenzyme
————————————————————-
Cofactors that are metal ions - called minerals. May be grouped as major or trace. metal ions are cofactors for several critically important enzymes. - DNA polymerase, hexokinase and adenylate cyclase (all require Mg2+)
- complexes I to V of electron transport chain (require Fe-S clusters)
- stored mainly within liver and bones

Question 43

P3: Be able to distinguish exergonic and endergonic reaction graphs

Answer 43

Positive ΔG°’: reaction endergonic, does not proceed spontaneously

Negative ΔG°’: reaction exergonic, does proceed spontaneously

Question 44

P3: What are the four common catalytic strategies / mechanisms of enzymes?

Answer 44

1. Covalent catalysis
   - active site contains a nucleophile that is briefly covalently modified
2. general acid-base catalysis
   - amino acids with ionizable side chains act as general acids or bases
3. Metal ion catalysis
   - ions (like Fe2+, Cu2+, Zn2+, and Ni3+) serve as an electrophilic catalyst, generate a nucleophile, or bind to the substrate
4. Catalysis by approximation and orientation
   - 2 substrates brought closely together to facilitate reaction

Question 45

P3: Define “active site”. Know what features all active sites share.

Answer 45

Location on enzyme where substrate binds and where chemical reaction takes place.

1. Are 3D crevices formed by multiple amino acid residues
2. Constitute a small portion of the enzyme’s total volume
3. Create unique microenvironments; water usually excluded
4. Involve a large number of noncovalent interactions

Question 46

P3: Explain why changing temperature, pH and salt concentration impact enzyme activity.

Answer 46

Temp - most enzyme-catalyzed reactions increase with increasing temperature - greater kinetic energy so enzyme/substrate interaction more likely
pH - most enzyme-catalyzed reactions occur within a narrow pH range. maintains ionization state for protein conformation and net charge. above or below optimal pH, enzyme activity reduced or lost
Salt concentration - cells generally isotonic (<0.9% salt), ions compete with amino acid residues to form noncovalent interactions, at certain concentration, protein denatures; enzyme activity lost

Question 47

P3: Is ATP hydrolysis an exergonic or endergonic process?

Answer 47

Exergonic

Question 48

P3: How does ATP’s phosphoryl-transfer potential compare to that of other biological important molecules?

Answer 48

• ATP phos. potential is in the middle. When compared to phospen. which ahs a better transfer potential due to a high negative delta G)

Tendency to transfer phosphate group to an acceptor molecule
due to structural differences between ATP and its hydrolysis products.
phosphoenolpyruvate hydrolysis ΔG°’ = -14.8 kcal mol-1

ATP hydrolysis ATP -> ADP + Pi ΔG°’ = -7.3 kcal mol-1
ATP -> AMP + PPi ΔG°’ = -10.9 kcal mol-1

Glucose 6-phosphate hydrolysis ΔG°’ = -3.3 kcal mol-1

Question 49

P3: Do enzymes alter ΔG°’? What about Keq?

Answer 49

Enzymes do NOT affect ΔG, as free energy of product(s) not altered

Enzymes do NOT affect reaction equilibrium constant (Keq)

Question 50

P3: Know how to determine an enzyme’s preferred substrate using KM values.

Answer 50

• KM is independent of [E]
• When [S] at KM, then enzyme at 1/2 Vmax
• Measure of enzyme substrate affinity with smaller KM - greater affinity
• Vmax and KM both influenced by environmental conditions

Question 51

P3: Understand why increasing reactants, or removing products, can be used to ensure a readily reversible pathway goes in the “correct” direction.

Answer 51

Thermodynamics! reactions proceed towards equilibrium - pathway direction is from higher to lower energy. The number of products is greater than number of reactants. Equilibrium inpacted by increasing reactants, removing products, altering environmental conditions, etc.

Question 52

P3: How do allosteric enzymes differ from Michaelis-Menten enzymes?

Answer 52

Michaelis-menten: have a single active site, generally catalyze 1 substrate reaction, governed by mass action, catalyze readily reversible reactions, not regulatory in nature
Allosteric: multiple active sites, catalyze multi-substrate reaction, governed by -environmental signals, more complex enzyme kinetics and quaternary structure. regulatory in nature and catalyze irreversible reactions like committed steps
(these 2 are almost flip flopped)

Question 53

P3: T vs. R state

Answer 53

T (inactive) or R (active)
inactive - low substrate affinity
active - high substrate affinity

Question 54

P3: Allosteric site

Answer 54

Have multiple active sites, so generally catalyze multi-substrate reactions

Activity governed by: (i) environmental signals, (ii) more complex enzyme kinetics, and (iii) a quaternary structure

Regulatory in nature, as catalyze irreversible reactions like the committed step in a pathway

Question 55

P3: Negative vs. Positive effector

Answer 55

effectors are small molecules that bind and alter enzyme activity
positive effectors (i.e. activators)
negative effectors (i.e. inhibitors)

Question 56

P3: Feedback inhibition

Answer 56

Reaction product (often final product) binds to allosteric enzyme, altering catalytic activity

Question 57

P3: Vmax

Answer 57

maximal velocity
influenced by environmental conditions
Vmax is dependent on [E]
When enzyme at Vmax, then all available enzyme bound to substrate

Question 58

P3: Transition state vs. Reaction intermediate

Answer 58

Enzymes lower a reaction’s activation energy (EA)* which facilitates the formation of the transition state
If more molecules reach transition state, then more product formed faster

Differs from intermediate as higher free energy (in energy saddle point)

Question 59

P3: Activation energy (EA)

Answer 59

Initial energy input required for a chemical reaction to occur

Question 60

P3: Gibb’s free energy (ΔG)

Answer 60

Whether or not the reaction occurs depends on Gibb’s free energy (ΔG)

ΔG = measure of useful energy that describes spontaneity of a reaction
Provides no information about reaction rate

Enzymes do not affect ΔG, as free energy of product(s) not altered

Question 61

P3: Entropy

Answer 61

Entropy of universe always increases (2nd law) – cannot decrease

Question 62

P3: Substrate

Answer 62

Type of ligand (i.e., molecule that binds to another [often larger] molecule for a biological purpose)

molecule chemically modified by enzyme during reaction

Question 63

P3: Why aren’t Michaelis-Menten enzymes used to regulate a pathway?

Answer 63

These enzymes have a single active site, so generally catalyze 1-substrate reactions. Activity governed by mass action - catalyze readily reversible reactions thus enzymes conforming to Michaelis-menten kinetics are NOT regulatory in nature

Question 64

P4: Understand how dietary proteins are digested. Do humans store AAs?

Answer 64

Must come from diet, cannot be synthesized by humans. Pepsin cleaves proteins into fragments (oligopeptides) responsible for 10-15% of dietary protein degradation. Digestion within stomach stimulates the gallbladder to release bile salts

AA are NOT stored for later use

Question 65

P4: Define “oxygenase”. Why is this enzyme necessary for metabolizing phenylalanine, tyrosine and tryptophan?

Answer 65

enzyme that oxidizes a substrate by transferring oxygen to it
Phenylalanine is converted into tyrosine by a monooxygenase
tyrosine then metabolized to fumarate and acetoacetate
tryptophan converted into acetoacetate by a dioxygenase

Question 66

P4: Does amino acid synthesis utilize the keto acids from glucogenic or ketogenic AAs?

Answer 66

Remaining amino acids considered both glycogenic and ketogenic

Question 67

P4: How does a keto acid differ from an amino acid?

Answer 67

• Ketogenic amino acid - yield major metabolic intermediates for fatty acid synthesis or cellular respiration (generate ATP)
• Glucogenic amino acids- yield major metabolic intermediates for gluconeogenesis (generate glucose or cellular respiration (generate ATP)

Question 68

P4: The urea cycle generates fumarate. What happens to this molecule?

Answer 68

fumarate is an intermediate of the citric acid cycle and can also be converted into oxaloacetate (via malate) in mitochondria

Question 69

P4: Why is N-acetylglutamate (NAG) required for CPSI activity?

Answer 69

In mammals, CPSI requires cofactor N-acetylglutamate (NAG) functions as a positive effector; CPSI cannot convert ammonia otherwise, NAG synthesis is stimulated by the amino acid arginine

Question 70

P4: What biomolecule monomer can be synthesized from aspartate, glycine and glutamine?

Answer 70

all 3 for de novo nucleotide synthesis
aspartate forms argininosuccinate but generates oxaloacetate

glycine generates pyruvate

glutamine generates alpha-ketoglutarate

Question 71

P4: Do digestive enzymes cleave covalent bonds or noncovalent interactions?

Answer 71

Digestive enzymes break covalent bonds in protein-containing foods.

Question 72

P4: Can humans metabolize essential AAs? What about nonessential?

Answer 72

Essential - must come from diet, cannot be synthesized by human enzymes.
Nonessential - Can synthesize from human enzymes; do not need to come from diet

Question 73

P4: The urea cycle generates urea. What happens to this product?

Answer 73

Arginine hydrolyzed into urea and ornithine and polar urea is excreted from body in urine and nonproteinogenic ornithine transported back to mitochondria

Question 74

P4: Where (organ(s) and organelle(s)) does the urea cycle occur in humans?

Answer 74

Begins in liver mitochondria then to cytoplasm then out by urine or back to mitochondria

Question 75

P4: Can all 7 major metabolic intermediates be metabolized via cellular respiration?

Answer 75

Yes, but may not always metabolize that way.

Glucogenic amino acids yield major metabolic intermediates for gluconeogenesis (generate glucose or cellular respiration (generate ATP)

Ketogenic amino acids yield major metabolic intermediates for Fatty acid synthesis or cellular respiration (generate ATP)

Question 76

P4: Know the 7 major metabolic intermediates, and which can be used to synthesize new fatty acids versus new monosaccharides

Answer 76

Pyruvate, α-ketoglutarate, fumarate, succinyl CoA, oxaloacetate, acetyl CoA and acetoacetyl CoA
Fatty acids can be synthesized by Acetyl CoA & acetoacetyl CoA

Question 77

P4: Glucogenic vs. Ketogenic AA

Answer 77

Glucogenic amino acids yield major metabolic intermediates for gluconeogenesis (generate glucose or cellular respiration (generate ATP
Amongst proteinogenic amino acids, 13 considered glucogenic

Ketogenic amino acids yield major metabolic intermediates for Fatty acid synthesis or cellular respiration (generate ATP)
Amongst proteinogenic amino acids, only 2 considered ketogenic (i.e., leucine and lysine)

Question 78

P4: CPSI

Answer 78

carbamoyl phosphate synthetase I
allosteric enzyme
In mammals, CPSI requires cofactor N-acetylglutamate (NAG)
Functions as a positive effector; CPSI cannot convert ammonia otherwise

Question 79

P4: Transamination vs. Deamination

Answer 79

First step involves removing nitrogen via transamination
α-amine group transferred to α-ketoglutarate, forming glutamate

Glutamate then deaminated to regenerate α-ketoglutarate and yield NH4+
Ammonium ions (NH4+) enter urea cycle

Glycine, serine and threonine can be directly deaminated

Question 80

P4: Albumin

Answer 80

a water soluble protein that transports amino acids by blood

Protein also transports fatty acids, bilirubin, calcium, etc.

Question 81

P4: Bile salts

Answer 81

-Not enzymes but act as protein-destabilizing agents within small intestine
-Interfere with bacterial disulfide bonds or membrane stability
-Important against foodborne pathogens
-Also help with absorption of dietary lipids and Fat-soluble vitamins

-Digestion within stomach stimulates the gallbladder to release bile salts

Question 82

P4: Specific vs. Nonspecific protease

Answer 82

specific protease as cleaves by large hydrophobic amino acid residues

nonspecific protease, preferential cleavage after phenylalanine and tryptophan

Question 83

P4: Complete protein food

Answer 83

then contains all essential amino acids
- Cannot be synthesized by human enzymes; must come from diet

Question 84

P5: Which AA donates its α-amine group to form most other AAs?

Answer 84

Glutamate donates it alpha amine group to form most amino acids via transamination

Question 85

P5: Understand how nonessential amino acid synthesis is regulated. **check

Answer 85

-regulation: may involve cumulative feedback inhibition
(usually, pathways are regulated by feedback inhibition)
-needs at least two other amino acids to act as suppressors

Question 86

P5: Understand how a protein is synthesized. What happens at each stage?

Answer 86

-Gene expression(DNA-RNA-Protein)
-synthesis occurs in Cytoplasm (prokaryotes); ER (eukaryotes)

1. Begins at start codons
2. involves ribosomes, mRNA, tRNA
3. Initiation, Elongation and termination

Question 87

P5: Are all genes in an organism expressed via translation at once?

Answer 87

Translation occurs on per gene/ small group of genes basis

Question 88

P5: Understand how translation is regulated

Answer 88

via molecules involved in protein synthesis (translation)

-binding of poly(A) binding proteins on mRNA
-sequestering of mRNA in the cytoplasm or processing bodies
-methylation of rNA
-phosphorylation of protein initiation factors
-RNA interference (RNAi)

Question 89

P5: Is the liver the only in the human body capable of synthesizing amino acids?

Answer 89

No!
-different nonessential amino acids are synthesized by different organs (synthesis=anabolism)
-liver: alanine, glutamine, arginine, tyrosine
-brain: glutamate, serine, proline
-kidneys: glycine, cysteine, asparagine, aspartate

Question 90

P5: Where do humans obtain most of the nitrogen our bodies need for amino acid synthesis?

Answer 90

majority of nitrogen through diet

Question 91

P5: How is nonessential amino acid synthesis are synthesized

Answer 91

Synthesis of the nonessential amino acids depends mainly on the formation of appropriate α-keto acids, which are the precursors of the respective amino acids. (cellular respiration is a main source of several keto acids)
-synthesized via transamination: glutamate donates the alpha amine group
-de novo AA synthesis: glutamate to glutamine
-cofactors are vital for synthesis

Question 92

P5: Besides ribosomes, what other proteins are involved in translation/ what are their roles? **Check

Answer 92

Ribonucleoprotein: particles that consist of small/large subunits
mRNA:
tRNA:

Question 93

P5: Where in a cell does translation occur in eukaryotes versus in prokaryotes

Answer 93

prokaryotes: cytoplasm
eukaryotes: ER

Question 94

P5: How do silent mutations and missense mutations differ? How are they similar?

Answer 94

silent: same amino acid/ synonymous mutation (goes unnoticed)
Missense: different amino acid/ nonsynonymous (the new amino acid is coded for)
-both involve changes to an individual and specific codon/ can switch chemical groups
-alters the sequence of mRNA

Question 95

P5: Do start codons calls for an amino acid? Which ones? What about stop codons?

Answer 95

-methionine/ AUG: start codon initiating translation
-UAA, UAG, UGA: stop codons/ DO NOT code for an amino acid

Question 96

P5: Can a person’s body synthesize a protein that contains essential amino acids

Answer 96

Humans can only synthesize nonessential amino acids, essential amino acids acquired from diet

Question 97

P5: Ester linkages are relevant to EF-Tu and RF1. What is the connection for both?

Answer 97

*need notes

Question 98

What is the meaning of a complete protein food

Answer 98

we must get the other nine amino acids (called “essential amino acids”) from the foods we eat. When a food contains all nine of these amino acids, it is called a “complete protein.”

Question 99

what does albumin mean

Answer 99

Albumin is the most common protein found in blood plasma. It helps to ensure blood stays in arteries and veins, and helps carry hormones, vitamins, and enzymes throughout the body

Albumin is made in the liver and quickly carried to the bloodstream.

Question 100

what is the difference between glucogenic vs. ketogenic AA

Answer 100

glucogenic amino acids produce pyruvate or any other glucose precursors during their catabolism

ketogenic amino acids produce acetyl CoA and acetoacetyl CoA during their catabolism.

Question 101

what is the nitrogenase enzyme complex

Answer 101

Nitrogenase is a complex, bacterial enzyme that catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia (NH3).

Question 102

what is the peptidyl transferase center

Answer 102

resides in the large ribosomal subunit and catalyzes the two principal chemical reactions of protein synthesis: peptide bond formation and peptide release.