Cell Bio Amino acids 1 & 2 Flashcards
Amino acid & proteins such as fats, proteins, and carbohydrates are comprised of which elements?
proteins are a bunch of ? together
which bonds exist between proteins?
Triacylglycerides comprise of?
carbohydrates comprise of?
C, H and O, just with diff. arrangements
proteins are a bunch of amino acids together
peptide bonds present between each amino acid
glycerol and 3 fatty acids are present in triacylglycerides
carbohydrates are just a bunch of monosaccharides combined together
proteins are the products of our ?
the central dogma of molecular biology incorporates?
PROTEINS
1. Proteins are **? in the living systems
2. how many physiological processes depend on these molecules - proteins?
3. Diverse and share fundamental common structural function of being?
Membrane proteins include?
proteins are the products of our genes
the central dogma of molecular biology includes DNA -> RNA -> Protein
Transcription -> Splicing -> Translation
Nucleus -> Ribosome -> ER -> GA -> vesicle
PROTEINS
1. ** IMP! Proteins are the most abundant and functionally diverse in the living systems
2. *ALL many physiological processes depend on these molecules - proteins?
3. Diverse and share fundamental common structural function of being *linear polymers of AA’s
Membrane proteins include transport proteins, channels, enzymes, signal proteins, hormone proteins, second messengers, structure proteins
AA, PEPTIDES, POLYPEPTIDES and PROTEINS
Proteins are biologically occurring sequencing of amino acid (AA) monomers linked by ?
- formed when the ? group of 1 AA reacts with the ? group of another AA
Peptides are distinguished proteins based on the ?
- Shortest peptides are ?, tripeptides, tetrapeptides
Peptides -> ? or fewer amino acids (and are peptides and proteins branched?)
and how many amino acids in proteins?
- Oligopeptide: which ones shorter between them?
- Polypeptide:
Proteins are biologically occurring sequencing of amino acid (AA) monomers linked by peptide bonds
- formed when the carboxyl group of 1 AA reacts with the amino group of another AA
Peptides are distinguished proteins based on the size of chain
- Shortest peptides are dipeptides, tripeptides, tetrapeptides
Peptides -> 50 or fewer amino acids WHEREAS proteins -> more than 50 amino acids and are branched (BOTH are not branched both linear AA’s)
- Oligopeptide (2-20) are shorter than polypeptides (21 - 50) - no need to memorize the specific #s
PEPTIDE BOND - Condensation Reaction
is condensation rxn spontaneous?
does it require ATP?
AA are composed of ? (3 things) -> which among these 3 things determines the role of AA in the protein
**AA’s ? determines how they interact with each other
R (side chain) is commonly one of #? side chains
at pH ? both amino and carboxyl groups are ionized
FAMILIES OF AMINO ACIDS
- the common AA are grouped a/c to whether their side chains are ?
- these #? AAs are given both #? letter and #?letter abbreviation (Thus: alanine = ? = ?)
MORE THAN >? AMINO ACIDS IN NATURE
how many seen in mammalian proteins?
Proteinogenic AA - how many of them?
*Standard amino acids encoded by? and can it be made in body?
Nonstandard amino acids are synthesized by chemical modification of ?
STOP-CODON also codes for another type of amino acid called? and its the #? proteinogenic AA
condensation rxn is NOT a spontaneous rxn
it requires ATP/ ATP dependent
AA are composed of
1. an amino group (NH2)
2. an acid (carboxyl group)
3. a distinct side chain (R-group) bonded to the alpha-carbon
-> SIDE CHAIN (R-group) bonded to the a-carbon determines the ROLE of AA in the protein
AA’s structure determines how they interact with each other
R (side chain) is commonly one of 20 side chains
at pH 7 both amino and carboxyl groups are ionized
FAMILIES OF AMINO ACIDS
- the common AA are grouped a/c to whether their side chains are acidic, basic, uncharged polar, nonpolar
- these 20 AAs are given both 3 letter and 1 letter abbreviation (Thus: alanine = Ala = A)
Proteinogenic AA - how many of them?
*Standard amino acids encoded by DNA and can it be made in body?
Nonstandard amino acids are synthesized by chemical modification of standard amino acids
STOP-CODON also codes for another type of amino acid called “Selenocysteine” and its the 21st proteinogenic AA
MORE THAN 300 AMINO ACIDS IN NATURE!
about 20 seen in mammalian protein
(we need to understand what are the polar AA and non polar AA, and y they are called that
histidine is a polar amino and will ask for specific characteristics of groups of amino acids (not asking to memorize which group is which AA)
nonpolar glycine, cysteine and proline - going to be discussing it.)
In proteins, most carboxyl and amino groups of amino acids are combined through ? which make them unavailable for chemical rxns
Therefore, the chemical nature of ? determines the role that amino acid plays in a ? (particularly how the protein folds into its ?)
The side (R-)chain distinguishes ?
-> R-group can be ?
In proteins, most carboxyl and amino groups of amino acids are combined through peptide bonds which make them unavailable for chemical rxns
Therefore, the chemical nature of side chain determines the role that amino acid plays in a protein (particularly how the protein folds into its native confirmation)
The side chain distinguises 1 AA to another AA
R group can be polar, nonpolar, negatively charged or positively charged.
AMINO ACIDS NON-POLAR SIDE CHAINS
- each have a nonpolar side chain that does not ? protons or participate in ?
- The side chains of these AA can be regarded as ? or ? which promotes ? interactions
- in protiens found in aqueoous solution, the side chains tend to cluster together in the interior of the ? (? effect)
which AA doesn’t have a side chain? due its lack of side chain it will make the AA?
- each have a nonpolar side chain that does not gain or lost protons or participate in H or ionic bonds
- The side chains of these AA can be regarded as oily or lipid-like or promotes hydrophobic interactions
- in proteins found in aqueous solution, the side chains tend to cluster together in the interior of the protein (hydrophobic effect)
The AA Glycine doesn’t have a side chain and due to its lack of side-chain it will be flexible, malleable .
AMINO ACIDS - PROLINE
Differs from other ? AAs
- side chain and alpha-amino N form a ?, (how many #s) - membered ring structure?
- ? instead of Primary amino group (called ? group)
The unique geometry of Proline:
- formation of the ? i.e., ?
- interrupts the ?-helices in ? proteins
PROLINE
Differs from other non-polar AAs
- side chain and alpha-amino N form a **RIGID, 5-membered ring structure?
- secondary instead of the Primary amino group (called imino group)
The unique geometry of Proline:
- formation of the fibrous structure i.e., collagen
- interrupts the alpha-helices in globular proteins
The UNCHARGED POLAR SIDE CHAINS
- have ? charge at physiologic pH
- which amino acids have a polar hydroxyl group? (participate in ? formation)
- which amino acids’ side chain contain carbonyl group (C double bond with O) and an amine group?
- side chain of cysteine contains a sulhydryl group (thiol, -SH group)
-> imp. for ? bonds formation btw proteinsc for stabilization
cysteine and tyrosine side chain can lose a ? at an alkaline pH
Cysteine: -SH bond is ?, but it‘s overall a ?
The UNCHARGED POLAR SIDE CHAINS
- have a 0 net charge at physiologic pH
- The amino acids have a polar hydroxyl group are Serine, threonine, tyroxine (participate in H+ bond formation)
- which amino acids’ side chain contain carbonyl group (C double bond with O) and an amine group? -> Asparagine & glutamine
- side chain of cysteine contains a sulhydryl group (thiol, -SH group)
-> imp. for disulfide bonds formation btw proteins
cysteine and tyrosine side chain can lose a proton at an alkaline pH
Cysteine: -SH bond is slightly polar, but it‘s overall a nonpolar molecule
AMINO ACIDS Charged - Acidic side chain
Proton donors: which amino acids do they include?
At physiological pH the side chains are:
* ? and ? charged
* aspartate and glutamate → ? charge of amino acid molecule
After donating a protien glutamic acid becomes ?
PROTON ACCEPTORS
At physiological pH the side chains are: ? and ? charged
Histidine‘s side chain:
Can be either ? charged or ?
depending on the ? pH
Important function as ?
AMINO ACIDS Charged - Acidic side chain
Proton donors: which amino acids do they include? -> glutamic acid and aspartic acid
At physiological pH the side chains are:
* Fully ionized and negatively charged
* aspartate and glutamate → negative charge of amino acid molecule
After donating a protein glutamic acid becomes glutamate
Histidine‘s side chain:
Can be either (+) charged or Neutral
depending on the environment‘s pH
imp. function as *buffer! (if pH below 6 then it accepts e- and if it rises above 6 then it donates an electron so histidine buffer system of body)
Other e.g. of AA w polar basic side chains are lysine and arginine (note: both end with -ine, same as am-ine)
NON-POLAR AMINO ACIDS AND POLAR AMINO ACIDS
Location of nonpolar amino acids in SOLUBLE protein and MEMBRANE protein
SOLUTION PROTEIN
- non-polar AA clusters on the ?
while polar amino acids cluster on the?
ON MEMBRANE PROTEIN
- non-polar amino acids cluser on the ?
SOLUTION PROTEIN
- non-polar AA clusters on the interior of the soluble protein
while polar amino acids cluster on the surface of soluble protein
ON MEMBRANE PROTEIN
- non-polar amino acids cluser on the surface of the membrane protein
AMINOACIDS DERIVATIVES
Tyrosine: (can be made into?)
-?
-?
Taurine:
- ?
Glutamate:
- ?→ an inhibitory neurotransmitter
Tryptophan:
-? → neurotransmitter, plays key role in digetion, mood, sleep, healing…
Histidine:
? → mediator of allergic reactions
Lysine:
-? → lipid oxidation
AMINOACIDS DERIVATIVES
Tyrosine:
-Triiodothyronine (T3) & thyroxine (T4) → thyroid hormones
-Dopamine
Taurine:
Bile acids
Glutamate:
GABA → is an inhibitory neurotransmitter
Tryptophan:
Serotonin → neurotransmitter, plays key role in digetion, mood, sleep, healing…
Histidine:
Histamine → mediator of allergic reactions
Lysine:
Carnitine → lipid oxidation (carnitine shuttle: transports the long chain FA form cytosol into mitochondrial matrix)
PEPTIDES with physiological relevance
just know their basic function and that they are peptide hormones
(note: proteins are more than 50 AA and peptides are until 50 AAs)
name 6 and thier basic func.
pneumonym: (OACBAM)
Oxytocin: peptide hormone (9 AA peptide) produced in the hypothalamus (uterine contractions and milk secretion)
- Antidiuretic hormone (ADH): 9 peptides produced in the hypothalamus and essential for the maintenance of water balance (ADH in nephron; diuretic reminds me of water)
- Creatine: tripeptide involved in energy production in muscle and cardiac cells
- Bradykinin: 9 peptides, vasoactive substance
- Angiotensin II, 10 pep, a potent vasoconstrictor
- Melanin: tripeptide, a pigment occurring in several tissues, synthesized from tyrosine via DOPA
POLYPEPTIDES with physiological relevance
list 4 and their basic func?
GGCA
Gastrin
- stomach hormone
- stimulates secretion of gastric glands
Glucagon
- produced by alpha-cells of the pancreas
- stimulates glycogenolysis
CCK (cholecystokinin)
- stimulates pancreas and liver secretion
- (bile from gall bladder)
Atrial Natriuretic Peptide (ANP)
- produced in the heart (atrium)
- essential for the regulation of blood volume and pressure
NOTE: STRUC OF AMINO ACID PEPTIDES AND PROTEINS V DIFF!
PROTEIN DIGESTION and AA METABOLISM
Unlike fats and carbohydrates, AA are not ?
AA must be obtained through:?
PROTEIN DIGESTION – Dietary protein
- starts in the ? aided by ? comprised of 2 things what are 2 things?
-> HCl: what does it do?
-> pepsinogen which is secreted in the stomach* is activated it gets converted from its inactive to active form called? which helps in ?
continues in the *? by ? enzymes
what are their active enzymes?
- pepsinogen
- chymotrypsinogen
- procarboxypeptidase
- prolelastase
most digestion happens in ? through pancreatic enzymes (and only pepsin breaks down in stomach relative to other enzymes)
PROTEIN DIGESTION and AA METABOLISM
Unlike fats and carbohydrates, AA are not stored in body
AA must be obtained through:
1. obtained from the diet (9 AA are essential)
2. released through the degradation of body protein
3. de nono synthesis (from intermediate metabolites)
PROTEIN DIGESTION – Dietary protein
Starts in the stomach → gastric juice (HCl and pepsinogen) HCl → kills bacteria and denatures protein (facilitates enzymatic
hydrolysis)
Pepsinogen is activated → pepsin → protein hydrolysis
Continues in the small intestine by pancreatic enzymes
what are their active enzymes?
- pepsinogen - pepsin
- chymotrypsinogen - chymotrypsin
- procarboxypeptidase - carboxypeptidase
- prolelastase - elastase
most digestion happens in small intestine through pancreatic enzymes (and only pepsin breaks down in stomach relative to other enzymes)
PROTEIN DIGESTION and ABSORPTION
STEP 1: Membranous-phase digestion
STEP 2: Enterocytes (brush border memb)
STEP 1: Membranous-phase digestion
- Membranous-phase digestion of ? and ?
- tripeptides and dipeptides may be ? either on the ? or within the ?
In CARBOHYDRATE HOWEVER, all disaccharide hydrolysis occurs at the ?
Regardless of the site at which the final hydrolysis of peptide occuurs, the product absorbed into the blood is ?
STEP 2: Enterocytes
- here at least #? diff. sodium cotransport proteins exist for the transport of AAs for ?, ? and ? AAs.
- A sodium cotransport process might be invovled in the absorption of dipeptides and tripeptides but this possibility is not ?
- oligopeptides enter the enterocyte through which protein/pathway?
- the dipeptides and tripeptides that go through carrier pathway go through **? which breaks down dipeptides and tripeptides into amino acids
PROTEIN DIGESTION and ABSORPTION
STEP 1: Membranous-phase digestion
- Membranous-phase digestion of carbs and peptides
- tripeptides and dipeptides may be hydrolyzed either on the apical membrane or within the enterocyte
In CARBOHYDRATE HOWEVER, all disaccharide hydrolysis occurs at the apical membrane
Regardless of the site at which the final hydrolysis of peptide occurs, the product absorbed into the blood is free AAs
STEP 2: Enterocytes
- here at least 3 diff. sodium cotransport proteins exist for the transport of AAs for acidic, basic, and neutral AAs.
- A sodium cotransport process might be involved in the absorption of dipeptides and tripeptides but this possibility is not well established
- oligopeptides enter the enterocyte through “peptidase”
- the dipeptides and tripeptides that go through “carrier” protein/pathway go through “**INTRACELLULAR PEPTIDASES” which breaks down dipeptides and tripeptides into *amino acids (END PRODUCT)
AA METABOLISM - DEGRADATION
In liver -> AA catabolism -> into ? (amine part of AA) and ? (the carbon skeletons of AA)
The carbon skeletons of the α-keto acids are converted to ?
- Which can be metabolized by central pathways of metabolism i.e., ?, ?, ? to
-> CO2 and H2O
-> Glucose, fatty acids or ketone bodies
All AA’s in excess of biosynthetic needs are ? -> AA are never ? !!
AA METABOLISM - DEGRADATION
In liver -> AA catabolism -> into ammonia (NH3/urea) (amine part of AA) and alpha-keto acids (the carbon skeletons of AA)
The carbon skeletons of the α-keto acids are converted to common intermediates of *energy-producing metabolic pathways
- Which can be metabolized by central pathways of metabolism i.e., **gluconeogenesis, glycolysis, TCA cycle to
-> CO2 and H2O
-> Glucose, fatty acids or ketone bodies
All AA’s in excess of biosynthetic needs are rapidly degraded -> AA are never STORED !!
