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89 Cards in this Set
- Front
- Back
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Biochemistry |
The science and study of molecules in living cells and organisms and their chemical reactions
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Metabolism |
The sum of all chemical reactions in living cells or organisms |
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Catabolism/ catabolic reactions |
the breaking down of molecules to make smaller ones. - gives off energy and oxidation and pathways ends with lysis (to cut) - sometimes produces / releases energy)
EX. protein goes to amino acids |
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Anabolism/ anabolic reaction |
synthetic reactions -> adding/ building up of molecules to make bigger ones. - pathway usually ends with genesis (to make , to build) - always requires energy |
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amino acids |
building blocks of proteins >40 amino acids are proteins 2-40 are peptides or polypeptides |
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what is porphyrines? |
Heme- (red) part of blood Not hemoglobin |
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How is a cysteine created? |
A disulfide bond made of two cysteines creates a cysteine |
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Proteins |
compounds composed of carbon, hydrogen, oxygen, nitrogen and sulfur atoms (chons)- sometimes sulfur |
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how are proteisn arranged? |
o -as strands or chains of aa bonded together which are: -no branches, straight- chained - sometimes composed of multiple chains interacting as 1 protein
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List 6 things about amino acids |
1. the building blocks of proteins and peptides 2. synthesis of neurotransmitters 3, synthesis of porphyrins (heme), purines, and pyrimidines (bases to our nucleotide) 4. synthesis of glucose, ketone bodies, and fatty acids 5. catabolized into ammonia and urea 6. 20 different L- alpha amino acids |
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What are the L- alpha- Amino acids? |
1. Aliphatic (all C and H atoms) 2. Hydroxy (OH group) 3. Sulfur Containing (contain s) 4. Acidic and amines (extra carboxylic acid group alone or with extra amine group) 5. Basic (extra amine group) 6. Aromatic (C ring) 7. Imino (ring with other atoms)
HAS A BAI |
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What is the side chain for Apliphatic? |
(all c and H atoms) Glycine, Alanine, Isoleucine, Leucine, Valine
GAILV |
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what is the side chain for Sulfur? |
(contain S) Methionine, Cysteine
MC |
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What is the side chain for Aromatic? |
(C ring) Phenylalinine, Tyrosine, Tryptophan
PTT |
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What is the side chain for Basic? |
(amine group) Lysine, Histidine, Arginine
LAH |
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What is the side chain for acid or amine group? |
(Carbox alone or with amine) Aspartic acid, asparagine, glutamine, glutamic acid
AAGG |
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What is the side chain for hydroxy? |
(OH) Threonine, Serine
TS or ST |
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What is the side chain for Imino? |
(within the ring) Proline
P |
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Diagram for L alpha amino acids |
COOH NH2 - C - H R
NH2 (amine) COOH (carboxylic acid) |
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What are the 3 branching amino acids in the brain that tells us whether we are starving or fasting? |
Valine, Isoleucine, Leucine
VIL |
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How are zwitterions created? (that have a net charge of 0 with equal amount of + and - charges) |
When internal acid-base reactions occur |
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Isoelectric Point |
The pH at which the zwitterion (neutral form) exists in a solution - net charge on aa is 0 |
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Acidic amino acid |
3-4 |
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Neutral amino acid |
6-7 |
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basic amino acid |
9-11 |
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What happens if pH is less than the isoelectric point? |
(high H+) (low pH) = aa form cations (overall positive charge0 |
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What happens if pH is more than the isoelectric point? |
(low H+) (high pH) = amino acids form anions (overall negative charge) |
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What determines the physical properties of amino acids? |
Based on their side chain (R or r group) |
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10 non- polar aa and hydrophobic, and found where |
(found inside protein) Aliphatics- (C + H) Glycine, Alynine, Leucine, Isoleucine, Valine
Sulfur (S) Methionine
Imino Proline
Aromatic - Tryptophan, tyrosine, Phenylalinine |
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5 polar aa and hydrophilic, and found where |
(found on surface of protein)
Serine, Threonine, cysteine, asparagine, Glutamine,
Polar acids: Aspartic Acid, glutamic acid (acid) Polar base: Lysine, Arginine, Histidine (basic) |
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What are the three major reactions of 2 amino acids? |
- most important is the formation of peptide bond - hydrogen bond -disulfide bond
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Peptide bond contains how many aa? |
2-40 |
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what happens with the amine group and carboxylic group join? |
Causes a release of water molecule (occurs in anabolic reaction)
amine + acid -> amide +H20 |
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Protein Functions |
- Catalyst (enzymes) - Structure (bones, muscles) - messengers (hormones, neurotransmitters) - Immunoproteins (antibodies) - transporters (blood, cells, cell membranes) - acid base balance (buffers) - fluid balance (osmosis) - energy |
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Primary structure of protein |
sequence of aa that are in specific order of which aa are joined together. (peptide bond) - sequence depends on the composition of their genetics :DNA/ genes |
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secondary structure |
non- covalent interactions/ attraction due to hydrogen bonding - occurs between aa within the peptide bond for stability. - will function best when they are at their most stable form |
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2 distinct shapes of the secondary structure |
alpha helix: stairway spiral connect of amino acids at every 4
Beta Pleated: Hydrogen bonding btwn side by side protein chain segments (intra or inter chain bonding) |
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Tertiary structure |
3D structure -globular = soluble in water, suspended in the blood or cells (ex. insulin, hemoglobin, transferrin)
- fibrous protein = insoluble in water but very storng intertwined (keratin, collagen, fibrin for blood clotting, and elastin)
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Disulfide Bonding |
Tertiary Structure
a strong covalent bond that holds sulfur together (ex. cysteine is created by 2 cysteine amino acids) |
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Electrostatic interactions |
Tertiary Structure
where negative attracts to the positive |
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Hydrophobic interaction |
Tertiary structure
nonpolar amino acids hang out together tucked away inside the cell |
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Quarternary Structure |
- proteins with 2 polypeptide chains (dimers) or more - they have poor functions individually, but when put together, they function well held with hydrogen and disulfide bonding |
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what is each polypeptide chain called? |
subunit monomer |
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What can 2 amino acids of the amine and acids group react to do? |
Create a peptide bond of the amide linkage |
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What is globin |
Globin is the protein that has 4 protein strands folded together: - 2 alpha - 2 beta (in adult) |
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What is heme (part of hemoglobin)? |
Heme is the prosthetic group (therefore it is a conjugated protein)
- tetrapyrrole 94 pyrole rings containing N atoms connected together - Fe2+ is center of tetrapyrrole
- double bonds in heme's structure causes it to absorb light at low end of spectrum (red)
- for every globin chain there is a heme (think of it like hemoglobin)
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How many amino acids are in the alpha strand (in globin)? |
141 aa |
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How many amino acids are in the strand beta (in globin)? |
146 aa |
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Hemoglobin |
Normal hgb: hgb alpha 2 beta 2
98% of normal Hgb = also called Hgb Al 2% of Hgb A2 of delta chains |
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What does deoxygenated Hgb from venus blood bind to? |
Deoxygenated hgb from venus blood binds to oxygen forming oxyhemoglobin in the lungs, then leaves via arterial blood.
- as oxygen increases, equilibrium shifts and favors it = more oxyhemoglobin |
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Oxygen Cooperative Kinetics |
When oxygen attaches to Hgb and changes shape (allosteric modification) to make it easier for more oxygen to attach |
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What happens when oxygen is released to tissues? |
Some oxygen is used immediately and some is picked up from myoglobin (muscle hemoglobin) for storage |
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2- 3 Biphosphoglycerate (BPG) |
a compound produced as a byproduct in glycolysis in red blood cells esp in anaerobic conditions |
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Explain the role of 2, 3 BPG in facilitating O2 release from hemoglobin |
increase in 2,3 BPG favors oxygen release from oxyhemoglobin |
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Living in higher altitudes |
- atmospheric pressure and oxygen is less
- bc of low oxygen at higher altitudes, there is an increase in 2,3 BPG due to glycolysis --> allows adaptation where oxygen isles s than sea level and provide more oxygen to the muscles |
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what happens when blood is exposed to air? |
Hgb undergoes oxidation (Fe +2 -> Fe +3) to "Methemoglobin"
- this is why our blood dries to a brown color |
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Carbon monoxide Poisoning |
common due to it being similar in size and structure to oxygen. Hemoglobin doesn't know the difference and attaches to it.
"cherry red" color of carboxyhemoglobin is in the red lips associated with CO poisoning
- reverse reaction Po2 must be increased |
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Bohr effect |
deoxyhemoglobin acts as a buffer in the blood |
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what does the bohr effect remove from tissues? |
removes CO2 from tissues |
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Where does the formation of carbonic acid happen? |
RBC, which splits into ions of + and - charge.
+ = protons, - = bicarbonate |
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The deoxygenated hemoglobin acts as a what? |
a buffer and binds to the protons and then delivers the protons to the lungs.
The oxygen in the lungs causes the hemoglobin to release the proton and instead bind to the oxygen |
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What happens with the protons and bicarbonates (+ and -) reform carbonic acids? |
It becomes CO2 and H2O out of the lungs |
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Identify and explain how one amino acid substitution results in Sickle Cell Anemia |
a genetic disorder where vaine (neutral non polar) replaces glutamic acid (polar) in the 6th residue of the beta chain.
- this makes heme stickier - changes the shape which causes the RBC to change
- body recognizes that there is something wrong with the RBC and will kill them as the spleen removes them and will lower the RBC count
- sticky patches attach to eacho ther, polymerization of Hgb and distorts the cell (hemoglobin S) |
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Glycosylated Hgb (Hgb Alc) |
- important for measuring diabetes
glucose enters the rbc and glycosylates and lysine residues of hgb is normally 5%. the level is dependent upon blood glucose levels in the previous 6-8 wees |
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Thalessanimias |
a genetic defect where you are missing partial or total absence of an alpha or beta chain of hemoglobin |
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Dietary Anemias |
- decrease in number of RBC count - impaired synthesis of Hgb (iron deficiency) - impaired production of RBC (folic acid deficit, B12 deficit, B6 deficit) |
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Alzheimer's Disease |
misfolding or refolding of beta amyloids protein forming aggregates or plaques in the brain tissue |
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Prions or Prions disease |
fatal neurodegeneration disease due to deposition of insoluble protein aggregates (plaques) in the neural cell. (mad cow disease) |
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Structure of L - Amino Acid |
COOH NH2 - C - H R |
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Structure of D - Amino Acid |
COOH H - C - NH2 R |
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How many different parts are there to the L- alpha amino acids? |
5 different parts (4 parts are identical in each aa) |
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When do amino acids exist as zwitterions? |
In the solid state |
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What does Neutral contain? |
equal numbers of COO- and NH3+ (can be polar or nonpolar) |
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What does Polar acidic contain? Give ex. |
two COO- and one NH3+ (extra COO- in side chain) (- charge)
ex. Aspartic acid and glutamic acid |
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What does Polar basic contain? Give ex. |
two NH3+ and one coO- (extra NH3+ in side chain) (+ charge)
ex. lysine, arginine, histidine |
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What is the peptide bond formation? |
RCOO- + RNH3+ -----> RCONHR + H2O acid amine -----> amide water |
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What do simple proteins contain? |
Only amino acids |
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what do conjugated proteins contain? |
amino acids (protein portion) and a prosthetic group (nonprotein portion)
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What happens when proteins change their conformational shape? |
Denaturation or formation of insoluble aggregates or plaques (aggregation) occurs |
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denaturation |
Rupture of H+ bonds, hydrophobic interactions and electrostatic interations - alcohol -acids -bases - heat |
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What is normal hgb? |
Hgb alpha2beta2 aka Hgb A1 (98% of normal hgb) |
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Symbol for oxyghemoglobin |
Hgb-O2 |
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What happens when O2 increases in oxygen transport? |
ex. lungs
the position of the equilibrium shifts to favor product formation (moves to right)
Hgb + O2 <----> Hgb-O2
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What happens when O2 decreases in oxygen transport? |
ex. muscle tissue
the equilibrium shifts favoring O2 release from Hgb- O2 (moves to the left)
Hgb + O2 <------> Hgb-O2
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How is oxyhemoglobin created? |
Deoxygenated hemoglobin from venous blood binds to oxygen, forming oxyhemoglobin (Hgb-O2) in lungs, then leaves via arterial blood
Hgb + O2 <---> Hgb-O2 (reaction is reversible) |
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Allosteric modification |
when hemoglobin undergoes a change in shape |
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How is the oxyhemoglobin dissociation curve shaped? |
In a sigmoid or S shape |
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In the Bohr effect, what does the formation of carbonic acid dissociate to? |
Protons (H+) and bicarbonate ions (HCO3-) |
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Reduced Hgb |
When the H+ binds with HGb forming Hgb-H |
