3-4 Biochem Flashcards
Why is Protein considered Life?
On a biochemical and molecular standpoint, the processes that define life are rooted in cellular activity wherein the work is done by proteins
The Structural Foundation of Proteins refers to the architecture of ___ and ___
Cells and Tissues
Which proteins provide a functional role?
Enzymes, Receptors, Carrier Proteins (Hormones and Neurotransmitters)
What is the function of enzymes?
Catalyze the vast majority of cellular processes and reaction, whether for growth or survival
Proteins also mediate signaling, helping cells communicate with each other, such as hormones and neurotransmitters. True or False?
TRUE
Amino acids are the building blocks of proteins. True or False?
TRUE
What bond joins amino acids together? Is it a Covalent Bond?
Peptide Bonds, Yes
Amino acids are composed of?
Amino Group (-NH2 ) (-NH3 + if not attached)
Side Chain (Functional Group)
Carboxyl Group (-COOH)
Glycine is the tiniest Amino Acid and has a side chain?
False, Glycine does not have a side chain
At physiologic pH (∼7.4), an amino acid typically exists in a zwitterionic form, where the molecule has both a ____ charge on the amino group and a ____ charge on the carboxyl group, thus is electrically neutral
Positive, Negative
Why is the Side chain considered the functional group?
It’s what makes the amino acid “unique.” It is variable per amino acid and provides different functions
Which parts of the amino acid interact to form a peptide bond?
Carboxyl Group of one amino acid and the Amino group of another Amino Acid
How do we classify Amino Acids in terms of Structural and Chemical Properties?
Aliphatic - Linear Structure
Aromatic - Cyclic Structure (Bulky/Big Chains)
Describe the Polarity of Amino Acids
Polar: Possess a side chain that is able to react to solutes in water (Hydroxyl, Sulfide, Amino Group, Carboxyl Group), found in outer surfaces of a protein
Non-Polar: Hydrophobic in nature and repel water, found in inner surfaces of a protein (away from the surrounding water)
Proteolysis alters the “secondary” structure and subsequently alters the proteins’ higher order structures as well.
False, the primary structure is altered
Differentiate Hydrophilic vs Hydrophobic Amino Acids
Hydrophilic: Dissolves well in water
Hydrophobic: Insoluble in Water and is Less Soluble in Blood but mixes well with lipids
At physiologic pH, Polar Amino Acids can have a positive (basic) or negative charge (acidic). True or False?
TRUE
What are the practical or operational groupings of Amino Acids
Small and Compact
Sulfur Containing
Branched-chain amino acids
Large, Aromatic
Provide specific examples of Amino Acids under each practical and operational grouping
Small and Compact (Glycine and Proline)
Sulfur Containing (Cysteine and Methionine)
Branched-chain amino acids (Valine, Leucine, Isoleucine)
Large, Aromatic (Tryptophan, Tyrosine, and Histidine)
Describe the characteristics of Glycine and Proline as small and compact amino acids
Forms Folds, Bends, Kinks in the structure of Polypeptide
What are the functions of branched-chain amino acids (BCAAs - Valine, Leucine, Isoleucine)
Play a vital role in neuronal metabolism, major amino acid food for the brain
All 3 act as energy reserves for the brain
Forms a big chunk of lean muscle mass. This is why there are BCAA supplements available for gaining muscle mass.
Where do hydrophobic amino acids tend to be found?
In the interior of typical plasma protein
When protein travels with the blood along the body, what elements are the protein exposed to?
Other cells, different molecules, compounds, acids and other proteins
Differentiate the interior and exterior of amino acids
Interior: Compact; hydrophobic amino acids (help stabilize structure) are here such as Gly, Phe, Val, Leu
Exterior: More exposed to surrounding environment; polar amino acids are here such as Glu, Asp, Tyr, Ser; have reactive side chains
Which amino acid has an oily or lipid like property and what does it promote?
Non-polar amino acid, promotes hydrophobic interactions
What phenomenon refers to the side chains of nonpolar amino acids clustering together in the interior of the protein?
Hydrophobic effect, which is the result of the hydrophobicity of the non polar R groups
Which part of the protein are the nonpolar R groups found?
Surface of the protein interacting with the lipid environment
What disease cause red blood cells to become sickle shaped rather than disc shaped?
Sickle cell anemia
Sickle cell anemia results from what?
from the replacement of polar glutamate with nonpolar valine at the sixth position in the β subunit of hemoglobin A.
What is the most common mutation associated with cystic fibrosis and what does it result into?
3-bp deletion which results into the loss of phenylalanine at position 508, weakening hydrophobic interactions leading to misfolding.
What protein component of LDL and HDL is responsible for interacting with tissue receptors?
Apoprotein, which possess polar amino acids in its interactive sites
Main difference between non-essential from essential amino acids:
Essential: Must be taken up through one’s diet because the body doesn’t have the enzymatic machinery to produce these amino acids
Non-essential: Made within the body
Examples of Non-essential amino acids
Glycine, proline
Essential Amino Acids Mnemonic
PVT - Phenylalanine, valine, threonine
TIM - Tryptophan, isoleucine, methionine
HALL - Histidine, arginine, leucine, lysine
Example of a conditionally essential amino acid
Arginine
What amino acids can be converted into both glucose and ketone bodies (glucogenic and ketogenic)?
IPTTT - isoleucine, phenylalanine, tyrosine, tryptophan, threonine
What amino acids can only be converted into ketone bodies (exclusively ketogenic)?
LL - leucine, lysine
What are the building blocks of peptides; joined by the peptide bonds?
Amino acids
What structure is the basic linear sequence of amino acids?
Primary
What structure is composed of the alpha helices, beta-plated sheets?
Secondary
What structure is composed of folds and domains, makes up a 3D conformation?
Tertiary
What are long sequence of amino acids joined together, interchangeable with the term protein?
Polypeptide
The sequence of amino acids in a polypeptide has directionality which starts from ______ and ends at _________?
N-terminus (amino terminus) and C-terminus (carboxyl terminus)
Tertiary structure is not just a helix or a sheet, they can fold over each other. True or False?
TRUE
What structure is applicable to proteins with multiple subunits/chains/polypeptide?
Quaternary structure
What connects each amino acid?
Peptide bond
In the secondary structure, the beta pleated sheets have linear arrangement of amino acids that are antiparallel to each other. True or False?
TRUE
Most of the plasma proteins dissolved in blood assumes what shape?
Tertiary structure
______ look like they are twisted into a coil when imagined in a 3D conformation
Alpha-helices / alpha helix
Arrangement wherein each of the amino acid side chains are arranged side by side.
Beta-pleated sheets
Which bonds stabilize the primary structure of amino acids?
Peptide bonds
Which bonds stabilize the secondary structure of amino acids?
Hydrogen bonds
________ are an expanded form of the alpha-helices where there is more complex arrangements of the alpha-helices and beta-pleated sheets
Supersecondary Structures
What are the different alpha helix motifs?
Helix-turn-helix (HTH)
Helix-loop=helix (HLH)
Coiled-coil
What causes the Helix-turn-helix (HTH) to have a turn/kink/bend?
The presence of proline residue
Explain why proline causes a kink/bend in the polypeptide structure.
Proline’s side chain continues onto the amino group
Differentiate Greek key from β-barrel.
Greek key: formed when a polypeptide chain doubles back on itself
β-barrel: formed when β-sheets are extensive enough to fold back on itself
In a β-α-β motif, two linear strands of β-sheets are connected by a stretch of an alpha-helix. True or False?
FALSE
Important structure that interacts with DNA and makes transcription an optimal process
Zinc finger
What is the difference of a hydrogen bond in the tertiary structure than that of in the secondary structure?
The hydrogen bonds form between the side chains instead of between the amino groups
Ionic bonds occur between two amino acids with identical charges. True or False?
FALSE
Give an example of an acidic amino acid.
Aspartate
Glutamate
Give an example of a basic amino acid
Histidine
Lysine
Arginine
Ionic bonds are also called _______ because of the similarity in how this is made.
Salt bridge
Disulfide bonds are formed between two _____ groups.
Sulfhydryl
A special type of interaction that is applicable for nonpolar amino acids.
Hydrophobic Interaction
The Van der Waals forces are the weakest forces or interactions but they also contribute to the stability of the proteins. True or False?
TRUE
What are the two (2) prototypical structures formed from the interaction of different amino acids?
Fibrous Proteins
Globular Proteins (globins)
This structure is present in proteins made up of 2 or more polypeptide chains.
Quaternary Structure
How many linear proteins or peptide chains is collagen composed of?
3
Collagen is an example of a _____ protein
Fibrous
Enumerate and differentiate the two (2) important components of collagen.
Glycine - smallest amino acid, creates folds to allow triple helix structure
Lysine - relatively long, forms cross-links which strengthen the 3 chains of collagen
Hemoglobin is an example of a ______ protein
Globular / globin
What are the four (4) globular subunits of hemoglobin?
2 β-chains and 2 α-chains
What happens to a protein when its primary structure is altered?
the protein becomes dysfunctional
What is an example of a primary structure alteration due to a point mutation?
Sickle Cell Anemia, where glutamate is replaced by valine
How does deletion or insertion mutations affect protein structure?
They create shorter or longer proteins.
What is a silent mutation, and how does it affect the protein?*
A silent mutation changes the primary structure but does not significantly affect the protein’s function.
What are the main components of a protein’s secondary structure?
Alpha helices and beta-pleated sheets.
What is a prion disease, and how does it affect protein structure?
Prion diseases are protein conformation diseases where normal alpha-helices are replaced by abnormal beta-pleated sheets, leading to aggregate formation in neurons.
How does altering the tertiary structure of a protein affect its function?
It can lead to misfolding of the protein, disrupting its function or structural integrity.
Differentiate between denaturation and misfolding of proteins at the tertiary level.
Denaturation results from the destruction of peptide bonds at the primary level, while misfolding involves disruption of interactions at the tertiary level without breaking peptide bonds.
What are the potential consequences of protein misfolding in neurons?
Accumulation of misfolded proteins can lead to cell injury, cell death, and neurological decline.
What is the consequence of disrupting the quaternary structure of a protein?
It can lead to a loss of function of that protein.
Which condition results from a dietary deficiency of vitamin C affecting collagen synthesis?
Scurvy, which undermines the conformational stability of collagen fibers
What makes proteins crucial for acid-base balance?
Structure: carboxyl groups (COOH/COO-) and amino groups (NH3+/NH2)
List the acidic and basic amino acids
Acidic: Aspartate & Glutamate | Basic: Histidine, Arginine, & Glutamate
Differentiate protonation and deprotonation
Protonation - donate or release protons ; Deprotonation - bind or accept protons
T or F. Acidic environment has no hydrogen ions.
F. “As the environment gets more alkaline = less and less H+ ions.”
What kind of environment/medium does deprotonation mostly occur?
relatively Alkaline environments/mediums
Primary buffer of blood pH
Histidine
At pH 7, the side chains of _____ are _% protonated and _% not protonated.
Histidine, 9, 91
Needed pKa of the primary buffer of blood pH to stay in its middle state
6
Plasma protein that can also buffer blood pH
Albumin
Characteristics of albumin that makes it suitable as blood pH buffer
High molecular weight = abundant amino acid residues participating in the protonation and deprotonation processes
What role do compounds containing O or N play in proteins?
Serve as hydrogen bond donors and/or acceptors
How does a change in pH affect proteins?
Alter hydrogen bonding, leading to structural and functional changes
The process of _______ and ________ alter hydrogen ions present in the functional groups of amino acids.
Protonation, deprotonation
Which functional groups in amino acids are affected by changes in pH through protonation and deprotonation?
Carboxylic group and amino group
What happens when proteins release or bind H ions?
Disruption of hydrogen bonds, forming new bonds and disrupting old ones
The disruption of hydrogen bonds in proteins can lead to a loss of __________.
Function
In the context of pH changes, proteins that are not designed to buffer may lead to __________ in tissues.
Dysfunction
What are the two types of protein structures affected by pH changes?
Secondary and tertiary structures
Disruption of hydrogen bonds in response to _____ can lead to protein structural changes.
Acidosis/Alkalosis
In critically ill patients, progressive protein dysfunction can lead to __________.
Multiple organ failure.
Patients who suffer from heart attack or severe blood loss, have tissues generating plenty of _______ due to lack of oxygen to be used.
Lactic acid
What changes occur in heart proteins during acidosis?
Proteins become protonated, disrupting their structure
What are the functional consequences of protein disruption in the heart due to acidosis?
Loss of contractility, impaired enzyme function, and misfolded receptors lead to compromised cell-to-cell communication
How does acidosis contribute to the weakening of the heart?
Disrupted protein function results in decreased contractility and overall heart function
Changes in pH can cause proteins in white blood cells to become __________, impairing immune response.
Sub-optimal
Besides pH, what other factors can alter the molecular structure of biological systems?
Temperature and other environmental parameters
What is the outcome of significant pH changes?
Loss of homeostasis, leading to multiple organ failure and potential death
What complications are seen during multiple organ failure?
Septic shock, severe shock, trauma, infections, stage 4 cancer, major surgery, and significant blood loss
What is the cumulative effect of the small changes caused by the fluctuation of a patient’s blood?
“Dying from a thousand cuts,” eventual death
Provide the three amino acids that are highly active in metabolism.
(ADE) Alanine, Aspartate, Glutamate
What is the prototypical glucogenic amino acid?
(A) Alanine
Amino acid that forms part of the building blocks of purine and pyrimidine molecules, as well as a precursor of heme.
(G) Glycine
