Exam 1: Biochemistry, Cell Biology, Amino Acids, & Peptide Bonds

What is biochemistry?

Biochemistry is the chemistry of life, applying chemistry to study biological processes at the cellular and molecular level.

What does the Central Dogma describe?

The Central Dogma describes the transfer of biological information from DNA to RNA to protein.

What is the process of converting DNA to RNA called?

Transcription

What is the process of converting RNA to protein called?

Translation

Why is biochemistry important?

Biochemistry explores the molecular mechanisms that underpin life, uniting all living beings through common biochemical principles.

What are the essential atoms for human life?

Oxygen, hydrogen, and carbon make up 98% of the atoms in any organism.

What are the building blocks of proteins?

Amino acids

How many naturally occurring amino acids are there in the human body?

20

What roles do proteins play in living organisms?

Proteins act as signal molecules, enzymes, structural components, and are essential for DNA replication and immune response.

What are nucleic acids made of?

Nucleic acids are made of nucleotides, which consist of a pentose sugar, a phosphate group, and a nitrogenous base.

What are the two types of nucleic acids?

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

What is the structure of DNA?

DNA consists of a double helix made up of deoxyribose, phosphate, and four bases: A, G, C, and T.

What is the structure of RNA?

RNA is a single-stranded polymer made up of ribose, phosphate, and the bases A, G, C, and U.

What are lipids?

Lipids are amphiphilic molecules that serve as storage forms of fuel and form barriers (membranes) in cells.

What is the primary function of carbohydrates?

Carbohydrates serve as an important fuel source for living organisms.

What is glycogen?

Glycogen is a storage form of glucose in animals.

What is the main difference between eukaryotic and prokaryotic cells?

Eukaryotic cells have membrane-enclosed compartments, while prokaryotic cells do not.

What is the function of the plasma membrane?

The plasma membrane separates the inside of the cell from the outside and regulates the transport of biomolecules.

What is the role of mitochondria in eukaryotic cells?

Mitochondria are the primary site of ATP generation.

What is the function of the nucleus?

The nucleus serves as the information center of the cell.

What is the function of lysosomes?

Lysosomes contain digestive enzymes that can digest material brought into the cell.

What is exocytosis?

Exocytosis is the process of transporting biomolecules out of the cell via secretory vesicles.

What is endocytosis?

Endocytosis is the process of bringing biomolecules into the cell by invagination of the plasma membrane.

What is the significance of weak interactions in biochemical processes?

Weak interactions are crucial for enzyme catalysis, insulin signaling, and DNA polymerization.

What are the three types of chemical bonds?

Ionic bonds, covalent bonds, and metallic bonds.

What is the most important component of biological systems?

Water, which makes up approximately 65% of the human body and 70% of cells.

What percentage of the human body is composed of water?

Approximately 65%

What role does water play in biochemical interactions?

Water acts as a medium, source, and carrier for biochemical interactions.

What type of bond is primarily found in water?

Covalent bonds between hydrogen and oxygen atoms.

What is the significance of water being a polar molecule?

It means that charge is not equally distributed, with oxygen carrying a slight negative charge and hydrogen carrying slight positive charges.

What is a hydrogen bond?

An interaction between a partial negative charge of oxygen in water and a partial positive charge of hydrogen in another molecule.

How does water affect ionic and hydrogen bonds?

Water weakens ionic and hydrogen bonds.

What is the hydrophobic effect?

The tendency of nonpolar molecules to cluster together in water, driven by an increase in the entropy of water.

What are the four fundamental non-covalent bonds?

Ionic bonds, hydrogen bonds, van der Waals forces, and electrostatic interactions.

What is the role of entropy in the clustering of hydrophobic molecules?

Entropy measures randomness; clustering of hydrophobic molecules releases water molecules, increasing entropy.

What is the pH a measure of?

The concentration of hydrogen ions (H+) in a solution.

What is the ion product of water (Kw)?

The mathematical product of the concentrations of hydrogen ions and hydroxide ions in water.

What defines an acid in terms of proton donation?

An acid is a proton donor, while a base is a proton acceptor.

What is the Henderson-Hasselbalch equation used for?

It relates the pH of a solution to the acid dissociation constant (Ka) and the ratio of concentrations of the conjugate base and acid.

What is the significance of buffers in biological systems?

Buffers help maintain stable pH levels in biological systems, such as blood.

What are proteins made from?

Proteins are polymers made from 20 different amino acids.

What are the two functional groups present in amino acids?

An ammonium group (—NH3+) and a carboxylate group (—COO−).

What is the role of hemoglobin and myoglobin?

They transport oxygen in the blood.

What is the significance of the L isomers of amino acids?

Only L isomers are found in proteins.

What happens to weak acids in solution?

Weak acids ionize to form a proton and a conjugate base.

What does a larger Ka value indicate?

A stronger acid.

What is the relationship between pH and pKa?

At pH > pKa, the conjugate base predominates; at pH < pKa, the acid predominates.

What is the role of water in disrupting hydrogen bonds?

Water competes for hydrogen-bonding capability, disrupting existing hydrogen bonds.

What are van der Waals forces?

Weak interactions between molecules that are neither polar nor charged.

What is the contact distance in van der Waals interactions?

The energy is most favorable at the van der Waals contact distance, where electron repulsion is minimized.

What is the impact of water on biological systems?

Water is crucial for biochemical reactions and influences the structure and function of biomolecules.

What is the significance of the polar nature of water?

It allows water to dissolve many important biochemicals and facilitates biochemical reactions.

How do non-polar molecules behave in water?

Non-polar molecules tend to associate with each other and are excluded from water.

What are amino acids?

Molecular building blocks of proteins with a central carbon atom bonded to an ammonium group, a carboxylate group, a hydrogen atom, and an R group.

What is the significance of L isomers in amino acids?

Only L isomers are found in proteins.

What are the two stereoisomer forms of amino acids?

D and L stereoisomers, which are mirror images of each other.

What is the isoelectric point (pI) of an amino acid?

The pH at which the charged groups on an amino acid are balanced and the amino acid is neutral.

What happens to an amino acid in a solution more acidic than its pI?

It exists as a positive ion.

What happens to an amino acid in a solution more basic than its pI?

It exists as a negative ion.

What is a zwitterion?

A neutral amino acid at its isoelectric point with both positive and negative charges.

How are amino acids classified based on their R groups?

Nonpolar (hydrophobic), polar neutral, polar acidic, and polar basic amino acids.

What characterizes nonpolar amino acids?

They have hydrogen, alkyl, or aromatic R groups and are hydrophobic.

What is the simplest amino acid?

Glycine, which has a hydrogen atom in place of an R group.

What are polar neutral amino acids?

Amino acids with R groups that contain hydroxyl, thiol, or amide groups.

What is unique about cysteine among amino acids?

It can form disulfide bonds that are important for protein stability.

What defines positively charged amino acids?

They have R groups that contain an amino group or guanidinium group, resulting in a positive charge at neutral pH.

What are the two negatively charged amino acids?

Aspartic acid and glutamic acid, which have acidic side chains typically negatively charged.

How many amino acids are considered nonessential?

11 amino acids can be synthesized in the body.

What are essential amino acids?

9 amino acids that must be obtained from the diet.

What is the primary structure of proteins?

The sequence of amino acids in a polypeptide chain.

What is the secondary structure of proteins?

Repeating structures formed by hydrogen bonds, such as alpha helices and beta sheets.

What is the tertiary structure of proteins?

The spatial arrangement of amino acid residues and disulfide bonds in a polypeptide.

What is the quaternary structure of proteins?

The arrangement of multiple polypeptide chains into a functional protein.

What is the directionality of peptides?

Peptides have a direction from N-terminal (ammonium group) to C-terminal (carboxylate group).

What forms a peptide bond?

An amide bond formed when the carboxylate group of one amino acid reacts with the ammonium group of another.

What are dipeptides, tripeptides, and tetrapeptides?

Dipeptides consist of two amino acids, tripeptides of three, and tetrapeptides of four amino acids.

What are polypeptides?

Long chains of amino acids formed by peptide bonds.

What is the role of histidine in proteins?

It contains an imidazole group that can be positively charged and is often found in enzyme active sites.

What is the pKa of histidine?

Approximately 6, allowing it to be uncharged or positively charged near neutral pH.

What happens to amino acids at low pH?

Both amines and carboxylic acids are protonated.

What happens to amino acids at high pH?

Both amines and carboxylic acids are deprotonated.

What is the significance of the R group in amino acids?

The R group determines the properties and classification of the amino acid.