Biochemistry | Cell Biology, Proteins, Enzymes

A set of flashcards reviewing Cell Biology, Protein Structure, Amino Acids, and Enzyme Kinetics based on Module 2 Pharmaceutical Biochemistry lecture notes.

Biochemistry

The study of the chemistry of life.

Cell Theory Rule 1

The cell is the most basic unit of life.

Cell Theory Rule 2

All living things are made up of cells.

Cell Theory Rule 3

Cells can only arise from previously living cells.

Prokaryotic Cell

A type of cell with no well-defined nucleus, such as bacteria.

Cytosol

The area where nucleic acids float in prokaryotic cells; also the fluid contained within the cytoplasm.

Eukaryotic Cell

A type of cell characterized by a well-defined nucleus.

Cytoplasm

Defined as "Everything Inside," it is the area between the nuclear and cell membranes containing cytosol and organelles.

Ribosomes

Organelles responsible for protein synthesis; they contain specific subunits.

Endoplasmic reticulum (E.R.)

An organelle that bridges the nuclear and plasma membranes, spanning from the middle to the outside of the cell.

Smooth E.R.

Responsible for the production/modification of lipids and membrane assembly.

Rough E.R.

Responsible for much of protein modification; appears rough due to the presence of ribosomes.

Mitochondrion

The "powerhouse" of the cell; contains enzymes for catabolism of biomolecules and production of $ATP$.

ATP

The usable energy produced by the mitochondrion.

Golgi apparatus

The "packaging counter"; secretes, modifies, and delivers products throughout and outside the cell.

Vacuoles

Organelles that store water and waste materials; they grow larger as plant cells age.

Microbodies

Small globe-shaped or globular organelles that contain a high concentration of enzymes.

Peroxisomes

A type of microbody that breaks down $H_2O_2$ into water and oxygen.

Lysosomes

Known as "suicidal sacs"; responsible for the elimination of unwanted waste using enzymes.

Cytoskeleton

A network of fibers that solidify the cell's framework, compared to the steel frames of a house.

Microfilaments

The smallest components of the cytoskeleton; the main reason for the cell's shape.

Intermediate filaments

Slightly wider fibers that strengthen the hold of the cytoskeleton.

Microtubules

Components made of tubulin proteins that provide motility for substances and structure (e.g., cilia and flagella).

Tubulin

The protein that makes up microtubules.

Cilia

Shorter, numerous hair-like structures responsible for cell movement.

Flagella

Longer, fewer structures responsible for the cell's movement or locomotion.

Nucleus

The center of genetic activity that contains the nucleic acids.

Cell Membrane

A semi-permeable phospholipid bilayer made of polar (hydrophilic) heads and nonpolar (hydrophobic) tails.

Hydrophilic head

The polar component of the cell membrane phospholipid bilayer.

Hydrophobic tail

The nonpolar component of the cell membrane phospholipid bilayer.

Cell Wall

An extra layer of protection beyond the cell membrane, absent in animals.

Cellulose

The material that makes up the cell wall in plants.

Chitin

The material that makes up the cell wall in fungi.

Peptidoglycan

The compound composed of various sugars found in bacterial cell walls.

Cell Cycle G1 Phase

The Gap phase instantly after cell division where a newly created cell produces organelles.

Cell Cycle S Phase

The Synthesis phase where DNA is synthesized to ensure new cells contain all previous genes.

Cell Cycle G2 Phase

The phase wherein the cell prepares for cellular division.

Interphase

The collective term for the G1, S, and G2 phases of the cell cycle.

M Phase

The Mitotic phase, which is the actual process of cell division.

Prophase

The first phase of mitosis where chromatins compress into chromosomes and the nuclear wall disappears.

Chromatin

Thread-like nucleic acids/genetic material seen during interphase.

Chromosomes

X-shaped structures formed when genetic material (chromatin) gets thicker during prophase.

Spindle fibers

String-like structures made of microtubules that attach to chromosomes during mitosis.

Metaphase

The phase where chromosomes align horizontally at the middle of the cell.

Metaphase plate

The center part of the cell where chromosomes line up during metaphase.

Anaphase

The phase where spindle fibers pull chromosomes apart toward the spindle poles.

Telophase

The reverse of prophase where chromosomes thin, spindle fibers disappear, and nuclear walls reappear.

Cleavage furrow

A dent formed between two dividing animal cells during telophase.

Cytokinesis

The total separation of the cell membrane resulting in two new cells.

Daughter cells

The final products of the cell cycle and cytokinesis.

Molecular Biology

Identified as Level 3 in the study of cells, focusing on the molecular level.

Biochemistry Focus

The study of the structure, function, and metabolism of biomolecules.

Proteins

One of the four primary biomolecules; polymers of amino acids.

Carbohydrates

One of the four primary biomolecules studied in biochemistry.

Lipids

One of the four primary biomolecules involved in membrane assembly.

Nucleic acids

Biomolecules contained within the nucleus, acting as the center of genetic activity.

Metabolism

The cycle of creation and breakdown of biomolecules.

Amino Acid Structure

Contains an amino functional group ($NH_2$) and a carboxylic acid group ($COOH$).

Proteinogenic amino acids

The 20 standard amino acids that are the building blocks of proteins.

Chiral

A property of a carbon atom that has 4 different substituents, giving rise to D and L isomers.

L-isomer

The common isomer of amino acids where the amino group is at the left.

D-isomer

The isomer of an amino acid where the amino group is at the right.

Amphoteric

A property of amino acids meaning they can act as both an acid and a base.

Bronsted-Lowry Acid

A proton donor, such as the $COOH$ group in an amino acid.

Bronsted-Lowry Base

A proton acceptor, such as the $NH_2$ group in an amino acid.

Zwitterion

The state of an amino acid when both the amino and carboxyl groups are charged, cancelling out to a net charge of 0.

Isoelectric pH ($pI$)

The specific pH where all amino acid molecules are zwitterionic.

Essential amino acids

Amino acids that cannot be synthesized by the human body; mnemonic: PVT TIM HALL.

Glucogenic amino acids

Amino acids that can be converted into glucose.

Ketogenic amino acids

Amino acids that can be converted into ketone bodies; includes Leucine and Lysine.

Nonpolar amino acids

Amino acids that are usually water-insoluble (hydrophobic) and consist mostly of carbon and hydrogen.

Glycine

The simplest nonpolar amino acid where the R group is $H$; it is not chiral.

Alanine

A nonpolar amino acid with a methyl R group.

Valine

A branched chain nonpolar amino acid whose skeletal structure looks like a "V".

Leucine

A branched chain nonpolar amino acid consisting of 4 carbons in the R group; it is ketogenic.

Isoleucine

A branched chain nonpolar amino acid; an isomer of Leucine abbreviated as "Ile".

Proline

The only secondary amino acid; formerly known as an "imino acid".

Phenylalanine

An aromatic nonpolar amino acid made of a phenyl group and alanine; abbreviated as "F".

Methionine

A nonpolar sulfur-containing amino acid with a thioether functional group ($R-S-R$).

Thioether

The specific functional group ($R-S-R$) found in Methionine.

Tryptophan

An aromatic nonpolar amino acid containing an indole ring; abbreviated as "W".

Indole ring

A 6,5 heterobicyclic ring system found in Tryptophan.

Polar amino acids

Amino acids that usually contain Hydroxyl ($OH$), Thiol ($SH$), or Amide groups.

Serine

A polar hydroxyl-containing amino acid; it has fewer carbons than Threonine.

Cysteine

A polar sulfur-containing amino acid with a thiol ($SH$) group.

Thiol

The functional group ($SH$) found in Cysteine.

Disulfide bond

A bond formed by the dehydrogenation or oxidation of two thiols ($-SH + HS- \rightarrow -S-S-$).

Hydrogenation

The reduction reaction involving the addition of Hydrogen to a disulfide bond to reform thiols.

Dehydrogenation

The oxidation reaction involving the removal of Hydrogen to form a disulfide bond.

Threonine

A polar hydroxyl-containing amino acid that has more carbons than Serine.

Asparagine

A polar amide-containing amino acid abbreviated as "N"; has one carbon less than Glutamine.

Glutamine

A polar amide-containing amino acid abbreviated as "Q".

Tyrosine

An aromatic polar amino acid containing a phenol; abbreviated as "Y".

Phenolic amino acid

Refers specifically to Tyrosine.

Acidic amino acids

Amino acids containing two carboxyl groups ($COOH$), allowing a possible charge of $-2$.

Aspartate

An acidic amino acid synonymous with aspartic acid; abbreviated as "D".

Glutamate

An acidic amino acid synonymous with glutamic acid; abbreviated as "E".

Basic amino acids

Amino acids whose identity is determined by the presence of nitrogen; can have a $+2$ charge.

Lysine

A basic amino acid with an R group containing 4 carbons and an amino group; abbreviated as "K"; it is ketogenic.

Histidine

A basic amino acid containing an imidazole ring; abbreviated as "H".