Cell and Molecular Biology Exam 1

7 Most Important Functional Groups for Life

hydroxyl, carbonyl, carboxyl, sulfhydryl, amino, phosphate, and methy, can replace hydrogen atoms attached to skeletons of organic molecules

Acetyl CoA

activated carrier that donates the carbon atoms in its readily transferable acetyl group to many metabolic reactions, including the citric acid cycle and fatty acid biosynthesis; the acetyl group is linked to the coenzyme A (CoA) by a thioester bond that releases a large amount of energy when hydrolyzed

Acid

A molecule that releases a proton when dissolved in water; this dissociation generates hydronium ions, thereby lowering the pH

Acidic Side Chains

Aspartic Acid and Glutamic Acid, within cells, side chains will have negative charges and be able to form ionic bonds with basic amino acid residues and other ionized molecules. They enhance the water solubility of the polypeptide as they are able to interact with the positive dipoles of water and other molecules, can be phosphorylated

Activated Carrier

a small molecule that stores energy or chemical groups in a form that can be donated to many different metabolic reactions, such as ATP, acetyl CoA, and NADH

Activation Energy

the energy that must be acquired by a molecule to undergo a chemical reaction

Active Site

region on the surface of an enzyme that binds to a substrate molecule and catalyzes its chemical transformation

Active Site

the region on the enzyme where the substrate binds

Adipose cells and tissue

humans and other mammals store their fat in adipose cells, adipose tissue also cushions vital organs and insulates the body

ADP

nucleoside diphosphate produced by hydrolysis of the terminal phosphate of ATP

Allosteric Inhibitors

bind to a region other than the active site (an allosteric site), they do not block the association of substrate with the active site, and they cause the enzyme to change shape to a less than optimal conformation

Allosteric

describes a protein that can exist in multiple conformations depending on the binding of a molecule (ligand) at a site other than the catalytic site, such changes from one conformation to another often alter the protein's activity or ligand affinity

Alpha glucose

polymers are helical

Alpha Helices

Many membrane-bound proteins cross the lipid bilayer as an alpha helix, which is the dominant pattern for membrane-bound enzymes and receptor proteins, in which a single polypeptide chain twists around itself to form a rigid cylinder stabilized by hydrogen bonds between every fourth amino acid, intertwined alpha helixes can form a stiff coiled-coil

Amino acid naming in a polypeptide chain

amino acid residues

Amino Acid Sequence

the order of the amino acid subunits in a protein chain, sometimes called the primary structure of a protein

Amino Acid

small organic molecule containing both an amino group and a carboxyl group; it serves as the building block of proteins

Amino

(-NH2, -NH3+)

Amphiphilic

possessing both hydrophilic and hydrophobic properties or sides

Amylase

enzyme that digests starch by hydrolyzing alpha linkages, cannot hydrolyze beta linkages in cellulose. To break b linkages, an organism would need to express a cellulase like cellobiase (animals do not express cellulases)

Amylopectin

a branched form of plant starch

Amylose

simplest form of starch

Anabolic Pathways

those that consume energy to build smaller molecules into larger ones and establish order (decrease entropy) within the living organism

Anabolism

set of metabolic pathways by which large molecules are made from smaller ones

Animal relationship with microbes that aid in cellulose digestion

symbiotic

Anion

a negatively charged ion

Antibody

protein produced by B lymphocytes in response to a foreign molecule or invading organism, binds to the foreign molecule or cell extremely tightly, thereby inactivating it or marking it for destruction

Antigen

molecule or fragment of a molecule that is recognized by an antibody

Apoenzyme

an enzyme on its own, without cofactors present, and inactive

Aqueous Solution

one in which water is the solvent, concentration of solutes is critical for chemical reactions because higher concentration means more collisions

Archaeon

Microscopic organism that is a member of one of the two divisions of prokaryotes; often found in hostile environments such as hot springs or brine

Artificial Intelligence

has become a major force in the world of bioinformatics, reducing compute times by several orders of magnitude in many cases

Asparagine and Glutamine

Polar side chains, similar to aspartate and glutamate (missing the -OH groups)

Atom

the smallest particle of an element that still retains its distinctive chemical properties

Atomic Force Microscope

drags a nano-scale probe across the surface of a specimen, detects bumps, valleys

ATP Composition

composed ribose (sugar), adenine (a nitrogenous base), and three phosphate groups

ATP

activated carrier that serves as the principal carrier of energy in cells; a nucleoside triphosphate composed of adenine, ribose, and 3 phosphate groups

Avogadro's Number

the number of molecules in a mole, the quantity of a substance equal to its molecular weight in grams

Bacillus

type of shape bacteria and archaea can adapt

Bacterium

Microscopic organism that is a member of one of the two divisions of prokaryotes; some species cause disease

Base

any substance that reduces the H+ concentration of a solution, molecule that accepts a proton when dissolved in water

Basic Side Chains

Lysine, Arginine, and Histidine, can form ionic bonds and dipole interactions, enhance water solubility, can be phosphorylated, positive charges

Beta glucose

polymers are straight

Beta Sheet

folding pattern found in many proteins in which neighboring regions of the polypeptide chain associate side-by-side with each other through hydrogen bonds to give a rigid, flattened structure, form rigid structures at the core of many proteins, antiparallel Beta sheets are most common, but parallel beta sheets are also present, and can stack to form an amyloid structure that resembles the type of insoluble aggregates observed in the neurons of individuals with different neurodegenerative diseases

Bilayer

the assembly that phospholipids take on when they are added to water with the hydrophobic tails pointing toward the interior, phospholipid bilayers are found in cell membranes

Binding Site

region on the surface of a protein, typically a cavity or groove, that interacts with another molecule(a ligand) through the formation of multiple noncovalent bonds

Bioinformatics

uses a computational approach to predict protein structure from amino acid sequences; this process is complex and requires significant computing power

Biomolecular Condensate

A large aggregate of phase-separated macromolecules that creates a region with a special biochemistry without the use of an encapsulating membrane

Biosynthesis

an enzyme-catalyzed process by which complex molecules are formed from simpler substances by living cells

Bright-Field Microscopes

series of lenses for magnification, light passes through the specimen into the objective lens

Buffer

mixture of weak acids and bases that maintains the pH of a solution by releasing and taking up protons

C-Terminus

the end of a polypeptide chain that carries a free carboxyl group

Capsule/ Slime Layer

adds protection, adhesion

Carbohydrate

simple sugars and polymers of sugars, serve mainly as fuel and building material

Carbonyl

(-COH, -CO-)

Carboxyl

(-COOH, --COO)

Catabolic Pathways

those that break down molecules to release energy and produce intermediate metabolites (smaller molecules that can be used to build up larger ones), release energy in a series of reactions, one reaction driving the next reaction

Catabolism

set of enzyme-catalyzed reactions by which complex molecules degraded to simpler ones with release of energy; intermediates in these reactions are sometimes called catabolites

Catalyst

substance that accelerates a chemical reaction by lowering the activation energy, enzymes perform this role in cells

Cation

a positively charged ion

Cell Respiration

process by which cells harvest the energy stored in food molecules; usually accompanied by the uptake of O2 and the release of CO2

Cell Theory

At a minimum, cells consist of a membrane and the contents therein, all organisms are composed of 1 or more cells, cells are the basic living units of function and organization, and all cells come from other cells

Cell Wall

tough structural reinforcement

Cell

The basic unit from which a living organism is made; an aqueous solution of chemicals enclosed by a membrane; has an ability to self-replicate

Cellular PrP

the healthy conformation; its functional domain is composed of alpha helices

Cellulose

A structural polysaccharide, major component of the cell walls of plant, differs from starch by the glycosidic linkages

Centrosomes

are the organizing centers of microtubules, important for mitosis

Change in Free Energy During a Process Related to Enthalpy and Entropy

Delta G = DeltaH - TDeltaS

Chaperones

helper proteins which are often needed to aid in proper folding of a polypeptides it's extruded from a ribosome; will prevent misfolding and ferry the polypeptide to the chaperonin

Chaperonin

a complex structure that will accept a newly synthesized polypeptide into an inner chamber; will change shape, contorting the polypeptide within, giving it a new stable conformation

Chemical Bond

an attraction that holds two atoms together

Chemical Group

a combination of atoms with distinct chemical and physical properties that influence the behavior of the molecule in which it resides

Chitin

another structural polysaccharide, is found in the exoskeleton of arthropods, also provides structural support for the cell walls of many fungi, unlike cellulose, animals can digest it, though very slowly

Chloroplast

Specialized organelle in algae and plants that contains chlorophyll and serves as the site for photosynthesis

Cholesterol

an important steroid, is a component in animal cell membranes, increases fluidity in cold environments and increases viscosity in hot environments, although essential to animals, high levels in the blood may contribute to cardiovascular disease

Chromatography

technique used to separate the individual molecules in a complex mixture on the basis of their size, charge, or their ability to bind to a particular chemical group. In a common form of the technique, the mixture is run through a column filled with a material that binds the desired molecule, and it is the eluted from the column with a solvent gradient

Chromosome

Long, threadlike structure composed of DNA and proteins that carries the genetic information of an organism; becomes visible as distinct entity when a plant or animal cell prepares to divide

Cilia

are found on many cell types, used to move mucus/secretions normally

Cis-Trans Isomers

have the same covalent bonds but differ in spatial arrangments

Coenzyme

Organic cofactors, small molecule that binds tightly to an enzyme and helps it to catalyze a reaction

Cofactors

like ions and other organic compounds (coenzymes) that most enzymes require to function, non-protein enzyme helpers

Coiled-Coil

stable, rodlike protein structure formed when two or more alpha helices twist repeatedly around each other

Colloid

a stable suspension of fine particles in a liquid

Common Traits in Eukaryotes

one nucleus, complex cytoskeleton, mitochondria, plastids in photosynthesizers (chloroplasts)

Competitive Inhibitors

molecules that bind to the active site of an enzyme, competing with the substrate, but if substrate concentration increases, it can outcompete the inhibitor, and the enzyme's maximal function will be restored

Complementary Base Pairs

A pairs with T using 2 hydrogen bonds, G pairs with C using 3 hydrogen bonds, or A pairs with U using 2 hydrogen bonds

Condensation Reaction

chemical reaction in which a covalent bond is formed between two molecules as water is expelled; used to bind polymers, such as proteins, polyssacharides, and nucleic acids

Confocal Fluorescence Microscopes

use fluorescent dyes and lasers to image a single plane, emitted light passes through a pinhole aperture, increasing resolution, computer constructs a 3-D image from multiple images capturing different planes of the specimen (z-stack)

Conformation

precise, three-dimensional shape of a protein or other macromolecule, based on the spatial location of its atoms in relation to one another

Contractile/Motor Proteins

movement, i.e. motor proteins are responsible for the undulations of cilia and flagella, actin and myosin proteins are responsible for the contraction of muscles, protein such as myosin or kinesin that uses energy derived from the hydrolysis of a tightly bound ATP molecule to propel itself along a protein filament or other polymeric molecule

Cooperativity

can amplify enzyme activity- once a substrate binds to one subunit, the other subunits can bind substrate more readily

Coupled Reaction

linked pair of chemical reactions in which free energy released by one reaction serves to drive the other reaction

Covalent Bonds

sharing of a pair of valence electrons by two atoms, atoms must remain close together in order for their valence shells to remain complete, strong and unaffected by the presence of water

Cryo-Electron Microscopy (cryoEM)

technique for observing the detailed structure of a macromolecule at very low temperatures after freezing native biological structures in ice

Cysteine

Polar side chains, contains a thiol group (-SH) and can form disulfide bridges (covalent bonds) with the thiol groups of other cysteine residues

Cytoplasm

Contents of a cell that are contained within its plasma membrane but, in the case of eukaryotic cells, outside the nucleus

Cytoskeleton

System of protein filaments in the cytoplasm eukaryotic cell that gives the cell shape and the capacity for directed movement; its most abundant components are actin filaments, microtubules, and intermediate filaments, anchors organelles, maintains cell structure, dynamically changes the shape of the cell, acts as transport lines for vesicles

Cytosol

Contents of the main compartment of the cytoplasm, excluding membrane-enclosed organelles such as the endoplasmic reticulum and mitochondria

Daltons

6.02 x 10^23 Da = 1 g, 1 Da is the mass of a proton or neutron

Dangers of Enantiomers

important for drug development, Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules, Usually only one drug enantiomer is considered so-called "biologically active" (meaning that this isomer was designed to have a desired effect on an organism), but both enantiomers will affect an organism in some manner, for example thalidomide