cell biology one

protein

function to provide chemical, mechanical, and transport types of work (the main labor force of the cell)

What product of the cell will give the cell its unique appearance, behavior, and function?

proteins

How many amino acids are there?

twenty

genome

all of the DNA that makes up a cell

What contains the entire program/genetic blueprint for a cell and the whole organism?

genome

cellular differentiation

process where the DNA directs growth, development, and specificity of the cell thru

model organism/system

typically a non-human species (or even non-living, like that of a computer or AI

macromolecules

large molecules (polymers) comprised of smaller building block molecules (monomers)

What do non-covalent bonds provide in polymers?

structure, such as the helical structure of proteins (weaker)

What do covalent bonds provide in polymers?

hold the strands together like glue (stronger)

Many proteins function by…

interacting with other proteins and molecules.

Interactions occur by…

one protein recognizing and binding to another.

enzymes

proteins (sometimes RNA molecules) that increase chemical reactivity by acting as catalyst; accelerate and regulate chemical reactions

metabolism

the sum of all chemical reactions needed to survive, grow, and reproduce (i.e. life)

activation energy

the small amount of energy needed to begin a reaction

An increase in ___________ can provide the activation energy needed to accelerate a reaction, but an enzyme.

temperature

What do enzymes provide for reactions?

a microenvironment that is energetically favorable by lowering the activation energy barrier

What do substrates do?

binds to an enzyme, then enzyme catalyzes the conversion of the substrate to a product(s)

active site

specific location on enzyme where substrate(s) will interact with it (bind to)

Is there a limit to how fast a reaction can occur?

yes

The rate that a specific number of enzyme molecules convert substrates to products depends on…

in part substrate and enzyme concentrations.

What would an increase in substrate amount do (within lower concentrations)?

speeds up binding to available active sites

enzyme inhibitors

when binded with, prevents enzymes from catalyzing reactions

competitive inhibitors

bind to the same site as the substrate (i.e. the active site), and thus block substrate binding

noncompetitive inhibitor

bind to a location other that the active site (allosteric site) preventing the substrate from binding to active site

allosteric

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

ligand

lysozyme

enzyme that cuts a specific six-sugar polysaccharide found in bacterial cell walls

positive regulation/feedback

results from regulatory molecules stimulating/increasing enzyme activity, as opposed to suppressing enzyme activity

What are some functions of a protein?

catalyze chemical reactions, allow for passage of nutrients and waste into and out of cell (communicating messages from one cell to another or from outside of cell to inside of cell), act as “ubers” moving molecules and organelles around within the cell or moving the entire cell from one location to another, fighting off foreign invaders (i.e. antibodies)

What is a protein’s function dependent upon?

the overall shape and structure of the molecule

What does a protein consist of?

one or more polypeptides twisted and folded into specific three-dimensional shapes/conformations

changing the structure of protein’s = ?

changes/destroys its function

titin (connectin)

the largest known human protein

amino acid sequence

amino acids assembled in a unique order per protein

What are the four parts of an amino acid?

central carbon, carboxyl group, amino group, and side chain

What differs in each amino acid?

side chain

What are the four types of side chains?

polar, nonpolar, acidic, basic

What categorizes a polar side chain?

hydrophilic; leads to hydrogen-bonding interactions

What categorizes a nonpolar side chain?

leads to hydrophobic interactions

What categorizes an acidic side chain?

leads to ionic and hydrogen-bonding interactions

What categorizes a basic side chain?

leads to ionic and hydrogen-bonding interactions

peptide bond

connecting one amino acid to another (a very strong covalent bond)

What is the primary amino group (-NH2) of one amino acid covalently joined to?

the carboxyl group (-COOH) of a second amino acid

Why are long polypeptide chains flexible?

due to the rotation of the peptide bonds and bonds within each amino acid

What does rotation allow a long polypeptide chain to do?

allows a protein to fold, bend, and twist in numerous ways; but some interactions put constraints on how a protein can fold and thus ultimately aid in determining the overall protein shape

What forms between the atoms that make up the polypeptide backbone and between the amino acid side chains?

weak noncovalent bonds

What types of noncovalent bonds form between the polypeptide backbone and amino acid side chains?

hydrogen bonds, electrostatic attractions, van der waals attractions, and hydrophobic interactions

denaturation

the loss of a protein’s normal conformation (shape/three-dimensional structure)

What can denature/unravel a protein?

alterations in temperature, pH, or other factors

renaturation

proteins return to their original shape after being denatured

How do forces (temperature change, pH, etc.) denature a protein?

disrupt the noncovalent (weak) interactions that maintain the protein’s shape and is usually accompanied by a loss of protein function

conformation

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

What happens when a protein is misfolded?

the formation of aggregates (amyloids) of protein that can damage cell and tissues

alpha helix(ces)

helical structure resulting from hydrogen bonding between adjacent/nearby (every fourth) amino acid

beta sheet(s)

sheet-like structure resulting from hydrogen bonding between adjacent segments that lie side by side

How does the alpha helix structure affect the side chain?

causes it to project away from helix and in a location that allow for the interaction with another region of the protein or other macromolecules

How does the beta sheet structure affect the side chain?

emerge from opposite sides of sheet because of adjacent amino acids related by rotation of 180 degrees