Chem Exam 7

Protein

A compound of high molar mass consisting largely or entirely of amino acids linked together

Amino Acid

A molecule that contains an amino group and a carboxyl group

Amino group

from ammonia (NH₃) but with hydrocarbon groups

Essential amino acid

An amino acid that must be obtained from the diet because it cannot be synthesized in sufficient quantities by the body

Essential for human life

Cannot be synthesized by the body

Must be obtained from the diet

How many amino acids?

20

Amino acids with a nonpolar R group has

hydrocarbons on its side chain

Classification of amino acid

based on side chain

• non-polar

• polar but no charge

• positive charge

• negative charge

Each amino acid can act as both acid and base

Zwitterion

An electrically neutral compound that contains both negatively and positively charged groups

Isoelectric point (pI)

The pH at which a given amino acid exists in solution as a zwitterion

• All amino acids with non-charge side chains have pI around 5.5-7.0

• All amino acids with + charge on side chains have pI greater than 7.5

• All amino acids with - charge on side chains have pI less than 3.5

Peptide

chains of two or more amino acids

Peptide bond

The amide bond joining two amino acid units in a peptide or protein

Formed when amino group of one molecule combines with carboxyl group of a different molecule

molecule of water is released in the reaction

N-terminus is written on left (free amino group)

C-terminus is written on right (free carboxyl group)

Polypeptide

a chain of about 50 or more amino acids

Proteins

compounds of high molar mass consisting largely or entirely of chains of amino acids

Two major classifications: fibrous and globular

Fibrous protein

insoluble in water

structural, connective, or protective functions

globular proteins

soluble in water

roughly spherical

primary struction

protein structure

the sequence of amino acids in a polypeptide chain or protein

Secondary structure

protein structure

fixed arrangement of the polypeptide backbone

a (alpha)-helix

B (beta)-pleated sheet

held together by hydrogen bonds between parts of the chain

Tertiary

protein structure

three-dimensional arrangement of the whole protein

held together by 4 different types of attractions

• ionic interactions- attractions between positive and negative charges on side chains

• hydrogen bonding

• disulfide linkages- bond between 2 thiol side chains

• dispersion forces- between non-polar side chains near each other because protein folding has put them away from contact with water and near each other

Quaternary structure

protein structure

arrangement of subunits that make up a protein

Ionic bonding (salt bridges)

bonding that results from electrostatic attractions between positively and negatively charged groups

hydrogen bonding

bonding between a highly electronegative oxygen atom or nitrogen atom and a hydrogen atom attached to another oxygen atom or nitrogen atom

disulfide linkage

a covalent bond that forms by the oxidation and linkage of two sulfure atoms from the side chains of two cysteine residues

dispersion force

a force caused by the instantaneous imbalance of electrons about a molecule

Denaturing proteins

change of the 3-dimensional structure of a protein

can be reversible or non-reversible

can be caused by

• heat

• UV radiation

• addition of acid or base

• addition of ethanol

• salts of heavy metals, like mercury, silver, or lead

• alkaloid reagents like tannic acid

Enzyme

a biological catalyst

Substrate

a compound on which an enzyme acts

Act on substrate

Form substrate/enzyme complex

Have active site where substrate binds

• lock-and-key model to explain enzyme activity

• induced fit model to explain enzyme activity

Enzyme Specificity

some enzymes act only on one substrate

some enzymes act on an entire class of structures

Enzyme Activity

based on substrate concentration

based on enzyme concentration

based on temperature

based on pH

Enzyme inhibition

irreversible-poison

reversible

• competitive inhibitor- resembles a substrate and competes for binding at active site

• non-competitive inhibitor- binds somewhere other than active site, disruption enzyme activity

• feedback inhibition- normal process that uses noncompetitive inhibitors to control enzyme activity

Competitive inhibitor

resembles a substrate and competes for binding at active site

non-competitive inhibitor

binds somewhere other than active site, disruption enzyme activity

feedback inhibition

normal process that uses noncompetitive inhibitors to control enzyme activity

Cofactor

nonprotein component of an enzyme necessary for enzyme to function

Coenzyme

cofactor that is an organic molecule

vitamin

a type of coenzyme essential in trace amoutns for normal metabolism

2 types: fat-soluble and water-soluble

Gene

basic unit of heredity

a region of DNA that codes for a specific function

Chromosome

an elongated, threadlike structure composed of protein and DNA that contains the genetic blueprint- genes are found on these

(long thread-like structure made of protein and DNA)

Nucleotides

monomer units that are linked together to form nucleic acids

can be further broken down to phosphoric acid, a pentose sugar, and a nitrogenous base

Nitrogen (nitrogenous base)

Based on pyrmidine (single ring structure) U, T, C

Based on purine (double ring structure) A, G

Sugar molecule

Phosphate ion

RNA (Ribonucleic acid)

Ribose

The nucleic acid responsible for using the genetic information encoded in DNA

DNA (Deoxyribonucleic acid)

Deoxyribose (no -OH on c2)

The nucleic acid that stores genetic information

Pyrmidine

A heterocyclic amine with two nitrogen atoms in a six-member ring

Purine

A heterocyclic amine consisting of a pyrimidine ring fused to a five-member ring with two nitrogen atoms (top half of a steroid structure)

What are the Nucleotides

Uracil (U) only in RNA

Thymine (T) is only in DNA

Cytosine

Adenine

Guanine

Structure

Primary

• sequence of 4 nucleotides

• Phosphate bonds of C 5’ of ring

• C 3’ of same ring bonds to another phosphate

• Continues on the length of the molecule

• Read left to right, top to bottom, 5’ end to 3’ end (5 prime to 3 prime direction going opposite directions- antiparallel)

Secondary

• double helix

• interior base pairs

  • Always C & G

  • Always A & T or A & U

• Backbone of sugar/phosphate chain

Replication

The process in which the DNA in a dividing cell is copied. 

Copying of DNA in cells as they are dividing

DNA strand opens up, unwinds- because of enzyme

Each strand of the original produces a complementary strand

Two strands are formed, each with half of the original strand

Transcription

The process in which RNA is synthesized from a DNA template

Formation of RNA from DNA

DNA again opens

• shorter length than in replication

• complementary RNA strand forms

• RNA strand is released

• DNA strand returns to double helix

3 Types of RNA

• mRNA- messenger, codes for proteins

• rRNA- ribosomal, makes up about 2/3 of ribosome structure

• tRNA- transfer, brings amino acids to ribosome

Ribosomes

• Structures inside cells 

• protein synthesis ‘factories’

Translation

The process in which the information encoded in RNA is used to direct the sequencing of amino acids to synthesize a protein

Codon- a set of 3 nucleotides on mRNA

Anticodon- set of 3 complimentary nucleotides on t RNA

Genetic code- identification which amino acid is specificied by specific group of 3 nucleotides

Synthesis:

• tRNA binds to correct amino acid (acceptor stem)

• mRNA holds growing amino acid chain

• next amino acid binds to previous one with peptide bond

• tRNA releases the next tRNA brings next amino acid

• growth continues until stop codon is reached

Mutation

Any chemical or physical change that alters the nucleotide sequence in DNA

Three types:

• Substitution- wrong nucleotide

• Insertion- extra nucleotide

• Deletion- nucleotide removed

Mutagen

A chemical or physical agent that causes mutations

Can be chemical or physical

Point mutation

A change in which one nucleotide is substituted, added, or deleted

Addition and deletion are more harmful than substitutions (adding or deleting shifts the entire amino acids over or back shifting the entire thing for the rest)

Virus

An infectious agent that is much smaller and simpler than bacteria

Enters a cell and inserts its own genetic information into the cell DNA or RNA

2 Types of viruses (DNA or RNA)

RNA can also be retrovirus, which is RNA that directs the synthesis of DNA in the host cell