Chapter 3 Bio: Nucleic Acids and Proteins

BSC2010

Nucleic acids are _____ macromolecules

informational

What are nucleic acids?

polymers that store, transmit, and express heredity (genetic information)

The monomers of nucleic acids are…

nucleotides

What is a nucleotide?

a pentose + N-containing base + phosphate group

What is a nucleoside?

a pentose + N-containing base

What is a pentose?

• a simple sugar with 5 carbons

• deoxyribose or ribose

What is DNA?

• deoxyribonucleic acid

• a deoxyribose pentose + a base + a phosphate group

• the deoxyribose pentose in missing an oxygen attached to the 2’ carbon; this is what makes it different from ribose

What is RNA?

• ribonucleic acid

• a ribose pentose + a base + a phosphate group

• has —OH on carbon 2’

What are N-containing bases?

• Pyrimidines- single rings (cytosine, thymine, and uracil)

  • C TUrtle eats single rings

  • “single rings” sounds like pyramids

• Purines- double rings (astatine and guanine)

  • AlliGator jumps through two PURE rings

• DNA and RNA have the same bases, except in RNA, thymine it replaces by uracil

• DNA always will have an equal number of pyrimidines and purines

What is the structure of a nucleotide?

one to three phosphate groups, a sugar, and a base

What are the functions of nucleotides?

• building blocks for DNA/RNA

• energy transfer, signaling (ATP, GTP)

Synthesis of a nucleic acid:

1. nucleotides bond in condensation rxns to form phosphodiester linkages (covalent bonds)

   1. always occurs by adding the 5’-phosphate end of the new nucleotide to the 3’-OH end of the nucleic acid

2. condensation rxn —> to form phosphodiester linkages (covalent bond)

3. nucleic acids grow in the 5’ to 3’ direction

4. the linkage between the #5 carbon of one ribose and the #3 carbon on the next ribose forms a chain of alternating sugar and phosphate molecules— the sugar-phosphate backbone

What are oligonucleotides?

• up to 20 monomers

• mostly RNA molecules

• small DNA or RNA oligonucleotides are important to initiate DNA replication

What are polynucleotides?

• longest polymers in the living world

• DNA and RNA are polynucleotides

What is a DNA/RNA strand?

• a single polynucleotide chain of DNA/RNA

• RNA is usually single strand

• DNA is a double strand; two strands come together by complementary base pairing

Structure of DNA:

• the two DNA strands are antiparallel

  • they run in opposite directions

  • their 5’ ends opposite of the molecule

• the two strands form a “ladder” that twists into a double helix

• sugar-phosphate groups form the sides of the ladder, and the hydrogen-bonded bases form the rungs!

Complementary base pairing of DNA enables…

DNA to store genetic information AND transfer this information to future generations

Base pairing between _____ involves ____

nucleotides involves hydrogen bonding

Complentary base pairing:

• adenine pairs with thymine

  • in RNA, adenine pairs with uracil

• guanine pairs with cytosine

• there is a fairly strong attraction of these bonds, but not as strong as covalent bonds

• base pairs can be separated by a small amount of energy

Structure of RNA:

• usually single stranded —> folds back on itself to form short double-strand regions

• folding occurs by complementary base pairing, so structure is determined by the order of bases

• the double-strand region gives the molecule a 3d shape that affects how it interacts with other molecules

What is Central Dogma?

• DNA is an information molecule: genetic information is encoded in the sequence of bases

• Central Dogma describes the one-way flow of genetic information within a biological system: DNA —> RNA —> protein

What are the functions of DNA?

1. Replication: DNA is copied into a new, identical DNA molecules that can be transmitted to daughter cells to offspring

2. Gene expression: sequences are copied to RNA (transcription) and specify amino acids sequences in proteins (translation)

What is DNA replication?

DNA is copied into a new, identical DNA molecules that can be transmitted to daughter cells and offspring

What is transcription?

information encoded in DNA base sequences is used to synthesize RNA

What is translation?

information in RNA base sequences is used to synthesize proteins

What does DNA replication and transcription depend on?

base pairing

How to read transcription/replication

• read from 5’ to 3’

• example: 5’- ATTGCTAG- 3’ = 5’- CTAGCAAT- 3’

• if a strand runs 3’ to 5’, the complementary strand runs 5’ to 3’ so flip it around

What are genes?

DNA sequences that encode specific proteins and are transcribed into RNA; not all genes are expressed in every cell

What is a genome?

a complete set of DNA in living organisms; not all DNA in the genome encodes genes

Proteins are polymers with…

variable structure

Major functions of proteins

1. enzymes- catalytic proteins

2. defensive proteins (antibodies)

3. hormonal and regulatory proteins— control physiological processes

4. receptor proteins— receive and respond to molecular signals

5. storage proteins store amino acids

6. structural proteins— physical stability and movement

7. transport proteins carry substances

8. genetic regulatory proteins regulate when, how, and what extent a gene is expressed

Every Dragon Holds Rare Stones, Shields, Treasures, Genes

Proteins are polymers made up of…

amino acids

How are amino acids identified?

by their side chains

side chains = unique chemical groups attached to the alpha carbon of each amino acid

How is the structure and function of a protein determined?

the SEQUENCE of amino acids making up the polypeptide chain

What are the two common functional groups of amino acids?

carboxyl and amino

the R group (side chain) differs in each amino acid

What are oligopeptides/peptides?

short polymers o 20 or fewer amino acids (some hormones and signaling molecules)

What are polypeptides?

larger polymers; proteins made up of one or more polypeptides

Amino acids are linked in ____ rxns to form _____

condensation exns; peptide bonds

In what direction does polymerization take place?

in the amino to carboxyl direction

How to read peptide bonds

read from N terminus to C terminus —> forms water —> condensation rxn

How can common amino acids be grouped?

• according to the properties conferred by their side chains

• the side chains differ in their charge, polarity, size, and functional groups

• proteins have HUGE structural diversity and specificity of interactions with other molecules and ions

The charged amino acids

1. positively charged: Arginine, Histidine, Lysine

   1. positive- All Hail Lizards!

2. negatively charged: Aspartic acid, Glutamic acid

   1. negative- Asp and Glu

The polar, uncharged amino acids

1. Serine

2. Threonine

3. Asparagine

4. Glutamine

5. Tyrosine

Some Tigers Always Growl Tonight

The nonpolar amino acids

1. Alanine

2. Isoleucine

3. Leucine

4. Methionine

5. Phenylalanine

6. Tryptophan

7. Valine

All Iguanas Love Making Pretty Tiny Vests

Glycine amino acid

small, and can fit into tight corners

Proline amino acid

forms a covalent bonds with hydrocarbon side chains, resulting in a ring structure

• proline more like pro ring

Cysteine amino acid

terminal sulfhydryl group, can react with another cysteine side chain to form a covalent bond called a disulfide bridge (—S—S—)

example: insulin has 3 S—S bonds

Among the four major macromolecules, proteins are…

the most active and the most diverse in structure and function

____ determines function

structure

How many levels of protein structure are there?

1. Primary

2. Secondary

3. Tertiary

4. Quaternary

Primary Structure

the sequence of amino acids; amino acids monomers are joined, forming polypeptide chains

Secondary Structure

1. repeated patterns in different regions, due to hydrogen bonding

2. alpha helix: right- handed coil

3. beta pleated sheet: 2+ sequences of amino acids that are extended and aligned in the polypeptide

both are determined by hydrogen bonding between the —NH and —CO groups of the amino acids that make up the primary structure

Tertiary Structure

• polypeptide chain is bent and folded; results in the definitive 3d shape

• structure is determined by the interactions between R groups

  • covalent disulfide bridges between cysteines

  • ionic bonds between charged side chains

  • hydrogen bonds between side chains

  • van der waals interactions between hydrophobic side chains

• functional groups on a protein’s exposed outer surface can interact with other molecules

Quaternary Structure

results from the ways in which 2+ polypeptide chains (subunits) bind together and interact

What are subunits?

many functional groups containing 2+ polypeptide chains

Example of quaternary structure

hemoglobin: binds oxygen in red blood cells; it has 2 alpha subunits and 2 beta subunits that assemble

What is denaturing?

heat or chemicals disrupt weak interactions in a protein, destroying secondary, tertiary, and quaternary structure

Factors that can cause denaturing:

• temperature

• concentration of H⁺ (pH)

• high concentration, charged substances

• nonpolar substances containing molecules

Can a protein return to normal after denaturing?

in some cases it can when it is cooled or the chemicals are removed— all of the information is contained in the primary structure

What is the function of a protein determined by?

by the protein’s structure and its binding characteristics

Amino acid side chains on the protein surface form…

weak bonds with functional groups on other molecules or ions

Typically, ____ molecules/ions can bind to a particular protein

just one or a few

What is a ligand?

• molecule or ion that binds to another molecule

• ligand bonding is specific and can involve several weak bonds, making a strong interaction

• binding can cause conformational change (change in shape), which affects the proteins function

• binding to a ligand changes receptor structure

What is R-group modification?

• Phosphorylation: a phosphate group is added on an amino acid residue

• includes serine, threonine, and tyrosine

• protein changes shape

What are cofactors?

nonprotein molecules or inorganic ions, often a metal ion, that some proteins require in order to function; includes coenzymes and ATP

What is proteolysis?

some proteins are nonfunctional when synthesized and must be cleaved to become functional

What are catalysts?

• substances that speed up (catalyze) chemical rxns without being permanently altered

• most catalysts are proteins (enzymes)

• enzymes lower the E_A in almost all chemical rxns

• think: speedy Cat

An enzyme…

does not cause a reaction to occur, it just increases the RATE of the reaction

Some enzymes change shape when…

substrate binds to them

Enzymes are specific, meaning…

each one catalyzes only one chemical rxn

Reactants are…

substrates: they bind to specific sites on the enzyme— the active sites

What is the enzyme-substrate complex?

held together by hydrogen bonding, ionic bonds, van der waals interactions, or temporary covalent bonding

How do enzymes impact E_A?

they lower it by inducing strain, substrate orientation, or by adding chemical groups

Cells can regulate…

synthesis of enzymes only when they are needed, and regulate the activity of enzymes

How can activity of enzymes be regulated?

1. active site regulation: inhibitors are molecules that bind to the active site, preventing the substrate from entering

   1. competitive inhibition: inhibitor is similar to the substance, but no reaction occurs; reversible

   2. irreversible inhibition: rare, mostly occurs in drugs

2. allosteric regulation: non-substrate molecule binds a site other than the active site (allosteric site)

   1. enzyme changes shape —> alters activity

   2. can activate or inactivate enzymes

Allosteric regulation

Allosteric sites can be modified…

by reversible covalent binding of a molecule

What is phosphorylation?

• a phosphate group is added by a protein kinase on an amino acid residue (serine, threonine, or tyrosine)

• alters a protein’s charge and conformation

• extremely important mechanism by which cells regulate enzymes and other proteins

Protein phosphates…

remove phosphate groups from proteins —> “off switch” to reverse the actions protein kinase