Molecules: proteins and nucleic acids

Lecture 5

proteins

polypeptides

amino acids

are organic molecules with amino group (-NH₂) and carboxyl group (

-COOH)

R groups

amino acids differ in their properties due to differing side chains, called

charge

polarity

size

shape

functional groups

side chains in amino acids differ through what?

protein folding

enzyme catalysis

protein-protein interactions

roles of charged amino acids

do not ionize and become charged

polar uncharged sidechains with amide groups do not what?

hydrocarbons

nonpolar amino acid sidechains are mostly composed of what?

hydrocarbons

consisting solely of hydrogen and carbon atoms

contributes to protein folding and stability

they form strong bonds (protein stability and shape)

unique cyclic side chain

What makes certain amino acids special cases?

peptide bond formation

amino acids in a protein (polypeptide) are linked together by peptide bonds between the carboxyl group and the amino group

primary

secondary

tertiary

quarternary

Various structures of proteins

polypeptide

polymer composed of amino acids linked together by peptide bonds

protein

one or more polypeptides precisely folded into a unique shape that carries out a specific function

primary structure

the linear sequence of amino acids

stabilized by: peptide bonds

secondary structure

repeated patterns in different regions, due to hydrogen bonding

stabilized by: hydrogen bonds between amino acid backbone atoms

a (alpha) helix

right-handed coil

b (beta) pleated sheet

two or more sequences are extended and aligned

hydrogen bond

is formed between the oxygen atom of a carbonyl group and the hydrogen atom of an amide group

tertiary protein structure

polypeptide chain is bend and folded, results in the definitive 3D shape

stabilized by: hydrogen bonds; disulfide bridges; van der waals interactions; ionic bonds. Primarily noncovalent interactions between side chain atoms

charged amino acids

Ionic bonds have what type of amino acids

polar uncharged amino acids

hydrogen bonds have what type of amino acids

nonpolar amino acids

van der waals has what type of amino acids

cysteine residue

a cysteine amino acid that is part of a polypeptide chain in a protein

• has sulfur-containing thiol (-SH) group in side chain

disulfide bond

becomes nonpolar and hydrophobic in tertiary structure

regulating protein function and activity

response to changes in cellular environment

formation and brokage of disulfide bond between cysteine residues has a role in:

quaternary structure

two or more polypeptide chains (subunits) bind together and interact

stabilized by interactions between side chain atoms

denaturation

impacts protein structure

denaturation

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

when they are cooled or the chemicals are removed

how can proteins return to normal after denaturation?

DNA and RNA

What are the two types of nucleic acids?

DNA

DNA or RNA?

double stranded helical structure

RNA

DNA or RNA?

single-stranded

DNA

DNA or RNA?

contains the sugar deoxyribose

DNA

DNA or RNA?

adenine (A), guanine (G), cytosine (C), and thymine (T)

RNA

DNA or RNA?

contains the sugar ribose

RNA

DNA or RNA?

adenine (A), guanine (G), cytosine (C) and uracil (U)

nucleic acids

are polymers called polynucleotides

polynucleotide

is made of monomers called nucleotides

pentose sugar (2 types)

nitrogenous base (5 types)

phosphate group (can have 1-3 phosphates)

nucleotides are composed of what?

pentose sugar

monosaccharides that contain five carbon atoms in their chemical structure

essential building blocks

ribose

a key component of ribonucleic acid (RNA) and several cofactors like ATP, NADH, and FADH₂

deoxyribose

a vital component of deoxyribonucleic acid (DNA)

pyrimidines

have a single ring structure and include cytosine, thymine, and uracil

purines

contain a double ring structure and consist of adenine and guanine

A,G,T,C

what are the four nitrogenous bases in DNA

A, G, C. U

what are the four nitrogenous bases in RNA

hydrogen bonds

nitrogenous bases pair with each other through what?

thymine (DNA)

uracil (RNA)

Adenine always pairs with what?

cytosine in both DNA and RNA

guanine always pairs with what?

phosphate groups

consist of a phosphorus atom bonded to four oxygen atoms

they form the sugar phosphate backbone that holds the nucleotide chain together

why are phosphate groups critical components of nucleic acids (DNA and RNA)

pentose sugar (2 types)

nitrogenous bases (5 types)

nucleosides are composed of what?

nucleosides

are essential precursors to nucleotides

nucleoside

a nitrogenous base covalently bonded to a pentose sugar molecule (ribose or deoxyribose)

nucleotide

a nitrogenous base, a pentose sugar molecule, and one or more phosphate groups attached to the sugar molecule

hydrogen

____ bonding interactions between complementary bases maintain shape

chargaffs rules

the ratios of adenine to thymine and guanine to cytosine are approximately equal in DNA molecules

antiparallel

one runs 3-5 direction, other 5-3

the two DNA strands in a double helix are

messenger RNA (mRNA)

typically linear, single stranded

carries genetic information from DNA to ribosomes

serves as a template for protein synthesis

transfer RNA (tRNA)

cloverleaf-like secondary structure (folds into a compact L shaped 3D structure

delivers amino acids to the ribosome for protein synthesis

ribosomal RNA (rRNA)

is a structural and functional part of ribosomes

DNA

provides directions for its own replication through base pairing rules

gene

DNA sequence that has instructions to synthesize another macromolecule

messenger RNA (mRNA)

each gene directs synthesis of a

RNA

DNA sequences are transcribed into what?