Nucleic Acids and Proteins Flashcards
nucleic acid
Huge long polymers with millions of monomers
not energy containing
not structural
carry information
Nucleotides
Sugar (ribose- 5C)
Base
Phosphate
Deoxyribose
Ribose sugar that is missing an oxygen from -OH (in DNA)
phosphate ester
Dehydration reaction w/ OH and H → phosphate ester
phosphodiester bond
2 esters on phosphate
backbone of strands of nucleic acids
3’ C of ribose and 5’ of another
2 bonds is between O-P=O
Purine
1 class of nucleotide Double ring structure Adenine (DNA and RNA)- 2 ring structure w/ NH2 and H (NO O) Adenosine = base + sugar (intermediate stage) Guanine (DNA and RNA)- 2 ring structure w/ NH2 and O
Pyrimidines
Single ring structure
Cytosine (DNA and RNA)
Thymine (DNA only)
Uracil (RNA only)
DNA
Always double-stranded and antiparallel
A + T (2 H bonds), C + G (3 H bond- stronger)
Always read or written 5’ → 3’
Twisted in a right-handed helix = B-DNA
Part closest to us goes up and to the right
5’ has phosphate on end, 3’ has hydroxyl on end
RNA
Single- stranded (only one 5’ end and one 3’ strand)
As if folds up form some intra-strand base pairs (H bonds)
Secondary structure
ATP
Adenine + sugar + 3 phosphates = adenosine triphosphate
Used in energy transfer
Energy is in the phosphate bonds
Precursor used in assembly of RNA
2’ carbon
on ribose- point of differentiation between a RNA molecule and a DNA molecule
RNA molecules have a OH group (hydroxy group)
DNA molecules only have a H group (dehydroxyl group- missing O)
3’ carbon
on ribose- point that creates nucleotide chains
Through dehydration synthesis, bonds to a phosphate group of another nucleotide to create a chain
base pairing, complementary sequence
hydrogen bonds used to pair bases
A-T (2 bonds)
C-G (3 bonds- very stable)
ZDNA
different structure, very uncommon
left-handed double helical structure in which the helix winds to the left in a zigzag pattern, unlike BDNA
nucleosides
base + sugar Adenosine: Adenine + sugar Guanosine: Guanine + sugar Cytidine: Cytosine + sugar Thymidine: Thymine + sugar Uridine : Urocil + sugar
amino acid
central asymmetric carbon (amino- NH2, H, acid- COOH, R group- varies)
20 exist, building blocks of proteins
all have L orientation (except glycine)
basic amino acids
Lysine (lys, K)
Arginine (Arg, R)
Histidine (his, H)
acidic amino acids
Glutamic Acid (Glu, E) Aspartic Acid (Asp, D)
polar, uncharged amino acids
Serine (Ser, S)
Threonine (Thr, T)
Tyrosine (Tyr, Y)
Nonpolar, hydrophobic amino acids
Leucine (Leu, L)
Alanine (Ala, A)
3 special function amino acids
Methionine, Cysteine, Proline
Methionine (Met, M)
Unusual because it contains sulfur
Is always the #1 amino acid on an amino acid chain
Cysteine (Cys, C)
Has a sulfhydryl side group (-S-H)
Only one that can form a disulfide bond (S-S) between two cysteines in a chain of amino acids –> strong
Proline (Pro, P)
Proline
Only amino acid to turn around and link up with itself
This “twist” tends to change the direction of the amino acid chain
Peptide bond
Chains of amino acids are formed by linking amino acids between the carboxyl group of 1 amino acid, and the amino group of 1 amino acid (dehydration) partial charges (- on O from amino group, + on H from acid group)
terminal end
all amino acid chains have an amino terminal end and a carboxyl terminal end
Known as an “N-terminus” and a “C-terminus”
Polypeptide chain
chain of amino acid if there’s a lot of them- aka protein
smaller chains- tetrapeptide, hexapeptide, etc.), we name them by the number of amino acids
Oligopeptides
18 amino acids linked together
Anfinson experiement
Isolated a protein known as native ribonuclease used in cutting up RNA
put in reducing agent to break disulfide bonds, left with cysteine
add heat–> protein denatures
cooled–> back to original form
–> information for functional shape is in the amino acid sequence
denature
unfolding of a protein Heat Changes in pH Detergent presence Changes in ionic conditions Changes in oxidation/reduction state
amino group
NH2, N terminus of peptide chain, not involved in linkage
carboxyl group
COOH , C terminus of peptide chain, not involved in linkage
weak bond interactions
contribute to the 3-D shape of proteins
hydrogen bonds- weak and covalent
ionic bonds- charged
Van der waals attraction- ideal spacing between atoms so that their nuclear protons are repelling, but other parts are attracting
Hydrophobic exclusion- polar surroundings with a non-polar components of a molecule. Meaning, that all of the non-polar components cluster together inside as they share hydrophobic properties
amino acid side chains
R group- can be positive, negative (charged), uncharged, polar, nonpolar
can bond with one another to hold a length of protein in a certain shape or conformation
polar- H bonds, charge- ionic bonds, hydrophobic- van der waals
primary structure (not all proteins have)
amino terminal end (N terminus) to carboxyl temrinal end (C terminus) e.g. ACTH – 39 AA
secondary structure (not all proteins have)
refers to localized arrangements of amino acids that are often seen in polypeptide structures
–> alpha helix OR beta sheet
tertiary structure (all proteins have)
held together by R group interactions (H bonds)
all proteins have tertiary structure
quaternary structure
more than one polypeptide
ex. hemoglobin- binds O and carries it around to tissues in the lungs–> has primary sequence, secondary structure, tertiary
embellishments
prosthetic groups- extra ex. heme in hemoglobin
covalent modification- ex. add a phosphate group in phosphorylation, Serine R group- inactive
Protein (ex. kinase- takes phosphate off of ATP–> becomes an active enzyme)
motifs and domains
between levels 2 and 3
motif- refers to structural part- helix and a curve, describes location (subregion in proteins that might bind to ATP)
domain- refers to functional idea (the function of that subregion that might bind to ATP)
alpha helix
secondary structure- ribbon or cylindrical structures
amino acids in chain (right handed helix), held together with hydrogen bonds which form along the backbone of the peptide bond
linkages are not on the R groups, on every 4th residue (aa) this is happening
beta sheet
secondary structure- zig zag pleats, arrows from N–>C
tend to occur in adjacent regions of a polypeptide chain and form flattened areas
can be anti-parallel or parallel
H bonds hold pleats together
metal co-factor
Small amount of metal (zinc here) that will help the enzyme be properly functional, can be placed anywhere
(Carbonic anhydrase uses a metal cofactor in its active site Nucleases need metal co-factor (RNase, DNase))
CAP (Catabolite Activator Protein)
Protein with 2 domains with different functions
Binds DNA with one part, binds cAMP with another part
chaperone proteins
help to facilitate the folding of other proteins without becoming part of the final structure (structural catalysts)
classes- Hsp70 and chaperonins
chaperonin- may form chambers and put a protein in a “box” and put a “cap” on and then misfolded protein comes out properly folded
binding site
Protein folding–> correct active site conformation
Enzyme has active site on the polypeptide and acts upon the substrate
The substrate fits into the active site of the protein
cyclic AMP (binding site)
Different parts of the cyclic AMP are interacting with specific R groups that are hanging out from the polypeptide chain itself
Must be folded in the way that cyclic AMP will be sitting at the right distance from bonds
protein folding disorders (misfolding)
particular protein (usually in the brain) are normally spherical, every now and then, one of them misfolds into flat shape
can recruit other proteins to fold into flat shape
–> aggregate
ex. Prion proteins in the brain
diseases are CJD (rare spontaneous misfolding), mad cow disease, scrapie
higher order structures
Proteins stick together in much bigger structures
Subunit– has the alpha helix etc. to make 3-D structure
2 together is a dimer, spheres, tubes, filament
Ex. actin (long helix chains) in myosin
ex. Collagen fibers comprised of individual polypeptides which link together to form bigger fibers
“family” of related enzyme
Serine protease
Proteins evolved from a single ancestor protein–> similarities in folding or shape
overlap- amino acids are shared by both elastase and chymotrypsin
X-ray crystallography- determine shape of proteins
Take purified sample of protein and coax to form a crystal
Shoot x rays through it, use detector that give a particular pattern, can figure out arrangement of atoms in the crystal
NMR
detects movements of small molecules (H, H2O) to calculate the location of where the molecules/atoms could be to get a shape of the protein
ribose
sugar used in DNA and RNA
2’ C- R group - if H=DNA if OH RNA
3’ C attaches to the next phosphate
zwitterion
2 ions- positive and negative–> overall is neutral
