Nucleic Acids and Proteins

Question 1

nucleic acid

Answer 1

Huge long polymers with millions of monomers
not energy containing
not structural
carry information

Question 2

Nucleotides

Answer 2

Sugar (ribose- 5C)
Base
Phosphate

Question 3

Deoxyribose

Answer 3

Ribose sugar that is missing an oxygen from -OH (in DNA)

Question 4

phosphate ester

Answer 4

Dehydration reaction w/ OH and H → phosphate ester

Question 5

phosphodiester bond

Answer 5

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

Question 6

Purine

Answer 6

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

Question 7

Pyrimidines

Answer 7

Single ring structure
Cytosine (DNA and RNA)
Thymine (DNA only)
Uracil (RNA only)

Question 8

DNA

Answer 8

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

Question 9

RNA

Answer 9

Single- stranded (only one 5’ end and one 3’ strand)
As if folds up form some intra-strand base pairs (H bonds)
Secondary structure

Question 10

ATP

Answer 10

Adenine + sugar + 3 phosphates = adenosine triphosphate
Used in energy transfer
Energy is in the phosphate bonds
Precursor used in assembly of RNA

Question 11

2’ carbon

Answer 11

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)

Question 12

3’ carbon

Answer 12

on ribose- point that creates nucleotide chains

Through dehydration synthesis, bonds to a phosphate group of another nucleotide to create a chain

Question 13

base pairing, complementary sequence

Answer 13

hydrogen bonds used to pair bases
A-T (2 bonds)
C-G (3 bonds- very stable)

Question 14

ZDNA

Answer 14

different structure, very uncommon

left-handed double helical structure in which the helix winds to the left in a zigzag pattern, unlike BDNA

Question 15

nucleosides

Answer 15

base + sugar	
Adenosine: Adenine + sugar
Guanosine: Guanine + sugar
Cytidine: Cytosine + sugar
Thymidine: Thymine + sugar
Uridine : Urocil + sugar

Question 16

amino acid

Answer 16

central asymmetric carbon (amino- NH2, H, acid- COOH, R group- varies)
20 exist, building blocks of proteins
all have L orientation (except glycine)

Question 17

basic amino acids

Answer 17

Lysine (lys, K)
Arginine (Arg, R)
Histidine (his, H)

Question 18

acidic amino acids

Answer 18

Glutamic Acid (Glu, E)
Aspartic Acid (Asp, D)

Question 19

polar, uncharged amino acids

Answer 19

Serine (Ser, S)
Threonine (Thr, T)
Tyrosine (Tyr, Y)

Question 20

Nonpolar, hydrophobic amino acids

Answer 20

Leucine (Leu, L)

Alanine (Ala, A)

Question 21

3 special function amino acids

Answer 21

Methionine, Cysteine, Proline

Question 22

Methionine (Met, M)

Answer 22

Unusual because it contains sulfur

Is always the #1 amino acid on an amino acid chain

Question 23

Cysteine (Cys, C)

Answer 23

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

Question 24

Proline (Pro, P)

Answer 24

Proline
Only amino acid to turn around and link up with itself
This “twist” tends to change the direction of the amino acid chain

Question 25

Peptide bond

Answer 25

``` 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) ```

Question 26

terminal end

Answer 26

all amino acid chains have an amino terminal end and a carboxyl terminal end Known as an “N-terminus” and a “C-terminus”

Question 27

Polypeptide chain

Answer 27

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

Question 28

Oligopeptides

Answer 28

18 amino acids linked together

Question 29

Anfinson experiement

Answer 29

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

Question 30

denature

Answer 30

``` unfolding of a protein Heat Changes in pH Detergent presence Changes in ionic conditions Changes in oxidation/reduction state ```

Question 31

amino group

Answer 31

NH2, N terminus of peptide chain, not involved in linkage

Question 32

carboxyl group

Answer 32

COOH , C terminus of peptide chain, not involved in linkage

Question 33

weak bond interactions

Answer 33

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

Question 34

amino acid side chains

Answer 34

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

Question 35

primary structure (not all proteins have)

Answer 35

amino terminal end (N terminus) to carboxyl temrinal end (C terminus) e.g. ACTH – 39 AA

Question 36

secondary structure (not all proteins have)

Answer 36

refers to localized arrangements of amino acids that are often seen in polypeptide structures --> alpha helix OR beta sheet

Question 37

tertiary structure (all proteins have)

Answer 37

held together by R group interactions (H bonds) | all proteins have tertiary structure

Question 38

quaternary structure

Answer 38

more than one polypeptide ex. hemoglobin- binds O and carries it around to tissues in the lungs–> has primary sequence, secondary structure, tertiary

Question 39

embellishments

Answer 39

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)

Question 40

motifs and domains

Answer 40

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)

Question 41

alpha helix

Answer 41

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

Question 42

beta sheet

Answer 42

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

Question 43

metal co-factor

Answer 43

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))

Question 44

CAP (Catabolite Activator Protein)

Answer 44

Protein with 2 domains with different functions | Binds DNA with one part, binds cAMP with another part

Question 45

chaperone proteins

Answer 45

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

Question 46

binding site

Answer 46

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

Question 47

cyclic AMP (binding site)

Answer 47

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

Question 48

protein folding disorders (misfolding)

Answer 48

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

Question 49

higher order structures

Answer 49

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

Question 50

"family" of related enzyme

Answer 50

Serine protease Proteins evolved from a single ancestor protein--> similarities in folding or shape overlap- amino acids are shared by both elastase and chymotrypsin

Question 51

X-ray crystallography- determine shape of proteins

Answer 51

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

Question 52

NMR

Answer 52

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

Question 53

ribose

Answer 53

sugar used in DNA and RNA 2' C- R group - if H=DNA if OH RNA 3' C attaches to the next phosphate

Question 54

zwitterion

Answer 54

2 ions- positive and negative--> overall is neutral