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Bio Fall > Nucleic Acids and Proteins > Flashcards

Nucleic Acids and Proteins Flashcards

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Biology 101 flashcards
1
Q

nucleic acid

A

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

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2
Q

Nucleotides

A

Sugar (ribose- 5C)
Base
Phosphate

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3
Q

Deoxyribose

A

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

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4
Q

phosphate ester

A

Dehydration reaction w/ OH and H → phosphate ester

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5
Q

phosphodiester bond

A

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

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6
Q

Purine

A 
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
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7
Q

Pyrimidines

A

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

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8
Q

DNA

A

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

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9
Q

RNA

A

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

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10
Q

ATP

A

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

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11
Q

2’ carbon

A

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)

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12
Q

3’ carbon

A

on ribose- point that creates nucleotide chains

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

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13
Q

base pairing, complementary sequence

A

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

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14
Q

ZDNA

A

different structure, very uncommon

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

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15
Q

nucleosides

A 
base + sugar	
Adenosine: Adenine + sugar
Guanosine: Guanine + sugar
Cytidine: Cytosine + sugar
Thymidine: Thymine + sugar
Uridine : Urocil + sugar
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16
Q

amino acid

A

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

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17
Q

basic amino acids

A

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

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18
Q

acidic amino acids

A 
Glutamic Acid (Glu, E)
Aspartic Acid (Asp, D)
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19
Q

polar, uncharged amino acids

A

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

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20
Q

Nonpolar, hydrophobic amino acids

A

Leucine (Leu, L)

Alanine (Ala, A)

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21
Q

3 special function amino acids

A

Methionine, Cysteine, Proline

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22
Q

Methionine (Met, M)

A

Unusual because it contains sulfur

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

23
Q

Cysteine (Cys, C)

A

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

24
Q

Proline (Pro, P)

A

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

25
Q

Peptide bond

A 
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)
26
Q

terminal end

A

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

27
Q

Polypeptide chain

A

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

28
Q

Oligopeptides

A

18 amino acids linked together

29
Q

Anfinson experiement

A

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

30
Q

denature

A 
unfolding of a protein
Heat
Changes in pH
Detergent presence
Changes in ionic conditions
Changes in oxidation/reduction state
31
Q

amino group

A

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

32
Q

carboxyl group

A

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

33
Q

weak bond interactions

A

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

34
Q

amino acid side chains

A

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

35
Q

primary structure (not all proteins have)

A

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

36
Q

secondary structure (not all proteins have)

A

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

37
Q

tertiary structure (all proteins have)

A

held together by R group interactions (H bonds)

all proteins have tertiary structure

38
Q

quaternary structure

A

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

39
Q

embellishments

A

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)

40
Q

motifs and domains

A

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)

41
Q

alpha helix

A

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

42
Q

beta sheet

A

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

43
Q

metal co-factor

A

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))

44
Q

CAP (Catabolite Activator Protein)

A

Protein with 2 domains with different functions

Binds DNA with one part, binds cAMP with another part

45
Q

chaperone proteins

A

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

46
Q

binding site

A

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

47
Q

cyclic AMP (binding site)

A

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

48
Q

protein folding disorders (misfolding)

A

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

49
Q

higher order structures

A

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

50
Q

“family” of related enzyme

A

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

51
Q

X-ray crystallography- determine shape of proteins

A

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

52
Q

NMR

A

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

53
Q

ribose

A

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

54
Q

zwitterion

A

2 ions- positive and negative–> overall is neutral

Bio Fall (21 decks)

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