Preview

Question 1

Infomational bio polymers

Answer 1

RMA DNA proteins
Sequence is the information
Have common generic structure: a common element(covalent bond)and a characteristic element(side-chains)
Shape: linear
Asymmetric monomers—>asymmetry of the polymer, the growth of the chain is unidirectional

Question 2

Advantage of linear structure for informational biopolymers

Answer 2

packaging and handling is more efficient than branched molecules

Question 3

2 major types of informational biopolymer monomer units

Answer 3

Nucleotides and amino acids

Question 4

Nucleotides

Answer 4

Common element: pentose sugar phosphate
Characteristic element: heterocyclic base
2 joining sites on common element: 5’—phosphate(negative charged) & 3’ OH(hydroxyl)
Deoxyribose: missing th 2’ hydroxyl of ribose compare with RNA (DNA is H), this absence makes DNA more resistant to chain cleavage by hydrolysis—greater stability

Question 5

5 heterocyclic bases of nucleotides

Answer 5

Purines: Adenine(A), Guanine(G)
Pyrimidines: Uracil(U), Thymine(T), Cytosine(C)

Question 6

The link between adjacent nucleotides

Answer 6

Phosphodiester
Ester linkage with 5’ OH and 3’ OH

Question 7

Amino acids

Answer 7

Characteristic element: since chain R group
Common element: NH2+CH+COOH
2 joining sites: NH2(amino terminus, positively charged) & COOH(carbonyl terminus, negatively charged)
Polymer growth is always add to the carbonyl end
3 main classes: Hydrophobic(8), Hydrophilic(9), Special(3)
Link: peptide bond

Question 8

Monomers need energized to incorporated into the growing polymer chain

Answer 8

Nucleotide monomers: nucleoside triphosphates (NTPs)
Ribo: ATP CTP GTP UTP
deoxyribo: dATP dCTP dGTP dTTP
The outer 2 phosphates are kicked out when the NTP is incorporated into a growing nucleic acid chain
Nucleoside monophosphate, diphosphate, triphosphate

Amino acid monomers: amino acyl-tRNA esters 酰基
High-energy ester bond
t-RNA is kicked out when the next amino acid is incorporated at the end of a growing protein chain

Linkage rection is catalyzed by a specific enzyme

Question 9

The enzyme is associated with a template biopolymer that directs the enzyme to incorporate the correct flavor monomer

Answer 9

Biopolymer template enzyme
DNA—————DNA———DNA polymerase
RNA—————DNA———RNA polymerase
Protein———mRNA———ribosome

Question 10

Biopolymer chain

Answer 10

RNA and protein are usually single polymer chains
DNA is usually duplex DNA (Antiparallel)

Watson-Crick base pairs: A-T/U C-G
DNA generally in a right-handed helix termed B-DNA
There is also A-DNA and Z-DNA

Question 11

DNA-binding proteins

Answer 11

DNA-binding proteins can make contact with base-pairs at major or minor grooves and identify specific sequences

Question 12

DNA strands can be separated and re-associated

Answer 12

Denaturation: seperated
Renaturation: reform H-bonds

Important in replication and transcription and also exported in experimental techniques

Tm: the temperature at which the DNA is 1/2 melted, depends on its base composition(numbers of H-bonds)
More G-C pairs, higher Tm

Question 13

DNA bend about its long axis

Answer 13

TATA box-binding protein (TBP): folding DNA into compact condensed structure

Question 14

The Central Dogma

Answer 14

DNA synthesis replication: Making a perfect copy
RNA synthesis transcription: rewriting in a different nucleotide font
protein synthesis translation: rewriting in a different language

Question 15

Bioploymer synthesis: templates and enzymes

Answer 15

process: biopolymer—template—enzymes

replication: DNA—DNA—DNA polymerase
transcription: RNA—DNA—RNA polymerase
translation: protein—mRNA—ribosome

Question 16

transcription

Answer 16

mRNA is the corresponding sequence of the non-template strand

exposed DNA strand directly interact with rNTP, catalyzes attack of 3’-OH on alpha-phosphate of incoming rNTP, beta-, gama- diphosphate dropped

structure of incoming rNTP:
base–pentose sugar—alpha, beta, gama phosphate

Question 17

Transcription bubble

Answer 17

RNA polymerase bind with promoter at the start site on template strand.

DNA locally unwinding (局部解旋) by helicase associated with RNA polymerase, create transcription bubble, one strand becomes template, the other becomes non-template strand.

transcription bubble moves along the DNA with RNA polymerase the original DNA duplex reforms behind RNA polymerase, the nascent RNA exist through a channel in the polymerase, 5’end first.

Question 18

RNA polymerase: starting and stopping

Answer 18

starting: certain DNA sequences called promoters

stopping: certain DNA sequences destabilize the attachment of RNA polymerase

Question 19

DNA replication

Answer 19

direct interaction between template DNA and incoming dNTP

Difference:
-Have origins, but no stop sites
-newly synthesized stands never separates from the template
-Both of the original DNA strands independently serve as template
-start with 1 molecule of double-stranded DNA and end with 2 molecules of double stranded DNA

Question 20

Translation

Answer 20

punctuation codons

start codon: AUG (codes Met)
stop codons: UAA UAG UGA (termination codons, not code for any amino acid)

Question 21

Relationship

Answer 21

template—energized monomer
DNA—dNTP
DNA—rNTP
mRNA—aminoacyl tRNA

for dNTP and rNTP:
direct interaction of template with next monomer molecule to be incorporated

for aminoacyl tRNA:
indirect interaction between template and next monomer to be incorporated (amino acid)
tRNA acts as an adaptor between template and growing chain

Question 22

Peptidyl transferase, ribozyme

Question 23

RNA world hypothesis

Question 24

Size of protein

Answer 24

average: ~300-400 amino acids
smallest: ~40
largest: ~30000 muscle protein titin

Question 25

Information flow

Answer 25

Genome-DNA
Protein primary structure
Protein 3D structure
Function
Cell biology

Question 26

2 major classes of amino acid side chain

Answer 26

hydrophilic: polar electronic charge distribution interact well with the polar solvent water

hydrophobic: non polar electronic charge distribution

Question 27

The hydrophobic effect-hydrophobic aggregation

Answer 27

the tendency of non polar molecules to be aggregated in water

The water molecules surrounding hydrophobic molecules, adopt a constrained, cage-like organization (lower entropy state)

hydrophobic molecules tend to coalesce (合并) under weak van der Waals intermolecular interaction, some water molecules released, the number of the constrained cage like structure decrease, causing net increase in entropy (shift to a higher entropy state), finally drives the formation of separate hydrophobic and aqueous phases

Question 28

Oil drop modle

Answer 28

each protein adopts only one or a small number of conformations

protein structures are based on the general oil drop model

Question 29

Directionality of protein

Answer 29

N-terminus to C-terminus
5’ to 3’ (coding DNA/RNA)

Question 30

alpha-helix

Answer 30

H-bond between C=O and N-H
n H-bond —> (n+4) amino acid
periodicity (3.6 residues per turn)

gross structure: straight rod

Question 31

beta-sheet

Answer 31

H-bonds link two adjacent beta-strands

strands maybe parallel or antiparallel

can create large surface

Question 32

structure driving interactions

Answer 32

Most are non covalent bonds:
H-bonds(secondary structure & among side chains)
Ionic bonds(among negative and positive side chains)
Van der Waals interactions (among hydrophobic side chains)

Covalent bond:
Disulfide bonds among cysteine’s sulfhydryl group(S-H) in side chain, disulfide bonds can be both intra-chain and inter-chain

Question 33

Motifs of protein structure

Answer 33

a) Coiled-coil motif
Heptad repeat: a common structure in protein, usually contain 7 repeated amino acids sequence, stabilize the proteins

b) EFhand/helix-loop-helix motif
a Ca++- binding motif 中心是一个Ca2+，两个alpha螺旋缠绕

c) Zinc-finger motif
common in transcription factors–binds to DNA/RNA
中心是一个Zn2+，链接一个alpha螺旋和两个反向的beta折叠

Question 34

Motifs vs. Domains

Answer 34

Motifs: small, local structures, not structurally independent entities (if cut away from the rest of the protein, do not have sufficient bonds to maintain its structure)
The rest of the protein also contributes to the stability of the local motif.

Domains: characteristic 3D structures larger than motifs, structurally independent entities, although covalently-joined to the rest of the protein.
The rest of the protein contributes little to the stability of a domain

Question 35

4 major structural classes of proteins

Answer 35

1.Fibrous proteins
2.Globular proteins
3.Integral membran proteins
4.Intrinsically disordered proteins: exist as random coils under physiological conditions
may adopt a specific secondary/tertiary structure upon binding to a well-structured partner protein

Question 36

Tertiary structure: domains

Answer 36

definition: >40aa-long region, compactly folded, can be made of various motifs
shows the modular nature of proteins

Question 37

Quaternary structure: Multimeric proteins

Answer 37

Next level: Supramolecular complexes can be > 1 MDa

Question 38

Supramolecular complexes

Answer 38

Large “molecular machines” made up of multiple distinct proteins, each of which may itself contain multiple subunits.
ex.transcription initiation complex

Question 39

Tertiary structure reveal evolutionary relationships

Answer 39

hemoglobin and myoglobin (in vertebrate), leghemoglobin(in plant): different amino acid sequence, similar 3-D structure, similar function(oxygen-binding protein)