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bio181 exam 2 review

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Biology

University/Undergrad

47 Terms

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- building blocks of proteins
central carbon structure is composed of:
1) amino group (-NH3) act as a base
2) carboxyl group (-COO) acts as an acid
3) hydrogen
4) R-group (side chain) functional group that caries among A.A.

polar uncharged: hydrophilic, oxygen
non-polar: hydrophobic, no oxygen, only C/H, N,S
polar charged:hydrophobic, no oxygen acidic (-)2AA, basic (+)3AA,

reactants(carboxyl, amino)---->products(peptide bond, polypeptide)

- dehydration synthesis occurs between carboxyl group and amino group
- covalent peptide bonds joins 2 A.A. together
- continues until there is a long chain of A.A. or a polypeptide

polypeptide chain
- linear chain of amino acids/primary structure
N-terminus - amino group
C-terminus: carboxyl group

1) backbone: N-C-C, N-C-C, N-C-C, etc.
2) directionality: polypeptides are labeled sequentially from N-terminus to the C-terminus
3)flexibility: peptide bonds can't rotate, but C-N bonds on either side can rotate

-> primary sequence has all info required for folding
folding = protein function
->protein folding is spontaneous - no energy
exp: ribonuclease

1) pentos sugar: 5 carbon -> labeled clockwise
2) phosphate group: represented by circle, bonded to 5'C
3)nitrogenous base: bonded to 1'C of sugar
- 5 bases found:
-> purines(2 rings)
->pyrimidines(1 ring)

pyrimidines: 1 ring,
- cytosine, uracil, thymine
purines: 2 rings, larger
- guanine, adenine

DNA= AT/GC rule
A:::T(2H bonds)
G:::C(3H bonds)

-> 2 strands are antiparallel
exp: 5'-TCG-3'
3'-AGC-5'

Stage 1: Initiation
- promoter region of DNA ad RNA polymerase binds to sigma factor
- RNA polymerase opens DNA double helix
- Template strand then synthesises mRNA by complimentary base pairings
Stage 2: Elongation
- initiation complete, elongation continues
- sigma realised from promoter continues from DNA
- RNA synthesises
Stage 3: Termination
- RNA polymerase encounters the terminator of the gene
- Hairpin forms in mRNA
- hairpin refolds through complementary base pairings
-RNA polymerase, mRNA, and DNA disassociate

read in groups of 3 nucleotide bases (codons) present on mRNA
makes 64 unique codons
Genetic Code: universal -> applies to all living things
- degenerate (redundant)
- more than 1 codon specifies for an amino acid
- is unambiguous: each codon specifies 1 amino acid only

->Conservative: first 2 bases in a codon are usually identical
->non overlapping:
- once ribosome looks onto first codon reading frame established and
reads each seperate codon 1 after another

exp: mRNA-> 5'-AUG AGG AGG UUA CGA AUG CAG CAG GGC UUU ACC-3'
(ribosomal binding site). (Start codon).

AUG-MET
CAG-GIN
CAG-GLY
UUU-PHE
ACC-THR

single stranded
- brings A.A. to ribosome as per the codon on mRNA

contains:
Hydrogen bonds
Stem loop
A.A. Attachment site

- sequence of A.A. that twist and fold
- Alpha helix: stabilized by H bonds and long length of backbone
B-pleated sheets: backbone parallel except where it bends 180 degrees, becomes crimped and pleated by H bonds

3-D shape of protein

stabilised by hydrogen bonds, ionic bond/polar interaction, hydrophobic effect, disolfide bridges, and Van Der Waals dispersion folds

multiple polypeptides that interact to form a single functional structure
- subunits: polypeptide
- stabilised by same bonds as tertiary

2'C attached to a -OH

2'C attached to -H, no oxygen

1) Primary: single nucleotide (A,G,C,U)
2) Secondary: forms stem and loop by folding back on itself
3) Tertiary: 2-D structure that folds into more complex, 3-D shapes

eukaryotic

prokaryotic