Lecture 4: Protein Structure I: Hierarchy And Primary Structure

Front 1

tripeptide

tetrapeptide

pentapeptide

Back 1

3-aa, 2-peptide bonds

4-aa, 3-peptide bonds

5-aa, 4-peptide bonds

Front 2

oligopeptide

Back 2

A few aas joined by peptide bonds

Front 3

polypeptide

Back 3

A long chain of aas joined by peptide bonds

Front 4

oligomeric

Back 4

multisubunit protien w/ indentical subunits

Front 5

protomeric

Back 5

multisubunit protien with at least some different someunits

Front 6

conjugated protiens

Back 6

contain chemical components in addition to aas

Front 7

prosthetic group

Back 7

non-amino acid part of a conjugated protein

Front 8

lipoprotiens

Back 8

conjugated protein with a lipid prosthetic group

Front 9

glycoprotein

Back 9

conjugated protein with a sugar prosthetic group

Front 10

metalloprotein

Back 10

conjugated protein with a specific metal

Front 11

protein length

Back 11

100 - several thousand aas

Front 12

Peptide bond formation

Back 12

Condensation

Carboxylic acid loses -OH and amino loses -H releasing H2O

Will not occur at physiological pH

Front 13

Levels of protein structure

Back 13

Primary: AA sequence

Secondary: Stable arrangements of AAs giving rise to recurring structural patterns

Tertiary: 3-d folding structure

Quaternary: Multisubunit arrangement

Front 14

polymorphic

Back 14

multiple forms of a protein in one species

Front 15

bioinformatics

Back 15

the use of computers to analyze biological data

Front 16

Consensus Sequence

Back 16

A DNA, or Amino Acid sequence consisting of residues that most commonly occur at each position in a set of similar sequences

Front 17

Homologs

Back 17

Members of a protein family

Front 18

Paralogs

Back 18

Homologs from the same species

Front 19

Orthologs

Back 19

Homologs from different species

Front 20

Signature sequence

Back 20

A segment of a protein sequence unique to a taxonomic group

Front 21

Hydropathy Plot

Back 21

<HI> plotted vs. residue #

Front 22

Positive inside rule

Back 22

Positively charged AAs (Lys, His, Arg) occur inside cell in transmembrane proteins

Front 23

Multiple Sequence Alignment (MSA)

Back 23

-Many Algorithms

-Output includes:

-Aligned sequences

-% Identity (>25% is high confidence)

-% Similarity (Some substitutions have low impact)

-E value (Probability match happened by chance, low: not by chance, high: by chance)

Front 24

Invariant positions

Back 24

-Identical in all positions

-indicates structural or functional importance

-(*)

Front 25

Conservative changes

Back 25

-Similar chemical or size properties

-(:) and (.)

Front 26

Graphical MSA plot

Back 26

-Quickly Id patterns and properties

-Colors indicate property, size indicates occurrence

-red: acidic

-blue: basic

-black: hydrophobic

Front 27

Consensus Sequence Plot

Back 27

-Representation of consensus sequence with more detail

-{x}: All AA except x

-[x,x,x,x]: Any in brackets allowed

-x(n): x repeated n times

-x(i,j): x repeated i to j times