lec 3 proteins

how many diff proteins do humans have

25 000

explain how proteins have a high degree of specifity

they have diff shapes and surfaces that allow to interact SELECTIVELY with other molecules

proteins have so many functions, list many types of proteins and their function briefly

Enzymes - catalysts that increase rate of chemical reactions

Structural proteins - physical support/shape

Transport proteins - move substances in/out cell

Signaling proteins - communication between cells

Storage proteins - resevoirs of amino acids (holds them readily)

Mobility proteins - contraction/movement

Regulatory proteins - control/coordinate cell function

Receptor proteins - enable cells to respond to stimuli

Defensive proteins - protect against disease

what are 4 levels of protein organization

primary (amino acid residues), secondary (a helix), tertiary (polypeptide chain), quaternary (assembled subunits)

what determines the 3D structure of a protein, and what determines the function of a protein

amino acid sequence determine 3D structure

structure determine function

what do u use to describe size of amino acid or peptide

MOLECULAR WEIGHT (MW)

units: Daltons DA or Kilodaltons kDA

whats the amino acid with highest vs lowest mass

highest mass: Tryptophan (W)

lowest mass: Glycine (G)

proteins are ____ made of ____ monomers

proteins are polymers made of amino acid monomers

how many diff standard amino acids are there and what 4 things do ALL amino acids have?

20

1. carboxyl group

2. amino group

3. single carbon atom (a-carbon)

4. unique side chain (R GROUP)

what happens to an amino acid’s charges at ph 7

the carboxyl group LOSES proton and becomes NEGATIVE

the amino group ACCEPTS proton and becomes POSITIVE

all amino acids except ____ have an asymmetric a carbon, so each aa can exist in either D or L form

glycine (symetrical a carbon)

are aa’s used in synthesis of protein on ribosome always D or L aa?

always L aa

specific properties of aa depend on the nature of their ____. they differ in:

R GROUP

differ in:

size, shape, charge, H bond capacity, hydrophobic character, chemical reactivity

what are some things unique to nonpolar amino acids? like where are they found, what do their side chains consist of, and they play an imporant role in what?

-usually BURIED in core of proteins or membranes, away from aqueous medium - GREAT for hydrophobic interactions and van der Waals forces

-hydrophobic side chains consist mostly of C and H atoms

-play important role in membranes by associating w lipid bilayer

examples of nonpolar amino acids?

Alanina Ala A

Valine Val V

Leucine Leu L

Isoleucine Ile I

Methionine Met M

Phenylalanine Phe F

Tryptophan Trp W

where are polar UNCHARGED amino acids found? what is this good for? what do their side chains tend to have

POLAR UNCHARGED aa found on SURFACE of proteins (great for H bonding)

-hydrophillic side chains have partial + or - charge allowing them to participate in chemical reactions, form H-bonds, and associate with water

what allows hydrophillic side chains of polar uncharged aa to participate in chemical reactions, form H-bonds, and associate with water

partial + or - charges

what are examples of polar UNcharged amino acids VS polar CHARGED amino acids

polar NO charge:

Serine Ser S

Threonine Thr T

Glutamine Gln Q

Asparagnine Asn N

Tyrosine Tyr Y

polar CHARGED:

Aspartic acid Asp D (negative)

Glutamic acid Glu E (negative)

postiive:

Lysine Lys K

Arginine Arg R

Histidine His H

within polar charge amino acids, which are positive and which are negative?

acidic are negative (think acidic donate H and become -)

basic are positive (think basic accept H and become +)

how do hydrophillic side chains of polar CHARGED aa act?

act as acids or bases that tend to be FULLY charged (unlike partial charge of polar uncharged hydrophillic side chains) under physiologic conditions, and these side chains form ionic bonds and often involved in chemical reactions

what are the 3 unique amino acids with special properties? what are the special properties

Glycine (Gly G) - side chain (R group) is only ONE H atom that can fit into hydrophillic OR phobic enviro

-Gly often found at sites where 2 polypeptides come into close contact

Cysteine (Cys C) - even tho side chain is polar uncharged, it has unique property of forming COVALENT bond with another Cys to form disulfide link

Proline (Pro P) - even tho side chain is hydrophobic, it has unique property of making KINKS in POLYPEPTIDE CHAINS and DISRUPTING SECONDARY structure

where is glycine often found

sites where 2 polypeptides come into close contact

what is the name of the process of elongating a chain of amino acids, and what explain the steps of the process

protein synthesis

-amino acids undergo CONDENSATION (dehydration) reaction where carboxyl of one aa react w amino group of another aa (H and OH combine to make water, then water removed)

-reaction summary: aa+aa = joined aa’s + H2O

-PEPTIDE BOND FORMED (joined the 2 aa’s C-N)

-repeat those steps with a new aa added each time, makes chain

-now u have polypeptide BUT not protein yet until chain completed and it FOLDS (making unique stable 3D structure that is biologically active)

what has to happen before a polypeptide can become a protein

FOLDING (create unique stable 3D shape thats biologically active)

describe what the primary structure is like

LINEAR STRAND of AMINO ACIDS (has all info needed for secondary structure)

primary structure sizes range vary, whats example of small one vs big one

small: Aspartame (dipeptide only 2)

big: Titan (33k aa)

what generates the secondary structure and what is the structure

local Hydrogen bonds among aa’s generate structure

structure: a helix and B sheet

describe the shape of the a helix (secondary structure), how many aa per turn, and between what groups the H bond forms

-SPIRAL, peptide backbone with R groups pointing out from the spiral

-3.4 aa per turn (peptide bonds of every 4th aa come close)

-H bond forms between NH of one aa and CO of next aa thats one turn away from first

what are the FOUR constraints affecting formation/stability of a helix? aka what are the factors that determine how a polypeptide chain will fold into an a helix?

1. Electrostatic repulsion/attraction between adjacent aa’s with charged R groups

2. Bulkiness of adjacent R groups

3. Interactions between R groups (3 or 4 residues apart)

4. Helix FORMERS (Leucine L, Methionine M, Glutamate E and helix BREAKERS (Proline P, Glycine G)

describe what a B sheet is and what are the locations called of the successive atoms of the polypeptide chain

B sheet - has several segments of a polypeptide strand lying SIDE BY SIDE in FOLDED/PLEATED conformation with R groups pointing out on alternating sides of sheet

-succesive atoms are located at “peaks” and “troughs”

which amino acids are B sheet formers

Isoleucine (I) Valine (V) Phenylalanine (F)

compare B sheet formation with a helix formation

-both stabilized by many H bonds, but B sheet formation can involve diff polypeptides or diff regions of SINGLE polypeptide

draw parallel vs antiparallel B sheet

parallel run same direction (angled bonds, weaker), antiparallel alternate (straight, strong, stable bonds)

what are the major structural elements in a protein

a helix and B sheet (60% of protein)

what are the most flexible portions of a polypeptide chain and the sites of GREATEST bio activity

hinges, turns, loops, finger-like extensions

what are Motifs

Motifs (folds) - UNITS of secondary structure consisting combinations of short stretches of a helices and B sheets CONNECTED by loops/turns (unrelated primary sequences can still form same motif)

proteins can be classified by these combinations of secondary

structures (motifs) into

Protein Families

what does tertiary structure describe?

the conformation of the entire polypeptide

what is secondary structure stabilized by and what is tertiary structure stabilized by? and how can u compare secondary vs tertiary number of possible conformations

SECONDARY: stabilized by H bonds of polypeptide backbone

TERTIARY: stabilized by covalent + noncovalent bonds between side chains of protein

secondary: limited to small number of conformations

tertiary: unlimited

what are two experimental methods to determine tertiary structure

1. X-ray crystallography (high resolution structures for LARGER proteins, but limit: proteins must be crystallized)

2. Nuclear magnetic resonance (NMR) spectroscopy (don’t require crystallization, provide info abt dynamic structural changes, can reveal drug binding sites, but DIFFICULT to use on larger proteins) BETTER FOR SMALLER

what are diff ways to represent tertiary structure, but what is usually omitted from the illustrations?

Ball and Stick model

Surface model (looks blobby)

Spiral and Ribbon model

-side chains (R groups) not in illustrations

tertiary structures are stabilized by covalent and non-covalent interactions, what are they (5)

Non-covalent: H bonds, Ionic bonds, van der Waals interactions, hydrophobic interactions

Covalent: Disulfide bridges (between cysteine residues)