Chapter 5: Amino acids, Peptides and Proteins Flashcards Preview

Introductory Biochemistry > Chapter 5: Amino acids, Peptides and Proteins > Flashcards

Flashcards in Chapter 5: Amino acids, Peptides and Proteins Deck (50):

Amino acids are amphoteric meaning what?

can act as a base or acid


At pH = 7 amino acids exist as zwitterions meaning?

- two ions on two different atoms in the same molecule


All amino acids have an acidic carboxyl group (-COOH) and a basic amino group ( -NH2).....therfore amino acids are classified by what?

- their R groups which make them different ! -Nonpolar: R contains, aromatic, aliphatic( carbon chains) and or sulfur groups - Polar, neutral: R contains -OH or an amide (NH2) -Acidic: R contains COOH..which donates H - Basic: R contains N that can accept H ***commonly written as structure at pH= 7 therefore R of acidic...would be say pH 7 it equals CH2COO-


All amino acids are abbreviated to the first three letters accept these four!

- Ile : Isoleucine - Asn: asparagine - Trp: tryptophan - Gln: glutamine


How are amino acid biologically active?

- chemical messengers : Neurotransmitters: glycine, glutamate, GABA, serotonin, melatonin L>Hormones: thyroxine, indole acetic acid - precursors to form complex N containing molecules (nucleotides, heme, chlorophyll ) - metabolic intermediates


How can amino acids be modified to form amino acid derivatives?

- carboxylation - hydroxylation - phosphorylation( of ser, thr and or tyr residues in proteins is used to regulate metabolic pathways) ( an OH is phosphorylated)


What does stereochemistry of aa's affect?

- structure of protein and therefore function


Asymmetric or chiral carbons?

- alpha carbon (first to attach to a attached to four things! ex: H, COOH, amino group and R group)



- molecules with chiral carbons ...they differ only in spatial arrangement of their atoms



- when isomers are mirror images of each other and cannot be superimposed on each other...they have identical physical properties but they rotate plane polarized light in opposite directions.


Optical isomers? L> dectrorotary L> levorotary

-rotate plane polarized light in opposite direction which is produced by passing unpolarized light through a special filter, the light waves vibrate in only one plane


What are the steps to titration of amino acids?

- draw it in its most acidic form ( fully protonated ....H) - Draw it gradually as it becomes more basic - determine isoelectric point (pI) the pH where the overall charge is zero..aka zwitterion


How do you determine the isoelectric point?

1. draw the aa in its most acidic form...aka fully protonated many pKa's does it have? 3. the one with the lowest pKa will lose a hydrogen first (usually, COOH) draw this new structure. 4. the next lowest pKa will lose its H.....draw this structure (usually the amino group) 5. the next lowest if it has an R group will now lose its H...draw this new structure *pKa= pH in this ! 6. examine the new structures......which ever structure has a net charge of zero you avg the pka values of either side and this gives you the pI.


Explain peptide bond formation! (characteristics of it?)

- bond?



- has a partial double bond character due to the peptide bond is rigid and planar... the alpha carbon is next the peptide bonded CdoublebondO

- there is rotation around the Calpha-N and the Calpha-C but not around the peptide bond 

-amino acid residues: amino acids that are part of a peptide or protein chain. 

- draw peptides from N-terminal to C-terminal...also name them this way


Amino acids are linked by a ___ bond between the ___ of one amino acid and the ___ of another. 

- covalent 

- alpha amino (-NH2) 

- alpha carboxyl (-COOH)


When peptide bonds are formed what is lost?

an H from  the amino group and an OH from the carboxyl group......which from water. aka its a dehydration 


The C-N bond of the peptide bond is much ___ and much more ___ than a typical carbon-nitrogen single bond. This is due to its___.

- Function of this?

- shorter, ridgid, resonance (goes from single to double bond) 

- the carbon nitrogen double bond is planar, flat and this makes it rigid....limiting the number of forms a protein/peptide can element of control basically....since there is this control in how proteins can fold and form shapes results in greater control and specificity of protein function! 


Proteins are classified by what?

structure, shape or composition


Protein functions? (7)

- catalysis(enzymes), structure(ex collagen), movement(ex actin), defense, regulation(binding a hormone molecule to conjugate receptors to change cellular function) , transport(carriers of molecules...across membranes etc...ATPase or hemoglobin), storage(reservoir of essential nutrients) and stress resposne(capacity of an organism to survive in a variety of abiotic stresses....ex cytochrome P450


What are the two shapes of proteins?

- globular and Fibrous 


Exlpain fibrous proteins

- long, rod shaped molecules tht are insoluble in water and physically tough.......structural and protective functions


Globular proteins?

- compact spherical moelcules that are water soluble...have dynamic functions...enzymes are this...immunoglobins, hemoglobin 


Two types of protein compositions?


- conjugated : simple protein combined with a non protein component(called a prosthetic group) ex: glycoproteins(contain a carb), lipoproteins, metalloproteins, phospoproteins, hemoproteins..

L> a protein without this group is called an apoprotein 

L> a protein combined with a prosthetic = holoprotein 

- simple: only contains aa's 


What are the classifications of protein structure?

- Primary, Secondary, Tertiary and Quaternary 


Primary structure?

- amino acid sequence 

-invariant residue : changes in aa seq that do not change peptide function 

- variable residue: mutations that change the aa seq and funciton 



Secondary Structure?

-consists of several repeating patterns

L> alpha helix and beta pleated sheets 


Secondary Structures: 

- alpha helix: ?

- right handed helix....3.6 residues per turn..pitcj= 54nm 

- hydrogen bonds between N-H and CdoublebondO are four residues apart and r groups extend outward from the helix



Secondary Structures: 

- beta pleated sheet?

- Beta strand. parallel( h bonds in polypeptide chain are arranged in the same direction) vs antiparallel(arranged in opposite directions)

-stabalized by H bonds between N-H and CdoublebondO of adjacent chains

- each beta strand is fully exteneded...antiparallel is more stable because the H bonds are more direct (colinear) 


Supersecondary structures or motifs?

- proteins that contain both alpha helix and beta pleated sheets

-many globular proteins are this.  

- BalphaB: 2 parallel b pleated sheets are connected by an alpha helix

- B-meander: two antiparallel sheets are connected by polar amino acids and glycines

- alpha alpha: two alpha helical regions separated by a nonhelical loop. 

- beta barrel: various b sheet configs fold back on themselves 

- green key: antiparallel b sheet doubles back on itself 


Tertiary structure??

(features 4)

- unique structure conformations of globular proteins!

1. amino acids far apart in primary structure can be close via folding

2. globular proteins are compact

3. large globlar proteins often contain domains - compact units with specific functions 

4. modular or mosaic proteins: contain umerous duplicate or imperfect copies of one or more domains that are linked in a series 


Tertiary structure stabilizing factors?

- hydrophobic interactions

- electrostatic interactions (salt bridges)

- hydrogen bonding

- covalent bonds (disulfide bonds)

- hydration: structured water forms a dynamic hydration shell that stabilizes the protein structure 


Quaternary Structure??

- several subunits....polypeptide chains

- oligomers and protomers=why multisubunits are common

- noncovalent bonding and covalent interactions hold the subunits in place 

- hydrophobic effect

- covalent cross links: disulfide bridges. desmosine and lysinonorleucine 

- allostery, ligand binding, allosteric transitions, effectors or modulators 



- control of the protein function via binding ligand.....triggering conformational changes tat alters its affnity to other ligands. 



Allosteric transitions?

- ligand induced conformational changes in proteins 

- ligands that trigger them= effectors or modulators 


Unstructured proteins? (IUPS: intrinsically unstructured proteins) 

- partially unstructured 


- natively unfolded proteins?

- no order of structure! 


IUP function?

- regulation of signal transduction, transcription, translation and cell proliferation....the disorder allows them to be more flexible and search for binding partners....they become more ordered once they find one. 


Protein denaturation?

- lost of 3-D structure ....interaction between aa residues are disrupted but peptide bonds are NOT BROKEN. 

- anything that can interfere with the stabalizing forces - denaturation 


List the denaturing conditons ? (8)

1. strong acid or bases: change in pH alters hydrogen bonding and salt bridge pattern (approching pI= parcipitation from solution) 

2. Organic solvents: water soluble solvents interfere with hydrophobic interactons

3. detergents: disrupt hydrophobic interaction causing proteins to unfold into extended chains (amphipathic..containing hydrophilic/phobic components) 

4. reducing agents: convert disulfide bridges to sulfhydryl groups. 

5. salt concentration: as it increases = few water molecules from increased interaction with proteins...therefore..solvation spheres form around the protein casuing them to salt out...parcipitate. 

6.heavy metal ions: disrupt salt bridges via ionic bonds, bonding with sulfhydryl groups changing structure. 

7. temp changes: as it increases mol vibration increases....hydrogen bonds break..protein unfolds. 

8. mechanical stress: stirring and grinding interactions disrupt features that maintain structure.


Traditional folding model? 


- interactions ebtween aa side chains alone force the molecule to fold.

- time happens in seconds... not in years 

- complexity 


molecular chaperones?


-bind to denatured or unfolded proteins

- protect unfolded proteins 

- asist protein folding rapidly, precisely and correctly 

- promote protein degradation when refolding isnt possible 


Most molecular chaperones are?

- HSPS: heat shock proteins




- skeletal and cardiac muscles 

- single protein component - globin 

- free heme  which is enclosed by the globin

L> affinity to O

- better at storage of O = greater affinity than hemoglobin



- spherical 

- transports oxygen from the lungs to every tissue in the body 

- four chains of hemoglobin 

- each has a heme binding unit 


Taut vs R states?

- Taut: deoxygenatated state

- R: oxygenated state 



- cleaves at the carboxyl end of peptides 



- cleaves peptide bonds at aromatic aas that contrib a COOH( Phe, Tyr, Trp)



- cleaves at the carboxyl end of Lysine and Arginine 




- tags the terminal amino acid! ..hydrolysis than cleaves the peptide bonds