Proteins Flashcards by Cornelia Blanc

What is the main component of proteins? / the basic unit of a protein

Amino acids

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What are proteins??

Polymeric Biomolecules composed of one or more Chains of Amino acids
linked covalently end to end by peptide bonds (amides).
Proteins have a very specific three-dimensional structure and carry essential functions in all biological process.

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the 4 major biomolecules?

Lipids, proteins, carbohydrates, nucleic acid

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What are biomolecules?

Molecules produced by living organisms that are essential to biological processes

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What are polymers / polymeric molecules?

Macromolecules consisting of many small similar molecules covalently bonded together

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Diff peptide and protein?

Peptides are smaller than proteins, consist of between 2 and 50 amino acids, whereas proteins >/=50 amino acids.

Peptides don’t have secondary, tertiary, and quaternary structures.

Proteins are formed from one or more polypeptides joined together. Hence, proteins essentially are very large peptides

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The central dogma

the central dogma
DNA —> RNA —> Proteins
(more?? expl?)

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where is the seq of amino acids encoded?

The sequence of amino acids in a protein is encoded in the DNA. Proteins
are one of the main effectors of genetic information.

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Are proteins imp in cellular functions?

Yes!!!! Proteins participate in all cellular functions

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How can proteins be divided into structural classes and which ones?

Based on 3D structure

Globular vs Fibrous

and

Membrane proteins and Intrinsically disordered proteins

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Diff Globular vs Fibrous proteins

Globular:
- Compact, spherical
- Water soluble
- Various functions, eg catalytic functions

Fibrous
- Long, Linear
- Insoluble in water
- Structural functions

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Membrane protein vs Intrinsically disordered protein

(????)

Membrane protein
- Soluble in membrane lipids
- Hydrophobic surface
- Diverse functions

Intrinsically disordered protein
- No stable structure
- Diverse functions

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Examples of protein functions?

Proteins can perform an immense variety of functions

Enzymes
* Catalysis of chemical reactions

Structural
* Fibrous scaffolds of the cytoskeleton
and extracellular matrix

Motor
* Generate movement

Transport
* Binding and transporting of
important molecules

Signaling
* Receptors and messengers of
cell’s communication network

Regulatory
* Control the function of other
proteins

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Amino acids
Expected learning outcomes:
* What are α-amino acids
* Why and how amino acids respond to changes in pH
* What are the different side-chains and how can they be divided
* What are the chemical properties of each group of side-chains (non-polar,
polar neutral, polar positive and polar negative)
* What are essential amino acids?

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Proteins are polymers of which kind of amino acids?

Proteins are biological polymers of 20 α-amino acids (monomers)
ALFA amino acids

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What are alfa-amino acids?

(α-amino acids. Amino-carboxylic acids.)
In α-amino acids, an amino group (NH2) in bound to the second carbon (α-carbon) after the carboxyl functional group (COOH). α-amino acids differ by their R group (side chain).

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What make the diff amino acids diff?

The R-group / side chain

What is the same for all amino acids and what do we call this?

They have an amino group and a carboxyl group

Backbone / ??????

Why do amino acids display acid/base behavior and what does the charge of an amino acid depend on?

Amino acids have weak ionizable groups (amino and carboxyl), thus its overall charge is dependent on the pH and the protonation state of the functional groups

What happens to the amino and carboxyl f grps when amino acid in water / neutral pH? (???)

carbonate is a weak acid –> neg ch ion
amino is weak base —> pos ion
when r w water

Describe the “char” of the Carboxyl and Amino grp in terms of protonation at neutral pH.

Carboxyl group (COOH): is a weak acid (pKa«7.0). It has low affinity for H+ and is
deprotonated (COO-) at neutral pH (~7.0).

Amino group (NH2): is a weak base (pKa»7.0). It has high affinity for H+ and is
protonated (NH3+) at neutral pH (~7.0).

What about the R-grp for net charge?

R group: Only amino acids with an acidic/basic at R group will have a net charge! = Only those that have ionizable grps in their R-chain will have a net charge!
Zwitterionic form (no net charge) (excluding the R grp I think)

WHat does the charge of free amino acid in solution dep on?

Descr protonation based on pH

EXCLUDING the R-grps

The charge of an amino acid in solution changes according to the pH!

pH &laquo_space;7 — Fully protonated (positive charge) — NH3+ and COOH

pH ~ 7 — Zwitter ion form. — NH3+ COO-

pH&raquo_space; 7 — Fully deprotonated (negative charge) — NH2 COO-

What are most proteins in living organisms synthesized from?

The majority of proteins in living organism are synthesized from a set of 20 amino acids (proteinogenic), each one with a different side chain

What attributes a proteins' chemical properties?

The side chain!

"Proteinogenic amino acids" means?

= amino acids that are incorporated biosynthetically into proteins during translation. "protein creating". Throughout known life, there are 22 genetically encoded (proteinogenic) amino acids, 20 in the standard genetic code

How are amino acids grouped/classified?

Proteinogenic amino acids can be grouped according to the properties of their side chain (polarity and charge at physiological pH)

What are the 4 diff grps of amino acids based on the properties of their side chain?

Non-polar Polar neutral Polar positive Polar negative Polar ones are water soluble -- hydrophillic, non-polar hydrophobic (right???) (polar neutral has net charge = 0, polar charged have net charge diff than 0)

Expl the diff polar grps of proteins (neutral, pos, neg) how & why charge

Neutral -- dont have weak a/b in the side chain Pos --- have weak base in side chain --- at around pH 7 ---> protonated ---> pos Neg --- have weak acid in side chain --- at around pH 7 ---> deprotonated --> neg

Which amino acid's side chain is considered borderline polar/non-polar?

Cysteine *The S-H bond in cysteine is borderline between polar and non-polar and will be considered both thorughout this course

How do the non-polar side chains interact with water?

They don't!! HYDROPHOBIC ---> want to avoid contact w water

Name the amino acids with non-polar side chains + some props/characteristics of their str

All w. non-polar: Gly (G) Ala (A) Val (V) Leu (L) Ile (I) Phe (F) Trp (W) Met (M) Pro (P) (Cys*** (C)) Gly – the simplest amino acid (R = H) -- only one that doesn't have a C in its side chain Val, Leu, Ile – branched chain amino acids (BCAA) Pro – secondary amino group (cyclic side chain) Phe, Trp – aromatic amino acids = have benzene ring in the R-grp

What amino acids have polar uncharged side chains?

Side chains (polar uncharged) Ser (S) Thr (T) Tyr (Y) Asn (N) Gln (Q) (Cys** (C)) Tyr – aromatic amino acid Cys* – thiol containing amino acid. Can form disulfide bonds

How do amino acids w. polar uncharged side chains interact w water?

* Interact with water (hydrophilic) * Form hydrogen bonds

Which are the aa w polar charged side chains? & which are pos/neg Descr their protonation at neutral pH

Side chains (polar charged) - His (H) - Lys (K) - Arg (R) - Asp (D) - Glu (E) * Asp, Glu – deprotonated at neutral pH (negative) * Lys, Arg, His – protonated at neutral pH (positive)

What kinds of interactions do aa w polar charged side chains partake in? Do they interact w water? What particular beh do they have?

* Interact with water (hydrophilic) * Form hydrogen bonds * Electrostatic interactions interact w water but since also have a charge, they can have ionic interactions, eg neg and pos amino acids tgthr... * Acid/base behavior (pK3)

Expl what is meant by "essential aa" & give examples of such.

Essential amino acids = amino acids that animals cannot synthesize from other precursors and therefore must be obtained in appropriate amounts from the diet * The remaining amino acids, can be synthesized endogenously, to a certain amount * CYS an TYR can be synthesized from MET and PHE * Birds, cats and ferrets: Arginine (R) is essential * Ruminants: rumen microbial metabolism can synthesize all essential amino acids, but… Valine (V) Leucine (L) Isoleucine (I) Methionine (M) Phenylalanine (F) Tryptophan (W) Threonine (T) Histidine (H) Lysine (K) (+ Arginine for Fe, birds, ferrets)

Is it only essential amino acids that should/must be obtained from food?

No! Not nec. To sustain growth and reproduction and depending on the species, age, physiological and environmental factors and pathological states the essential and non-essential amino acids must also be obtained in sufficient amounts from the diet! non-essential only means we CAN prod it just bc of that doesnt mean dont need to consume, may not prod enough

Why do we need to consume proteins?

we need to consume to use their amino acids to make our own proteins -- not to use them as they are break down ---> amino acids ---> make our own proteins