The name’s Bond. Peptide Bond. We’ve talked about “condensation” as a gas turning into a liquid, but my favorite type of condensation is when protein letters (amino acids) “condense” by joining together to form a peptide bond. And they can keep doing this to make a long chain of amino acids that can fold up into a functional protein.
Amino acids, like all matter for that matter, are made up of atoms which are the basic units of elements (things like carbon (C), hydrogen (H), nitrogen (N), & oxygen (O)) – see the Periodic Table for a full menu. Different elements have different numbers of tinier things called protons. These +-charged subatomic particles hang out in a central core called the nucleus (along with neutral neutrons) and their positive pull helps reign in a cloud of negatively-charged electrons that whizzes around them.
The outermost electrons are called valence electrons. They’re furthest from the nucleus’ pull, have the most energy, and can interact with electrons from other atoms. Since opposite charges attract, protons have electron pulling power, but so do other +-charged things in other molecules.
So electrons can get attracted to other molecules and drag the rest of their molecule along with them to investigate. Like it enough and the 2 molecules might end up sharing a pair of electrons to form a covalent bond. They can even share 2 pairs to form a double bond or 3 for a triple. Since both atoms are invested in these bonds, they’re strong, especially when they have multiple electrons in the game (like in a double bond)
You can think of a covalent bond as a kind of reign – the more electronegative, the tighter the reign and add a second like you have in a double bond and that’s some strong reigning-in potential! So double bonds are stronger than single bonds and they’re shorter.
Another consequence of double bonding is that it prevents twisting. Whereas a single bond’s rotatable, a double bond’s kind like if you stand across from someone and try to shake both hands while twisting around. Molecules can’t do that sort of contortionism. So, as a result, movement around a double bond is restricted
Another thing about electron-sharing is that. when atoms share electrons, they don’t always do so fairly. One of them may hog the shared electrons and we say the hogger is ELECTRONEGATIVE.
Oxygen’s one of those really hoggy ones. And in biochemistry it shows up a lot. And a lot of the time it shows up double-bonded to a carbon (C). We call such a -(C=O)- a carbonyl. You’ll find these a lot of places in biochemicals – it’s 1 of most important “functional groups” because the O pulling e- density away from the C makes the C more reactive because it’s positively desperate for some electron-rich friends (we call such things electrophiles and you can learn more about them here – http://bit.ly/2KXq9OU
A functional group’s just a commonly-found atomic combo that has certain properties that it keeps regardless of what it’s stuck onto. Like how you could tape a spoon to anything and still (albeit potentially with great difficulty) scoop ice cream with it, whereas you could tape a fork to it and not have luck – but the fork would still have its fork-useful-ness. More here: http://bit.ly/2IXlz0i
So, going back to this “biochemical spoon of sorts.” O had 6 electrons “of its own” going into the bond, so even with those 2 electrons of is going towards the double bond, it still has 2 “lone pairs” of electrons that attract hydrogens that are attached to electronegative things like N or O and are thus (δ+). When an electronegative atom with a lone pair (like the O in a carbonyl) is attracted to an H attached to an electronegative thing, you get something called a hydrogen bond (H-bond). It’s not a strong bond like the covalent bond (no actual electron sharing, just attractions) but they can add up. There’s structural strength in numbers – and there are lots H-bonds in proteins!
But that O needs its scaffold and that’s where carbon (C) comes in. It has 4 electrons “of its own” to share. It can give 1 to each of 4 other atoms to form 4 single bonds, or double or triple up to connect more strongly to fewer atoms. When it forms a double bond, like in a carbonyl, that takes 2 electrons, so it still has 2 left.
when C=O is attached to an alkyl group “R” (H or C attached to Rest of molecule) on 1 side it’s called an ACYL & still has free side. And depending on what that free side’s attached to, we give it different names.
If it’s attached to OH we call it a CARBOXYL. Since when an H is attached to a hoggy O it can come and go, a carboxyl can exist in 2 forms: if O’s bound to H it’s a CARBOXYLIC ACID. When that acid acts as an acid (donates an H+) we call the O deprotonated and call it a CARBOXYLATE (which is the conjugate base of the carboxylic acid – more on acids and bases: http://bit.ly/2Zj3mFe
Without the + of the H+, the carboxylate is negatively charged, so we call it an ANION (as opposed to positively-charged things which we call cations).
When the (C=O) is attached to nitrogen (N) we call it an AMIDE. N is similar to O in a lot of ways – both are electronegative and have lone pair(s) of electrons – but O has 2 lone pairs whereas N only has 1 (and 1 more electron free for bonding). So N can also form H bonds when that lone pair’s not in use. And sometimes an N uses its lone pair to snatch up a proton like the ones acids pass out.
You’ll find both of these – carboxyl & amide when you start linking up amino acids. Amino acids revolve (literally & figuratively) around a central carbon (Cα). C can form up to 4 bonds & Cα makes use of all of em. On 1 side it bonds to an *amino* (nitrogen/hydrogen) group 👉 other side a carboxylic *acid* group (-COOH) 👉 AMINO ACID!
The other 2 bonds? 1’s to H & other’s to an “R GROUP” (aka SIDE CHAIN) 👉 part that makes each of the 20 aa unique. More about each of them starting http://bit.ly/2pQ77hI
Amino acids join carbonyl (C=O) group of one to amino group of other ⏩ “CONDENSE” to form PEPTIDE BOND (aka amide bond) – individual amino acids have carboxyl groups and when they link up they swap that carboxyl for an amide. On net this requires the loss of an OH (from the carboxylic acid) & an H (from the amine group) so, 2 H & 1 O – H2O – water. So this is also known as a dehydration reaction – but when your cells do it they don’t directly lose water cuz they do it stepwise.
PEPTIDE BONDS are special because they’re resonance-stabilized. Chemicals want stability & a great source of stability is RESONANCE (delocalized e⁻ sharing). In order for electrons to be shared through resonance they have to have their electron clouds synced up just right – you need them to all be on the same plane (planar). Think of a hose – if you want water to flow through the hose you can’t have the hose pinched – atoms have to stay “flat” to share. So they trade charge stabilization for some restriction of movement.
ELECTRONEGATIVE (e⁻ hogging) O of carbonyl pulls so hard it drags e⁻ density from N (which has a lone pair) even though there’s a C between them. This e⁻ delocalization is very stabilizing BUT it can only occur if atoms are lined up in the same “plane” – so the peptide bond is PLANAR – no rotation is allowed
Each time you join 2 amino acids, you lose the carboxyl (but keep the carbonyl!), gain an amide, & form one of those planes. And keep combining amino acids like this & you get a “chain of planes” connected at Cα “nodes.” Because of that whole resonance stabilization needing stiffness, there’s NO rotation about C-N bond. BUT you DO have rotation around other backbone bonds. These ⟳ are between 2 planes so we call them DIHEDRAL ANGLES (aka TORSION ANGLES). And, like a Geek sorority, they have Greek names.
🔹 phi Φ 👉⟳ about N-Cα
🔹 psi Ψ 👉 ⟳ about Cα-C
🔹🔹tips 4 remembering 👉 psi sounds like it could start w/C & looks kinda like a sideways C on a stick 🤷♀️
These ⟳ are possible bc you can rotate “freely” around single bonds, BUT they aren’t really “free” bc of STERIC HINDRANCE – basically 2 atoms can’t be in same place – the bigger the side chain, the less the flexibility
Actual angles bonds take are usually less “random” because the backbone’s perfectly placed H-bonding groups can interact to form “secondary structure” (like helices & strands) when they take on characteristic angles. In fact, you can look at something called a Ramachandran plot which shows the angles taken by atoms in a molecule. When we’re solving a crystal structure we often check that the angles are geometrically solid & one of the things you’ll see in the “report card” for a structure is “Ramachandran outliers” If people are interested, maybe I’ll do a post on these plots…
a couple other cool things:
The C-N bond has partial double bond character, so it’s shorter than normal C-N bond but longer than a C=N bond
Since the O is stealing electron density, and electrons are negative, the O becomes partly ➖ (δ-) & the things it steals from (N & H) become partly ➖ & N & its H partly ➕(δ+). High hydrogen bond (H-bond) potential! So the protein backbone is peppered with evenly-spaced H-bond donors (the N-Hs) and acceptors (the carbonyl O) – so you can get consistent H-bonding patterns perfect for things like forming the alpha helices & beta strands that give proteins their secondary structure!
Amino acids may wed thru a peptide bond 👫 BUT it’s not quite a love story! Forming these bonds is energetically unfavorable (that whole decreased entropy thing) so small pieces of RNA called transfer RNA (tRNA) act as matchmakers, binding to aa’s carboxyl group & making it more attractive to amino groups ⏩ bring them to an multisubunit RNA/protein enzyme called RIBOSOME where condensation occurs. We call this process of using an RNA template to put together amino acids to form a protein TRANSLATION and you can learn much more about it here: http://bit.ly/31IwofL