BIOMG 3310 Quiz 1 - QUICK STUDY

Glycine, Gly, G

Aliphatic (non-polar)

Most simple, optically inactive

Hydrogen for R

Alanine, Ala, A

Aliphatic (non-polar)

Methyl for R, a simple functional group to start just like "A" starts alphabet

Valine, Val, V

Aliphatic (non-polar)

Simple, R shaped like a V

Leucine, Leu, L

Aliphatic (non-polar)

Valine extended with one methyle

Isoleucine, Ile, I

Aliphatic (non-polar)

"Lopsided Valine"

Proline, Pro, P

Aliphatic (non-polar)

3 Carbon chain to N

Special Structure found in turns

Ring-stacking!

Methionine, Met, M

Sulfur Containing

Starts every protien

3 Carbons with a thioether

methyl blocked sulfhydryl

Cysteine, Cys, C

Sulfur Containing

Sulfhydryl alanine

reactive, can form disulfides

Ionizable Group (-/neutral)

Phenylalanine, Phe, F

Aromatic

Alanine with phenyl group

y reminds of aromatics

Tyrosine, Tyr, Y

Aromatic

hydroxylated

phenylalanine, one of 3 "T"s

that has "Y" in its name so it is an aromatic

Ionizable Group (-/neutral)

Tryptophan, Trp, W

Aromatic

one of 3 "T"s with a "Y" so it is aromatic, will

"tryp" you up because it is hard to remember,

has a 3 carbon start to N (or indole ring on methylene)

Serine, Ser, S

Aliphatic hydroxyl

"hydroxyl alanine"

Threonine, Thr, T

Aliphatic, "threo" parts are methyl, hydroxyl, and hydrogen on a single C

Aspartate, Asp, D

Acidic

"carboxyl alanine"

"ate" -> acidic

Ionizable Group (-/neutral)

Glutamate, Glu, E

Aspartate plus one methylene, side chain length is signified by alphabetical ordering of the first letter in the names (G is after A)

Ionizable Group (-/neutral)

Arginine, Arg, R

Basic

3 carbon chain linked to a C full of only N's (no H's & C has 4 bonds) through an N

Ionizable Group (neutral/+)

Lysine, Lys, K

Basic

3 carbon chain plus one methylene to amino, it lies ("Lys") about the 3 carbon trend

Ionizable Group (neutral/+)

Histidine, His, H

Basic

3 carbons to N and loop back through C 'n' N

Ionizable Group (neutral/+)

Asparagine, Asn, N

Amide derivatives of acids - loose OH for NH2 to loose charge

amide derivative of aspartate

Glutamine, Gln, Q

Amide derivatives of acids - loose OH for NH2 to loose charge

amide derivative of glutamate

What are the four main categories of biomolecules?

- Lipids

- Carbohydrates

- Nucleic Acids

- Proteins

Why did natural selection result in metabolic reactions that are too slow for life?

So they can be controlled and/or regulated by catalysts.

Compare the size scale of biochemistry relative to the universe.

Biochemistry: Atoms/chemistryUniverse: Measured in lightyears

Explain why humans and plants need each other to exist.

Interdependent processes of human metabolism (produces CO2 and H2O) and plant photosynthesis (produces carbs and O2).Plants need CO2 and H2O; humans need carbs and O2.

Compare the conditions of Earth and the core of a star. Justify why one is suitable for nuclear fusion and the other for chemical bond formation.

Earth isn't as hot as the core of stars so the temperature is suitable for chemical bond formation, whereas the hot temperature at the core of stars allows nuclear bond formation.

Justify the truth of the statement, "We are made of stardust".

Nuclear fusion in star cores produces the lighter elements that we are made of, such as hydrogen.

Memorize the equation that expresses pH in terms of [H+].

pH = -log10 [H+]

Memorize the Henderson-Hasselbalch equation in both log and inverse log forms.

10^(pH - pka) = [unprotonated/protonated]

Determine the dominant charge form of an ionizable group, given its pKa value and the pH.

pH < pKa → protonated

pH > pKa → unprotonated

pH = pKa → equally protonated/unprotonated

Protonated: + / 0 (His, Lys, Arg)

Unprotonated: 0 / - (Asp, Glu)

Describe the formation of a peptide bond (what specific groups are involved, what are the reactants, and what are the products).

COO- loses an oxygen, NH3+ loses 2 hydrogens. The product is a peptide and H2O

Describe the thermodynamic basis for the hydrophobic interaction (what type of energy is the driving force).

Water entropy is the driving force. If protein is folded, water has more opportunity to make H-bonds with other water molecules. Polar AAs are on outside of folded protein chain, nonpolar AAs are on the inside.

Isozyme/isoenzyme/isoform

From the same organism, catalytically and structurally similar enzymes, but AA sequence is slightly different (example: LDH and CPK)

Define "primary structure" and explain why it is important and what it can be used for

The AA sequence that can be used to eventually determine the 3D shape of a protein.

Define homolog

two genes with sequence similarity, regardless of function, share a common ancestor

Define paralog

related genes in the same species

Define ortholog

genes in different species with clear similarity in sequence and function

Understand why the comparison of primary structures of orthologs provides evolutionary relationships among organisms.

Orthologs descend from a common ancestor but are found in different species, which can help draw connections back to evolution.

Describe bioinformatics.

Uses large datasets to better understand how life works

What is AlphaFold?

It is a protein folding prediction algorithm that represents a significant step forward in protein folding prediction; recent advancements in 3D protein structure prediction.

List three main ways the atomic-level 3D structure of proteins can be determined.

- X-ray diffraction of protein crystals

- NMR of protein dissolved in buffer.

- Cryo electron microscopy

Describe light.

light is an electromagnetic wave produced by an oscillating electric field that produces mutually perpendicular oscillating electric fields and magnetic fields

Describe "the phase problem"

the loss of crucial phase information during a diffraction experiment (like X-ray crystallography), making it impossible to directly determine the structure of a molecule from the measured diffraction intensities alone

What are the six categories of non-covalent interactions?

1. Hydrogen bonds

2. Electrostatic (ion pair, salt bridges)

3. Disulfide bonds (covalent, think cystine)

4. Weak and weakly covalent bonds (ion-dipole, dipole-dipole, and London dispersion forces (van der waals))

5. Ring stacking (w/ Proline!)

6. Hydrophobic Interactions

Hydrogen bonds

form between backbone atoms of the polypeptide chain to stabilize alpha-helices and beta-sheets (secondary structures)

Electrostatic bonds

interaction of amino acids based on their charge

Disulfide bonds (covalent)

tertiary and quaternary structure

cysteine

London Dispersion Forces

stabilize the hydrophobic interior of globular proteins by attracting nonpolar side chains

Dipole-Dipole forces

(alongside hydrogen bonds) attract polar uncharged side chains

Ion-dipole forces

occur between charged amino acids and polar groups or water, contributing to protein folding and function in aqueous environments

Ring-stacking

dipole-dipole interaction between two aromatic groups

Hydrophobic interactions

drive protein folding by forcing nonpolar (hydrophobic) amino acid side chains to cluster in the protein's interior, away from water, creating a stable, hydrophobic core

ionizable groups in amino acids

1. terminal carboxyl group

2. terminal amino group

3. Asp and Glu acids

4. His

5. Cys

6. Tyr

7. Lys

8. Arg

terminal amino

(unprotonated/protonated) = (neutral/+)

terminal carboxyl

(unprotonated/protonated) = (-/neutral)

If pH >>> pKa

H+ is "off" (deprotonated)

If pH <<< PKa

H+ is "on" (protonated)

If pH = Pka

[unprotonated] = [protonated]

rate = 1/2

condensation reaction

forms peptide bond

hemoglobin

tetramer that transports oxygen

myoglobin

monomer that stores oxygen; allows transport of oxygen to mitochondria

prosthetic groups

non-amino acid group covalently bonded to protein

holoprotein

protein with a prosthetic group (the WHOLE protein)

Apoprotein

just the protein itself (no prosthetic group)