What is a molecule?
A structure of multiple atoms linked by covalent bonds
What is a covalent bond?
The sharing of electrons to complete an outermost shell
What is electronegativity?
The tendency of an atom to attract electrons to complete its shell
What is the result of a very electronegative atom sharing an electron with relatively non electronegative atom? What is the result in less extreme cases?
Polar vs. Non polar covalent bonding
What is an ion?
When an atom has different number of electrons than protons?
What is a cation?
What’s its charge?
Give examples
When the atom has more protons than electrons (positive charge)
Na^+, K^+, Mg^2+, Ca^2+
What is an anion?
What’s its charge?
Provide an example
When the atom has more electrons than protons (negative charge)
Cl^-
What is an ionic bond?
Why is it weak in water?
When one extremely electronegative atom, steals the electrons away from a lesser electronegative atom (NaCl is an example), NOT A COVALENT BOND WHERE THEY SHARE
Weak in water because the two ends are attracted to opposite ends of the polar water molecule and become seperated
What does it mean to be “hydrophilic?”
Having a tendency to mix with, dissolve in, or be wetted by water
“Water-loving”
What does it mean to be “hydrophobic?”
Having a tendency to repel and not absorb, not mix well, or not dissolve in water
“Water-fearing”
What are hydrogen bonds?
What do they give the property of?
Hydrogen atoms holding a slight positive charge, having an attraction for an atom with a negative charge.
Give the property of cohesion or a tendency to stick together in a substance
What is the process of denaturing?
Breaking down all non-covalent bonds but leaving the covalent ones intact
What is the backbone of all organic molecules?
Carbon
What is the max number of covalent bonds a carbon atom can for with other atoms?
4
What aspect of carbon bonding contributes to the functional diversity of organic molecules?
The Geometry
What functional groups (moieties) are frequently attached to carbon chains in biomolecules? What do they do?
Hydroxl- (polar); Carbonyl-; and Amino- (ionic)
They alter molecular characteristics
What are the four organic molecules?
Proteins, Nucleic Acids, Carbohydrates, and Lipids
What are sugars? What are they used for? What can they be linked to form?
Sugars are carbohydrates that can be used as a source of energy. They can be linked into complex carbohydrates
Are Lipids Hydrophobic or Hydrophilic?
Hydrophobic
What are Triacylglycerols?
What are they made up of?
Lipids that store energy and are made up of glycerol and fatty acids
What are fatty acids?
What do they always have at one end?
What are they composed of?
Linear hydrocarbon chains of variable length.
Always have a carboxyl group at one end.
Composed of repeated C2H4 elements
What is a defining aspect of unsaturated fatty acids?
They have one or more carbon-carbon double bonds
What force is responsible for the tight packing of fatty acids in lipids?
What is this force?
Van der Waals forces
A type of weak, noncovalent bond
What do the spatially spread out bonds allow for in a carbon molecule? Why is this useful?
Rotation, allows for different shapes and structures to be built from carbon molecules
What is an isomer?
Two molecules that have same chemical formula but different structures
What are double bonds?
What are their deficiencies in organic molecules?
Double Bonds are the sharing of two electrons
This type of bond does not twist and rotate well like with a single bond
What are Proteins polymers of?
Amino Acids
What are Nucleic Acids polymers of?
Nucleotides
What are Carbohydrates polymers of?
Sugars (saccharides)
What do Lipid membranes consist of?
Fatty Acids bonded to other organic molecules
C2H4 blocks
What is the makeup of a Hydroxyl group? Provide chemical structure
An Oxygen and a Hydrogen together with a single bond
-OH
What are two very important characteristics of hydroxyl groups?
They are polar and reactive!
They can add these features to an organic molecule (most important difference between DNA and RNA)
What is the makeup of a Carbonyl group? Provide chemical structure
Carbon double bonded to Oxygen
C == O
What is the makeup of a Carboxyl group? Provide chemical structure
Carbon with two oxygen and hydrogen
-COOH
What is special about a Carboxyl group at physiological pH?
They can donate their proton (Hydrogen) and become a fully ionized group
What is the makeup of a Amine group? Provide chemical structure
Nitrogen and Hydrogen with a double bond
=NH
Why is “big” better if you are a molecule?
- Storage (energy, information)
- Build/Attach, construct bigger things
- Bring things together, make stuff happen
What are six carbons in a chain referred to as?
Hexoses
What are three examples of Hexoses
Glucose, Galactose and Fructose
Do monosaccharides have many or few hydroxyl groups? What effect does this have on them?
They have many hydroxyl groups that makes them polar and hydrophillics
What happens when monosaccharides are linear?
They have a C=O bond at end making them an aldose
Or have it at position two, making them a Ketose
What are monosaccharides in a pair?
Disaccharides
What is a nucleotide composed of?
3 things
5 carbon-sugar, phosphate group, and a base
What are the four bases of DNA?
Adenine, Guanine, Cytosine and Thymine
What base is different in RNA when compared to DNA?
RNA has Uracil instead of Thymine
What are DNA and RNA polymers of? How are these substances linked?
Nucleotides linked by phosphodiester bonds
Do nucleic acid strands have polarity? What are on the ends of these strands?
Yes they do have polarity, with a 5’ - phosphate group at one end and a 3’ hydroxyl group at the other end
How do nucleic acid strands (bases) mix with one another? What is this method in detail?
Hybridize through base H-bonding (hydrogen bonding)
Guanine to Cytosine
Adenine to Thymine or Uracil
What do the physical differences in DNA and RNA affect?
Structure, stability and reactivity
What does DNA do?
stores and transmits genetic information
How is information coded in DNA?
Coded in sequence of DNA bases, that can be replicated using base pairing
How do you build a big molecule (simply put)?
Make a polymer
What are some examples of lipids? How are lipids bound?
Fats (butters) and Oils
Bound through Hydrocarbon chains
What are two important features of lipids?
- Energetics favor separation from water
- Compact storage of energy source
Are fatty acids polar or nonpolar?
Very non-polar
What does an unsaturated fatty acid contain? What does the absence of this thing create?
Unsaturated fatty acids contain a C=C bond
Without this bond you have a saturated fatty acid
What does a C=C bond do in a fatty acid?
Creates a bend in the structure. Cannot be straight.
What does a bend in the molecules do in a substance (particularly fatty acid)?
Doesn’t allow molecules to sit close together, meaning they cannot compact well.
Unsaturated fatty acids (ex. oils) liquid at room temp
Why do Triacylglycerol molecules have no charge?
On average, the positive and negative charges average each other out
Describe van der Waals forces
Fatty acid molecules are uncharged, but the constant motion of elections leads to regions of slight positive/negative charges. Charges in turn attract or repel elections in neighboring molecules, setting up areas of positive and negative charges in those molecules as well. Molecules temporarily polarized. Such molecules weakly bind to one another because of the attraction of opposite charges
Process of DNA turning into mRNA
Transcription
Process of mRNA forming macromolecules like proteins
Translation
What is DNA necessary for?
The transmitting of genetic information
What are the three covalently linked parts in a nucleotide?
- (Nitrogenous) Base
- Ribose (aka Sugar)
- Phosphate group(s)
Describe the Ribose part of a nucleotide including it’s position relative to other two parts and the numbering of its carbon atoms
It’s located in the middle between Phosphate groups and nitrogenous base group
The numbering of carbons runs to 5’ with 1’ being the Carbon connected to to the base group
Provide difference between the 2’ carbon position in DNA and RNA
In DNA, there is no oxygen atom in 2’ position; just a hydrogen atom – D = deoxy (lacking oxygen, deoxyribose nucleic acid)
In RNA, there is an Oxygen present making it a hydroxyl group that is present
What is always linked to the 5’ Carbon position in DNA and RNA?
Phosphate group(s)
What is a nucleoSide?
Nucleotide without the phosphate group(s)
What are the (nitrogenous) bases of DNA and RNA rich in?
Nitrogen
What are the double ring structure bases in nucleotides? What are they referred to as? How do you remember them?
Adenine and Guanine have double ring structures
Called Purines
Remember “Pure As Gold” Pur, A, G
What are the single ring structure bases in nucleotides? What are they referred to as? How do you remember them?
Thymine, Cytosine, and Uracil
Called Pyrimidines
Remember “Pyramids are built for you (U) to see (C)”
Pyramid, U, C
How many hydrogen bonds are used to connect the different pairings of nucleic acid bases? Which connection is more stable?
Adenine and Thymine (or Uracil) held together by two hydrogen bonds
Guanine and Cytosine held together by three hydrogen bonds (this one slightly more stable)
Describe nucleotide polymerization
Using energy from triphosphate hydrolysis you can attach the phosphate group at position 5’ of the ribose and attach it to the hydroxyl group at the 3’ position of another ribose by pulling water out (condensation)
5’ ALWAYS ADDED TO 3’
How do you break apart nucleic acids?
Through hydrolysis - putting water into the connections
What is the bond connecting 5’ phosphate group of one nucleic acid to 3’ hydroxyl group of another?
Phosphodiester bond
Give three comparisons of DNA vs RNA
DNA: Long double stranded structures for storing information (compact-able)
RNA: Often complex base pairing for doing things (3D structure)
DNA: stable molecule (for storage)
RNA: Reactive molecule (has two hydroxyl groups)
DNA: can do simple duplication
RNA: assists in chemical reactions
Describe proteins
Linear polymers of amino acids that form three-dimensional structures with specific functions
What do the 20 common amino acids consist of?
5 things
-a (alpha) carbon connected by covalent bonds to:
- Amino Group
- Carboxyl Group
- Hydrogen Atom
- Side Chain or R group
How are amino acids connected? What do they form upon connecting?
Amino acids connected by peptide bonds to form proteins
What is the definition of the primary structure of a protein?
Its amino acid sequence
What does the primary structure of a protein determine? What does this then determine?
Primary structure determines how protein folds, which in turn determines how it functions
What are the two types of secondary structures of proteins?
a (alpha) helices
b (beta) sheets
How do the two types of secondary structures of proteins form?
Form from peptide backbone H-bonding between nearby amino acids
What is the definition of hydrolysis? What is the term that means the opposite of this?
Hydrolysis - Water goes in
Opposite is condensation
Where are the alpha carbons in this chain? What’s the order to remember where alpha carbons are?
R H R | | | H3N+--CH--C--N--CH--COO || O
Alpha carbons are (from left to right) the first and third carbons
Remember order N-C-C as the middle carbon (immediately following Nitrogen atom) is the alpha carbon in a chain
What is the direction of synthesis of a peptide chain? What is always added to the end?
Direction of synthesis is how peptide chains form, similar to how nucleic acids are connected.
An amino group is always added to the carboxyl end
What gives each protein its characteristics?
The order and composition of the side chains
“Which ones, where?”
What are the four levels of structure in a protein?
Primary, Secondary, Tertiary, and Quaternary
How many amino acids can be found in between a backbone to backbone H-bond?
3.6 amino acids/turn
How do side chains contribute to protein shape and function?
1) side chains have different sizes
2) side chains have distinct polarities
3) some amino acids have “special properties”
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Cytesine
Nonpolar
Cys
Can form disulfide bonds: a covalent bond (outside cells)
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Glycine
Nonpolar and aliphatic
Gly
Only a single Hydrogen as R group
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Alanine
Nonpolar and aliphatic
Ala
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Valine
Nonpolar and aliphatic
Val
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Leucine
Nonpolar and aliphatic
Leu
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Methionine
Nonpolar and aliphatic
Met
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Isoleucine
Nonpolar and aliphatic
Ile
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Serine
Uncharged and Polar
Ser
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Threonine
Uncharged and Polar
Thr
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Proline
Uncharged and Polar
Pro
Ring like structure but still not aromatic
- Covalently linked to backbone in two places which forces bends, breaks alpha helices (dog biting its own tail)
- In other words, very stiff and bent
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Asparagine
Uncharged and Polar
Asn
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Glutamine
Uncharged and Polar
Gln
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Lysine
Positively Charged Group
Lys
Holds a positive charge at the bottom of the linear chain in the R group
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Arginine
Positively Charged Group
Arg
Has a positive charge in the second to last position of the linear chain in the R group
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Histidine
Positively Charged Group
His
Creates a ring-like (but not aromatic) structure in the R group that holds the positive charge in the bottom right
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Aspartate (Aspartic Acid)
Negatively Charged Group
Asp
Holds a fully ionized carboxyl group at the end (lacks hydrogen proton)
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Glutamate (Glutamic Acid)
Negatively Charged Group
Glu
Holds full ionized carboxyl group at the end (lacks hydrogen proton)
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Phenylalanine
Nonpolar, Aromatic Group
Phe
Holds hexagon like ring at the bottom of chain
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Tyrosine
Nonpolar, Aromatic Group
Tyr
Holds a Hydroxyl group below the hexagon like ring at the bottom of the chain
What classifier group does the following amino acid R group fall in to? Also provide its three letter code and a unique feature if possible.
Tryptophan
Nonpolar, Aromatic Group
Trp
Holds a pentagon like construct sharing a side to a hexagon like ring at the bottom of the chain
What can polar amino acids form?
Hydrogen Bonds
What can fully charged side chains form?
Ionic Bonds
Which three organic molecules are cell membranes composed of?
Lipids, Proteins, and carbohydrates
What happens when phospholipids are placed in an aqueous environment? What is the term for this characteristic?
They spontaneously form structures such as micelles and bilayers
Known as being amphipathic (polar and nonpolar)
What is membrane fluidity influenced by? (3 things)
- Length of fatty acid chains
- Presence of carbon-carbon double bonds in fatty acid chains
- Amount of cholesterol
The plasma membrane is a selective barrier that controls what? How does it drive work?
The movement of molecules between the inside and the outside of the cell
Drives work through electrochemical gradients
What is passive transport?
The movement of molecules by diffusion directly through the plasma membrane (simple diffusion) or be aided by protein transports (facilitated diffusion)
Describe membrane fluidity as temperature changes
Fluidity lower at low temps and higher at higher temps
What kind of charge does phosphate carry?
Negative Charge
What are phospholipids composed of?
- Two hydrocarbon chains
- A glycerol backbone
- A phosphate group
- A head group of some type
What are phospholipids composed of?
- Two hydrocarbon chains
- A glycerol backbone
- A phosphate group
- A head group of some type
What do phospholipids with “straight” tails make? What is the shape of their structure. Is the inside of the structure hydro-phillic or phobic?
Make Micelles
A structure of multiple “ice cream cones” being packed together
Outside head groups is hydrophillic, while the inside is all hydrophobic
What is a liposome?
A phospholipid bilayer that surrounds a central space. “Ball with the middle space carved out”
What is a liposome?
A phospholipid bilayer that surrounds a central space. “Ball with the middle space carved out”
-hydrophillic on the inside and out
Do phospholipids in membranes contain saturated or unsaturated fatty acids?
Unsaturated
What does cholesterol do?
Stiffens membranes
What are the four discussed jobs of proteins in a membrane? Provide a brief description of each
Transporter - allow items to pass from one end to another
Receptor - detect a signal from inside membrane to do something on outside
Enzyme - facilitate some sort of chemical reaction
Anchor - attach cell to something on the outside
What are integral membrane proteins?
Transmembrane proteins that span the entire membrane (go through it)
What are peripheral membrane proteins?
Temporarily associated with either the internal or the external side of the membrane (usually through covalent bonds)
What are the three parts of a transmembrane protein?
Transmembrane
Extracellular
Cytoplasmic
“Pooh bear stuck in the tree”
How to peripheral membrane proteins hold on?
“holding on” by hydrophobic regions
What is an electrochemical gradient?
A high concentrations of protons (a “chemical”) and positive charge on one side of a membrane
What is passive diffusion?
If there is a high concentration and a low concentration on opposite sides of a membrane, a motive force will try and equalize the two sides through passive diffusion (going through lipid portion of the membrane)
What is osmotic pressure?
Water pushing against gravity in order to equalize high and low concentrations generating force
Does a more stable configuration (in terms of chemical bonds) have lower or higher potential energy?
Always have lower
-as a result, energy is required to break a covalent bond because going from a lower energy state to a higher one requires an input of energy
How might you keep a membrane fluid in colder temperatures?
- Have shorter length lipids
- More double bonds
This makes is harder for van der walls forces to align strands and for them to be compact together
How might you decrease membrane fluidity in hotter temperatures?
Have longer lipid strands and have less double bonds (more saturated fatty acids)
-this allows van der walls forces to take effect and hold the strands together rather than rupture and rip
Lipids are impermeable to what?
Polar/charged molecules
What “calls the shots” of what gets through a membrane?
Membrane proteins
List the three things a differential in molecule/ion concentration across a membrane can do.
- Can be dissipated to do work (e.g. make ATP)
- Can be used to transmit information fast
- Can be used to transport molecules across the gradient (antiporter)
What is the nucleus in a cell used for?
Storehouse for the cell’s genetic information
Also site of RNA synthesis
What is the mitochondria used for?
Site of most ATP synthesis
- outer membrane
- inner membrane
- intermembrane
- mitochondria membrane
Describe the plasma membrane in a cell
Composed of phospholipids and proteins and regulates the passage of materials into and out of hte cell
Describe chloroplasts of a plant cell
Help plant cells utilize sunlight as energy to synthesize sugars
What are ribosomes used for in the cell?
Protein synthesis
What is the golgi apparatus used for?
Modifies and sorts proteins and lipids before they head to their final destination
What do lysosomes do in the cell?
Degrade macromolecules
What does the endoplasmic recticulum do?
involved in protein and lipid synthesis
What is exocytosis? What is endocytosis?
- expelling things from inside cell
- bringing things into the cell