Chapter 2: Life's Chemistry and the Importance of Water Flashcards
What is the difference between atoms, elements, and molecules?
Element: A substance made up of only a single atom
Molecules: A combo of elements(ex. H2O)
Protons and electrons experience a force of _____________________(1)
(1) Electrostatic attraction
What is the atomic number?
The number of protons in an atom, used to determine an atoms identity
The dry weight of nearly 98% of all biological molecules on Earth is composed of which 6 atoms?
PONCHOS
Phosphorus, oxygen, nitrogen, carbon, hydrogen, Sulfur
How many electrons can each shell in an atom hold?
First shell: 2 electrons
Second shell: 8 electrons
Third shell: 18 electrons
Only electrons in the _____________(1) are involved in chemical reactions. Filling the _____________(1) is an energetically stable state.
(1) valence shell
How many covalent bonds does hydrogen want to from?
1
How many covalent bonds does oxygen want to from?
2
How many covalent bonds does sulphur want to from?
2
How many covalent bonds does nitrogen want to from?
3
How many covalent bonds does carbon want to from?
4
How many covalent bonds does phosphorus want to from?
5(or 3)
Why can phosphorus from either 3 or 5 bonds? Why can’t nitrogen do the same thing?
It can separate the pair of electrons in its outer shell(“lone pair) enough so that an extra pair of electrons can squeeze in. Its third shell gives it some flexibility.
Nitorgen’s lone pair of electrons is too close to all the other electrons. Its outer shell is the second shell not the third.
________________________(1) in molecules can rotate freely, but _______________________(2) cannot. This affects the shapes that molecules can take on
(1) Single bonds
(2) Double and triple bonds
In organic molecules, the ________________(1) represent carbon atoms
(1) Ends of the line segment
What are the four types of bonds, ranked in order of strength?
(Ranked strongest to weakest)
- Covalent bond(electrons share din orbitals
- Ionic bonds(Electrons transferred from one atom to another)
- Hydrogen bonding(between N, O, F)
- Van der Waals interactions
What are the two important simplifications made in bio?
- Everything is an aqueous solution(in water). This explains why covalent bonds are stronger than ionic(because ionic would dissociate in water)
- Limited set of atoms, only looking at PONCHOS
What are hydrophobic interactions?
The interaction between non polar substances
What is electronegativity?
The ability of an atom to attract electrons
Ex in water, oxygen is an electron hog because it has a high electronegativity
Describe covalent bond polarity
In a polar covalent bond, the electrons spend more time around the more electronegative atom. This results in partial charrges(but not formal charges) on each of the bonded atoms. We indicate partial charges in a bond using the s symbol.
What is the eelctronegatvity difference for polar covalent and non-polar covalent bonds?
Non polar covalent bonds: less than 0.5
Polar covalent bond: 0.5 or greater
Polar molecules can from ____________________(1)
(1) hydrogen bonds
What does a dotted/dashed line represent?
Hydrogen bond
What are the interactions between two non polar molecules?
Van der Waals or hydrophobic interactiosn
___________________(1) molecules are hydrophilic. ____________________(2) molecules are hydrophobic.
(1) polar
(2) non polar
Why do polar molecules dissolve in water?
Polar molecules dissolve in water because they form hydrogen bonds with water molecules.
Why do non polar molecules group in water?
Nonpolar molecules group together in water because the water molecules form hydrogen bonds with one another
Is water polar or non polar?
polar
Where does energy come from?
The sun/photosynthesisW
Why do living organisms need energy?
Metabolic functions, carry out chemical reactions
What is a chemical reaction?
Making a molecule and/or breaking up a molecule
What is metabolism?
All the chemical reactions occurring in an organism
What is an anabolic reaction?
The linking of simple molecules to from complex ones. It requires net energy input. Energy is captured in the chemical bonds that form
Ex. polymerization
What is a catabolic reaction?
The beaking of complex molecules down into simpler ones. The energy stored in the chemical bonds is released
Ex. depolymerization
What is an endergonic reaction, in terms of energy and entropy?
Energy input required, entropy decreases
What is an exergonic reaction, in terms of energy and entropy?
Energy released, entropy increases
Are anabolic and catabolic reactions endergonic or exergonic?
Anabolic: endergonic
Catabolic: exergonic
What are the three factors that contribute to increasing disorder(entropy)?
- Addition of heat(increased molecular motion)
- Phase changes(solids have less entropy than liquids and gases)
- Breaking molecules/polymers apart
What is a spontaneous chemical reaction?
A chemical reaction that is spontaneous can proceed without outside assistance.
The second law of thermodynamic states that in any reaction that proceeds spontaneously, there is always an increase in total entropy
How are catabolic and anabolic reactions linked?
The energy released in catabolic reactions is often uses to drive anabolic reactions to do biological work. This allows reactions that decrease entropy to proceed(since they are non spontaneous)
When is delta G positive and negative?
If delta g is positive the reaction requires energy
If delta g is negative, the reaction releases energy
Nearly all of the chemical reactions inside living organisms are _______________________(1)
(1) reversible reactions
Do acidic molecules accept or donate protons? Why is this?
Acidic molecules donate protons or H+ ions. This is usually due to the breaking of very polar covalent bonds between a hydrogen atom and an electronegative artom.
Do basic molecules accept or donate protons? Why is this?
Basic molecules accept protons as they are capable of forming covalent bonds, or accepting, one or more H+ ions. This is often due to the presence of lone pair electrons
What is pH?
pH measures the concentration of H+ present in a solution. It is a property of a solution, NOT of an acid or acidic group
pH = -log[H+]
What are buffers?
Buffers help to minimize changes in pH when small amounts of H+ ions or OH- ions are added or removed.
Living cells keep the pH of their cells constant, and a pH close to _____(1). This is referred to as the ________________________(2).
(1) 7
(2) physiological pH
What is protonated and deprotonated mean?
Protonated: with H+
Deprotonated: without H+, dissociated
Carbon often forms the _____________(1) of complex molecules because it is the most versatile element and can make up to _____(2) covalent bonds.
(1)backbone
(2) 4
