Unit #1 Review Session Cards sheet 2 Flashcards
What are hydrophobic interactions, and why are they important for living organisms?
They are nonpolar and not charged; they interact with other hydrophobic molecules
- Water repels them / pushes hydrophobics away
- Water excludes these molecules forcing them to associate with each other
*H2O determines shape of biopolymers
Why do water and oil separate after you shake them up?
Water will force/push oil away
*Oil is nonpolar
Ex: water pushes hydrophobic molecules away and forms shape of protein
*Protein shape not right = disorder b/c can’t function right
What is a mole (to a chemist)?
Quantity of a chemical that contains avogadro’s number
*Easier to weigh molecules than count them
What is pH and why is it important to living organisms?
- name of 2 ions
- scale
- neutral
- which way means what
H2O → H+ + OH-
Water (pH = 7) → proton/hydrogen ion + hydroxyl
0————7————14
pH scale runs from 0 to 14
7 is neutral
From 7 to 0…the number of OH- decreases and the number of H+ increases
Solution becomes more acidic
From 7 to 14…the number of OH- increases and the number of H+ decreases
Solution becomes more basic
In living systems, pH must remain constant
pH of blood = 7.4
What is the difference in [H+] between a solution whose pH is 5 and a solution whose pH is 8?
5-6-7-8
X 10 each time to the right
1000 or 10^3 more protons in 5 than 8
What is a buffer?
Minimizes change in H+ or OH- concentrations in a solution
What is the formula for determining pH?
pH = -log [H+]
Which pH ion is acidic and which is base?
proton / hydrogen ion = acidic
hydroxyl = basic
Why is life based on carbon?
Needs 4 electrons Shares them (covalent bond)
C IS A great covalent bonder
*forms backbone of many biopolymers
What is a functional group (in organic chemistry) and why are they so important?
Groups of atoms that confer certain chemical properties on the molecules in which they are found
Please list the 7 most important functional groups in biological molecules.
- OH hydroxyl
- CO carbonyl
- COOH carboxyl
- CH3 methyl (nonpolar)
- SH sulfhydryl
- PO4 phosphate (add energy)
- NH2 amino (basic)
What is a macromolecule, and what features do all macromolecules have in common?
Large molecule
Polymer of similar polar units
What types of macromolecules do you find in living organisms?
Polymers ( - monomers)
Polysaccharides (carbohydrates)
- Monosaccharides
- Disaccharides
Proteins
*Amino acids
Lipids
*Fat is made of fatty acids and glycerol
Nucleic acids
*nucleotides
What is a dehydration reaction?
Used to build a polymer from its monomers
H+ and OH- → H2O
What is an anabolic reaction?
What is a catabolism reaction?
Reaction that builds
*ex: dehydration
Catabolism: reaction breaks down hydrolysis
What is a hydrolytic reaction?
Used to break down a polymer into its monomers
Add water into bond to separate
Ex: Bread into water
Digestion of food
What is a carbohydrate, and what functions do carbohydrates perform?
Sugar functions:
Source of energy
Structure
Signaling - these molecules are used for cell to cell communication
Why are carbohydrates good for storing energy?
C-H
Carbohydrates have a large number of C-H bonds
What is an isomer?
Isomer: molecules with the same structural formula, but atoms are arranged differently
C6H12O6 is the structural formula for three sugars:
Glucose
Fructose
Galactose
** atoms are arranged differently
Difference between isomers and isotopes?
isomers =
molecules
same structural formula
different arrangement
isotopes =
element
different # of neutrons
different atomic masses
suffix: “ose”
sugar
suffix: “ase”
enzyme
What is the difference between a structural isomer and a stereoisomer?
Structural isomers: have functional groups attached to different C (which C the O is on)
Stereoisomer: have functional groups attached in different orientations, but functional groups on the same C (which side the hydroxyl is attached to the carbon)
What is a transport disaccharide?
Made from 2 monosaccharides
These disaccharides are made by plants to keep the sugars from being metabolized as they pass down to the roots for storage
*plant cells would grab and use monosaccharides for energy
Maximizes the amount of sugar that gets stored in the root
What is the similarity between starch, glycogen and cellulose?
Starch, glycogen, and cellulose are all polymers of glucose
What is Alpha and Beta glucose?
Alpha glucose: hydroxyl on bottom
Beta glucose: hydroxyl on top
What linkages do the following have?
starch
glycogen
cellulose
Starch: 1-4 linkage
Glycogen: 1-6 linkages
Cellulose: 1-4 linkages
What kind of glucose are the following:
starch
glycogen
cellulose
Starch: polysaccharide polymer of alpha-glucose
Glycogen: polysaccharide polymer of alpha-glucose
Cellulose: polysaccharide polymer of beta-glucose
Where do the following occur / made by ?
starch
glycogen
cellulose
Starch: produced by plants
Glycogen: produced in liver made by animals
Cellulose: made by plants
(cell walls)
Soluble or insoluble in water:
starch
glucose
cellulose
Starch: insoluble
Glycogen: soluble
Cellulose: insoluble
What is the structure of …
starch
cellulose
Form long chains
no coils
used as a structural molecule
Chain of glucose units is unbranched
folds into coils due to hydrogen bonding
Why is starch insoluble in water?
Its hydrogen bonds to itself so no hydrogen bonds are available to interact with water
Water will exclude or repel starch
What is carbo-loading and how does it work?
Strategy used by athlete, e.g marathon runner
Diet before the race designed to load up on glycogen - lots of carbs, pasta, grains
Muscle will have a good supply of sugar in the form of glycogen for the race
Glycogen will also store a lot of water
Why is it so much harder to digest cellulose than starch?
We do not have the enzyme to break down cellulose
Cellulose goes out the way it went in - roughage
Not a source of energy
Why do beans give you gas?
Beans contain raffinose sugars with alpha galactose 1-6 links that humans cannot digest easily
bacteria can ferment these sugars, but give off gas as a result
What are proteins?
Proteins are polymers of amino acids linked together by dehydration
What functions do proteins perform?
Structural (hair, finger nails)
Energy storage (casein in milk)
Catalyst - enzyme increases rates of reactions
Transporter
Signaling molecules
Defense (immune system)
How many amino acids are there?
20
What are amino acids, and what are the five groups of amino acids?
Amino acid - subunit of a protein
5 R groups
- ionizable (acidic and basic)
- polar
- non-polar
- aromatic (c-containing rings)
- special function
Why do we say that proteins are made “N to C”?
Proteins are made N to C
Link amino of the incoming amino acid to the COOH (carboxyl) of the chain of amino acids
Amino is the NOSE , carboxyl is the TAIL
Why is the structure of a protein so important?
What happens if the structure is wrong?
What determines the shape?
Structure of a protein determines its function
If a protein doesn’t fold correctly, it will not work
Ex: genetic disorders
Sequence of amino acids determines the shape of the protein
So
The sequence of the amino acids MUST BE CORRECT
What is a primary structure of a protein?
sequence of amino acids in a protein (determined by sequence of nucleotides in DNA)
This sequence ultimately determines the 3D shape of the protein
What is a secondary structure of a protein?
amino acid chain takes on a shape due to hydrogen bonds between amino and carboxyl groups
What is a tertiary structure of a protein?
protein assumes 3D shape due to interactions between the R groups with water
What is a quaternary structure of a protein?
Do all proteins contain these?
some proteins require two more more polypeptide chains in their structure; final shape of a protein with two or more subunits (polypeptide chains (chains of amino acids)
Not all proteins have quaternary structures but all have one through three
What is a motif, and what is a domain and how do they differ (when talking about protein structure)?
Protein motif: combination of secondary structures in a protein
Incapable of functioning independently
Used to infer functions of unknown protein
Domain: structurally independent section of a protein that has a certain function connected to other domains by a single polypeptide chain
*Many proteins are a combination of various domains
Why do proteins fold into their tertiary structure?
Tertiary structure is due to interactions between water and R groups
Hydrophobic amino acids pushed to middle of protein
Hydrophilic amino acids pulled out to interact with water
What types of bonds help proteins maintain their tertiary structure?
Tertiary structure of protein is due to interactions of R groups with water
- Polar amino acids exposed on the outside of a protein
- Nonpolar pushed inside the protein, away from water
*Hydrogen bonds with water, between N and C of
backbone, between R groups
- Van Der Waals interactions
- Disulfide bridges
Why do proteins fold into their final structure faster than we expect?
Chaperonins - proteins that help other proteins fold into their tertiary structure
What are nucleic acids?
Polymers of nucleotides that contain information in the sequence of their nucleotides
DNA - deoxyribonucleic acid
RNA - ribonucleic acid
What are the functions of DNA?
DNA stores genetic information in the sequence of its nucleotides
What are the functions of RNA?
RNA retrieves data
What are nucleic acids made of?
Nucleotides (4 diff kinds) - [monomer]
- Phosphate
- 5C sugar
- Nitrogenous base (N)
P
I
S – N
Nucleic acid - nucleotides put together in a certain order
[polymer]
- dehydration reaction
What are the two kinds of bases found in nucleic acids?
Purines
angles are pure
adenine (A)
guanine (G)
Pyrimidines ** CUT the Py** Thymine (T) Cytosine (C) Uracil (U)
What bases do you find in DNA and what bases do you find in RNA?
DNA contains: A, G, T, C
RNA contains: A, G, U, C
- *no thymine is RNA**
- *N uracil in DNA**
What function do bases serve in nucleic acids?
Order of bases code information
or
Order of bases in DNA stores genetic information A T, C, G
What is the primary structure of a nucleic acid?
DNA: 2 antiparallel strand of nucleotides - ladder [bases (connected to sugar) = rungs , phosphates and sugars = sides]
RNA: 1 strand of nucleotides (A,T,C,G)
DNA is made out of DNA nucleotides (A,T C,G)
RNA is made out of RNA nucleotides (A,U,C,G)
Why do we say that nucleic acids are made 5’ to 3’?
Incoming nucleotide 5’ PO4 (nose) joins the 3’ end OH (tail) of nucleotide chain
Why do we care that nucleic acids are made 5’ to 3’?
Bases are read 5’ to 3’
Nucleic acids have a distinct directionality and we can refer
to either end specifically
5’ AATTTTCCGG 3’
What are the main differences between DNA and RNA?
Sugar Nitrogen bases # of strands Stability Function Catalytic property Structure
DNA: -deoxyribose -ATCG -2 -More stable -Store genetic information -no -Primary structure: “ladder” No secondary structure Tertiary structure: double helix
RNA -ribose -AUCG -1 -unstable -Retrieves information -Yes (rare) *ribozymes -Complicated structure, depends on type of RNA Some RNA have secondary structure that allows it to be catalytic *probs evolved first*
What holds the backbone of a nucleic acid together?
Phosphodiester bonds between the P and S of the “backbone” - these are covalent bonds
Between nucleotides
Chargaff’s Rule:
what bonds exist and how many?
Apples in trees (A-T) : 2 h bonds
Cars in the Garage (C-G) : 3 h bond
H bonds in between the nucleotides
carbons in nucleic acid
and glucose?
Nucleic acids = 5 Carbon
Glucose = 6 Carbon
What compounds are the 5’ and 3’ side near ?
Phosphate = 5’ Hydroxyl = 3’
** always add to 3’ **
What is the 3˚ structure of a DNA molecule?
Double helix
What holds the two strands of a DNA molecule together?
hydrogen bonds
Nucleotides as a whole = covalent bonds
Why can’t RNA form a double helix ?
RNA is only one strand of nucleotides
Ribose is too big and bulky
Why does RNA adopt complicated shapes?
Interactions between nucleotides cause the formation of a number of different shapes, depending on the type of RNA
What is a ribozyme?
RNA with catalytic activity
Why do most biologists believe that RNA came before DNA?
Can catalyze reactions
Can replicate itself
RNA polymerase is older than DNA polymerase
