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BIO 121 Terzaghi > Unit #1 Review Session Cards sheet 2 > Flashcards

Unit #1 Review Session Cards sheet 2 Flashcards

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1
Q

What are hydrophobic interactions, and why are they important for living organisms?

A

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

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2
Q

Why do water and oil separate after you shake them up?

A

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

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3
Q

What is a mole (to a chemist)?

A

Quantity of a chemical that contains avogadro’s number

*Easier to weigh molecules than count them

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4
Q

What is pH and why is it important to living organisms?

  • name of 2 ions
  • scale
  • neutral
  • which way means what
A

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

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5
Q

What is the difference in [H+] between a solution whose pH is 5 and a solution whose pH is 8?

A

5-6-7-8
X 10 each time to the right

1000 or 10^3 more protons in 5 than 8

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6
Q

What is a buffer?

A

Minimizes change in H+ or OH- concentrations in a solution

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7
Q

What is the formula for determining pH?

A

pH = -log [H+]

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8
Q

Which pH ion is acidic and which is base?

A

proton / hydrogen ion = acidic

hydroxyl = basic

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9
Q

Why is life based on carbon?

A 
Needs 4 electrons
Shares them (covalent bond)

C IS A great covalent bonder

*forms backbone of many biopolymers

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10
Q

What is a functional group (in organic chemistry) and why are they so important?

A

Groups of atoms that confer certain chemical properties on the molecules in which they are found

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11
Q

Please list the 7 most important functional groups in biological molecules.

A
  • OH hydroxyl
  • CO carbonyl
  • COOH carboxyl
  • CH3 methyl (nonpolar)
  • SH sulfhydryl
  • PO4 phosphate (add energy)
  • NH2 amino (basic)
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12
Q

What is a macromolecule, and what features do all macromolecules have in common?

A

Large molecule

Polymer of similar polar units

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13
Q

What types of macromolecules do you find in living organisms?

A

Polymers ( - monomers)

Polysaccharides (carbohydrates)

  • Monosaccharides
  • Disaccharides

Proteins
*Amino acids

Lipids
*Fat is made of fatty acids and glycerol

Nucleic acids
*nucleotides

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14
Q

What is a dehydration reaction?

A

Used to build a polymer from its monomers

H+ and OH- → H2O

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15
Q

What is an anabolic reaction?

What is a catabolism reaction?

A

Reaction that builds
*ex: dehydration

Catabolism: reaction breaks down hydrolysis

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16
Q

What is a hydrolytic reaction?

A

Used to break down a polymer into its monomers

Add water into bond to separate

Ex: Bread into water
Digestion of food

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17
Q

What is a carbohydrate, and what functions do carbohydrates perform?

A

Sugar functions:
Source of energy
Structure
Signaling - these molecules are used for cell to cell communication

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18
Q

Why are carbohydrates good for storing energy?

A

C-H

Carbohydrates have a large number of C-H bonds

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19
Q

What is an isomer?

A

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

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20
Q

Difference between isomers and isotopes?

A

isomers =
molecules
same structural formula
different arrangement

isotopes =
element
different # of neutrons
different atomic masses

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21
Q

suffix: “ose”

A

sugar

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22
Q

suffix: “ase”

A

enzyme

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23
Q

What is the difference between a structural isomer and a stereoisomer?

A

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)

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24
Q

What is a transport disaccharide?

A

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

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25
Q

What is the similarity between starch, glycogen and cellulose?

A

Starch, glycogen, and cellulose are all polymers of glucose

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26
Q

What is Alpha and Beta glucose?

A

Alpha glucose: hydroxyl on bottom

Beta glucose: hydroxyl on top

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27
Q

What linkages do the following have?

starch
glycogen
cellulose

A

Starch: 1-4 linkage

Glycogen: 1-6 linkages

Cellulose: 1-4 linkages

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28
Q

What kind of glucose are the following:

starch
glycogen
cellulose

A

Starch: polysaccharide polymer of alpha-glucose

Glycogen: polysaccharide polymer of alpha-glucose

Cellulose: polysaccharide polymer of beta-glucose

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29
Q

Where do the following occur / made by ?

starch
glycogen
cellulose

A

Starch: produced by plants

Glycogen: produced in liver made by animals

Cellulose: made by plants
(cell walls)

30
Q

Soluble or insoluble in water:

starch
glucose
cellulose

A

Starch: insoluble

Glycogen: soluble

Cellulose: insoluble

31
Q

What is the structure of …

starch
cellulose

A

Form long chains

no coils

used as a structural molecule

Chain of glucose units is unbranched

folds into coils due to hydrogen bonding

32
Q

Why is starch insoluble in water?

A

Its hydrogen bonds to itself so no hydrogen bonds are available to interact with water

Water will exclude or repel starch

33
Q

What is carbo-loading and how does it work?

A

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

34
Q

Why is it so much harder to digest cellulose than starch?

A

We do not have the enzyme to break down cellulose

Cellulose goes out the way it went in - roughage

Not a source of energy

35
Q

Why do beans give you gas?

A

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

36
Q

What are proteins?

A

Proteins are polymers of amino acids linked together by dehydration

37
Q

What functions do proteins perform?

A

Structural (hair, finger nails)

Energy storage (casein in milk)

Catalyst - enzyme increases rates of reactions

Transporter

Signaling molecules

Defense (immune system)

38
Q

How many amino acids are there?

A

20

39
Q

What are amino acids, and what are the five groups of amino acids?

A

Amino acid - subunit of a protein

5 R groups

  1. ionizable (acidic and basic)
  2. polar
  3. non-polar
  4. aromatic (c-containing rings)
  5. special function
40
Q

Why do we say that proteins are made “N to C”?

A

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

41
Q

Why is the structure of a protein so important?

What happens if the structure is wrong?

What determines the shape?

A

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

42
Q

What is a primary structure of a protein?

A

sequence of amino acids in a protein (determined by sequence of nucleotides in DNA)

This sequence ultimately determines the 3D shape of the protein

43
Q

What is a secondary structure of a protein?

A

amino acid chain takes on a shape due to hydrogen bonds between amino and carboxyl groups

44
Q

What is a tertiary structure of a protein?

A

protein assumes 3D shape due to interactions between the R groups with water

45
Q

What is a quaternary structure of a protein?

Do all proteins contain these?

A

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

46
Q

What is a motif, and what is a domain and how do they differ (when talking about protein structure)?

A

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

47
Q

Why do proteins fold into their tertiary structure?

A

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

48
Q

What types of bonds help proteins maintain their tertiary structure?

A

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
49
Q

Why do proteins fold into their final structure faster than we expect?

A

Chaperonins - proteins that help other proteins fold into their tertiary structure

50
Q

What are nucleic acids?

A

Polymers of nucleotides that contain information in the sequence of their nucleotides

DNA - deoxyribonucleic acid
RNA - ribonucleic acid

51
Q

What are the functions of DNA?

A

DNA stores genetic information in the sequence of its nucleotides

52
Q

What are the functions of RNA?

A

RNA retrieves data

53
Q

What are nucleic acids made of?

A

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
54
Q

What are the two kinds of bases found in nucleic acids?

A

Purines
angles are pure
adenine (A)
guanine (G)

Pyrimidines
** CUT the Py**
Thymine (T)
Cytosine (C)
Uracil (U)
55
Q

What bases do you find in DNA and what bases do you find in RNA?

A

DNA contains: A, G, T, C
RNA contains: A, G, U, C

  • *no thymine is RNA**
  • *N uracil in DNA**
56
Q

What function do bases serve in nucleic acids?

A

Order of bases code information

or

Order of bases in DNA stores genetic information A T, C, G

57
Q

What is the primary structure of a nucleic acid?

A

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)

58
Q

Why do we say that nucleic acids are made 5’ to 3’?

A

Incoming nucleotide 5’ PO4 (nose) joins the 3’ end OH (tail) of nucleotide chain

59
Q

Why do we care that nucleic acids are made 5’ to 3’?

A

Bases are read 5’ to 3’

Nucleic acids have a distinct directionality and we can refer
to either end specifically

5’ AATTTTCCGG 3’

60
Q

What are the main differences between DNA and RNA?

Sugar
Nitrogen bases
# of strands
Stability
Function
Catalytic property
Structure
A 
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*
61
Q

What holds the backbone of a nucleic acid together?

A

Phosphodiester bonds between the P and S of the “backbone” - these are covalent bonds

Between nucleotides

62
Q

Chargaff’s Rule:

what bonds exist and how many?

A

Apples in trees (A-T) : 2 h bonds
Cars in the Garage (C-G) : 3 h bond

H bonds in between the nucleotides

63
Q

carbons in nucleic acid

and glucose?

A

Nucleic acids = 5 Carbon

Glucose = 6 Carbon

64
Q

What compounds are the 5’ and 3’ side near ?

A 
Phosphate = 5’
Hydroxyl = 3’

** always add to 3’ **

65
Q

What is the 3˚ structure of a DNA molecule?

A

Double helix

66
Q

What holds the two strands of a DNA molecule together?

A

hydrogen bonds

Nucleotides as a whole = covalent bonds

67
Q

Why can’t RNA form a double helix ?

A

RNA is only one strand of nucleotides

Ribose is too big and bulky

68
Q

Why does RNA adopt complicated shapes?

A

Interactions between nucleotides cause the formation of a number of different shapes, depending on the type of RNA

69
Q

What is a ribozyme?

A

RNA with catalytic activity

70
Q

Why do most biologists believe that RNA came before DNA?

A

Can catalyze reactions
Can replicate itself
RNA polymerase is older than DNA polymerase

BIO 121 Terzaghi (8 decks)

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