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Flashcards in Everything Deck (149)
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1
Q

What is a molecule?

A

A structure of multiple atoms linked by covalent bonds

2
Q

What is a covalent bond?

A

The sharing of electrons to complete an outermost shell

3
Q

What is electronegativity?

A

The tendency of an atom to attract electrons to complete its shell

4
Q

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?

A

Polar vs. Non polar covalent bonding

5
Q

What is an ion?

A

When an atom has different number of electrons than protons?

6
Q

What is a cation?
What’s its charge?
Give examples

A

When the atom has more protons than electrons (positive charge)
Na^+, K^+, Mg^2+, Ca^2+

7
Q

What is an anion?
What’s its charge?
Provide an example

A

When the atom has more electrons than protons (negative charge)
Cl^-

8
Q

What is an ionic bond?

Why is it weak in water?

A

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

9
Q

What does it mean to be “hydrophilic?”

A

Having a tendency to mix with, dissolve in, or be wetted by water

“Water-loving”

10
Q

What does it mean to be “hydrophobic?”

A

Having a tendency to repel and not absorb, not mix well, or not dissolve in water

“Water-fearing”

11
Q

What are hydrogen bonds?

What do they give the property of?

A

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

12
Q

What is the process of denaturing?

A

Breaking down all non-covalent bonds but leaving the covalent ones intact

13
Q

What is the backbone of all organic molecules?

A

Carbon

14
Q

What is the max number of covalent bonds a carbon atom can for with other atoms?

A

4

15
Q

What aspect of carbon bonding contributes to the functional diversity of organic molecules?

A

The Geometry

16
Q

What functional groups (moieties) are frequently attached to carbon chains in biomolecules? What do they do?

A

Hydroxl- (polar); Carbonyl-; and Amino- (ionic)

They alter molecular characteristics

17
Q

What are the four organic molecules?

A

Proteins, Nucleic Acids, Carbohydrates, and Lipids

18
Q

What are sugars? What are they used for? What can they be linked to form?

A

Sugars are carbohydrates that can be used as a source of energy. They can be linked into complex carbohydrates

19
Q

Are Lipids Hydrophobic or Hydrophilic?

A

Hydrophobic

20
Q

What are Triacylglycerols?

What are they made up of?

A

Lipids that store energy and are made up of glycerol and fatty acids

21
Q

What are fatty acids?
What do they always have at one end?
What are they composed of?

A

Linear hydrocarbon chains of variable length.
Always have a carboxyl group at one end.
Composed of repeated C2H4 elements

22
Q

What is a defining aspect of unsaturated fatty acids?

A

They have one or more carbon-carbon double bonds

23
Q

What force is responsible for the tight packing of fatty acids in lipids?
What is this force?

A

Van der Waals forces

A type of weak, noncovalent bond

24
Q

What do the spatially spread out bonds allow for in a carbon molecule? Why is this useful?

A

Rotation, allows for different shapes and structures to be built from carbon molecules

25
Q

What is an isomer?

A

Two molecules that have same chemical formula but different structures

26
Q

What are double bonds?

What are their deficiencies in organic molecules?

A

Double Bonds are the sharing of two electrons

This type of bond does not twist and rotate well like with a single bond

27
Q

What are Proteins polymers of?

A

Amino Acids

28
Q

What are Nucleic Acids polymers of?

A

Nucleotides

29
Q

What are Carbohydrates polymers of?

A

Sugars (saccharides)

30
Q

What do Lipid membranes consist of?

A

Fatty Acids bonded to other organic molecules

C2H4 blocks

31
Q

What is the makeup of a Hydroxyl group? Provide chemical structure

A

An Oxygen and a Hydrogen together with a single bond

-OH

32
Q

What are two very important characteristics of hydroxyl groups?

A

They are polar and reactive!

They can add these features to an organic molecule (most important difference between DNA and RNA)

33
Q

What is the makeup of a Carbonyl group? Provide chemical structure

A

Carbon double bonded to Oxygen

C == O

34
Q

What is the makeup of a Carboxyl group? Provide chemical structure

A

Carbon with two oxygen and hydrogen

-COOH

35
Q

What is special about a Carboxyl group at physiological pH?

A

They can donate their proton (Hydrogen) and become a fully ionized group

36
Q

What is the makeup of a Amine group? Provide chemical structure

A

Nitrogen and Hydrogen with a double bond

=NH

37
Q

Why is “big” better if you are a molecule?

A
  • Storage (energy, information)
  • Build/Attach, construct bigger things
  • Bring things together, make stuff happen
38
Q

What are six carbons in a chain referred to as?

A

Hexoses

39
Q

What are three examples of Hexoses

A

Glucose, Galactose and Fructose

40
Q

Do monosaccharides have many or few hydroxyl groups? What effect does this have on them?

A

They have many hydroxyl groups that makes them polar and hydrophillics

41
Q

What happens when monosaccharides are linear?

A

They have a C=O bond at end making them an aldose

Or have it at position two, making them a Ketose

42
Q

What are monosaccharides in a pair?

A

Disaccharides

43
Q

What is a nucleotide composed of?

3 things

A

5 carbon-sugar, phosphate group, and a base

44
Q

What are the four bases of DNA?

A

Adenine, Guanine, Cytosine and Thymine

45
Q

What base is different in RNA when compared to DNA?

A

RNA has Uracil instead of Thymine

46
Q

What are DNA and RNA polymers of? How are these substances linked?

A

Nucleotides linked by phosphodiester bonds

47
Q

Do nucleic acid strands have polarity? What are on the ends of these strands?

A

Yes they do have polarity, with a 5’ - phosphate group at one end and a 3’ hydroxyl group at the other end

48
Q

How do nucleic acid strands (bases) mix with one another? What is this method in detail?

A

Hybridize through base H-bonding (hydrogen bonding)

Guanine to Cytosine
Adenine to Thymine or Uracil

49
Q

What do the physical differences in DNA and RNA affect?

A

Structure, stability and reactivity

50
Q

What does DNA do?

A

stores and transmits genetic information

51
Q

How is information coded in DNA?

A

Coded in sequence of DNA bases, that can be replicated using base pairing

52
Q

How do you build a big molecule (simply put)?

A

Make a polymer

53
Q

What are some examples of lipids? How are lipids bound?

A

Fats (butters) and Oils

Bound through Hydrocarbon chains

54
Q

What are two important features of lipids?

A
  • Energetics favor separation from water

- Compact storage of energy source

55
Q

Are fatty acids polar or nonpolar?

A

Very non-polar

56
Q

What does an unsaturated fatty acid contain? What does the absence of this thing create?

A

Unsaturated fatty acids contain a C=C bond

Without this bond you have a saturated fatty acid

57
Q

What does a C=C bond do in a fatty acid?

A

Creates a bend in the structure. Cannot be straight.

58
Q

What does a bend in the molecules do in a substance (particularly fatty acid)?

A

Doesn’t allow molecules to sit close together, meaning they cannot compact well.

Unsaturated fatty acids (ex. oils) liquid at room temp

59
Q

Why do Triacylglycerol molecules have no charge?

A

On average, the positive and negative charges average each other out

60
Q

Describe van der Waals forces

A

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

61
Q

Process of DNA turning into mRNA

A

Transcription

62
Q

Process of mRNA forming macromolecules like proteins

A

Translation

63
Q

What is DNA necessary for?

A

The transmitting of genetic information

64
Q

What are the three covalently linked parts in a nucleotide?

A
  1. (Nitrogenous) Base
  2. Ribose (aka Sugar)
  3. Phosphate group(s)
65
Q

Describe the Ribose part of a nucleotide including it’s position relative to other two parts and the numbering of its carbon atoms

A

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

66
Q

Provide difference between the 2’ carbon position in DNA and RNA

A

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

67
Q

What is always linked to the 5’ Carbon position in DNA and RNA?

A

Phosphate group(s)

68
Q

What is a nucleoSide?

A

Nucleotide without the phosphate group(s)

69
Q

What are the (nitrogenous) bases of DNA and RNA rich in?

A

Nitrogen

70
Q

What are the double ring structure bases in nucleotides? What are they referred to as? How do you remember them?

A

Adenine and Guanine have double ring structures

Called Purines

Remember “Pure As Gold” Pur, A, G

71
Q

What are the single ring structure bases in nucleotides? What are they referred to as? How do you remember them?

A

Thymine, Cytosine, and Uracil

Called Pyrimidines

Remember “Pyramids are built for you (U) to see (C)”

Pyramid, U, C

72
Q

How many hydrogen bonds are used to connect the different pairings of nucleic acid bases? Which connection is more stable?

A

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)

73
Q

Describe nucleotide polymerization

A

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’

74
Q

How do you break apart nucleic acids?

A

Through hydrolysis - putting water into the connections

75
Q

What is the bond connecting 5’ phosphate group of one nucleic acid to 3’ hydroxyl group of another?

A

Phosphodiester bond

76
Q

Give three comparisons of DNA vs RNA

A

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

77
Q

Describe proteins

A

Linear polymers of amino acids that form three-dimensional structures with specific functions

78
Q

What do the 20 common amino acids consist of?

5 things

A

-a (alpha) carbon connected by covalent bonds to:

  • Amino Group
  • Carboxyl Group
  • Hydrogen Atom
  • Side Chain or R group
79
Q

How are amino acids connected? What do they form upon connecting?

A

Amino acids connected by peptide bonds to form proteins

80
Q

What is the definition of the primary structure of a protein?

A

Its amino acid sequence

81
Q

What does the primary structure of a protein determine? What does this then determine?

A

Primary structure determines how protein folds, which in turn determines how it functions

82
Q

What are the two types of secondary structures of proteins?

A

a (alpha) helices

b (beta) sheets

83
Q

How do the two types of secondary structures of proteins form?

A

Form from peptide backbone H-bonding between nearby amino acids

84
Q

What is the definition of hydrolysis? What is the term that means the opposite of this?

A

Hydrolysis - Water goes in

Opposite is condensation

85
Q

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
A

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

86
Q

What is the direction of synthesis of a peptide chain? What is always added to the end?

A

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

87
Q

What gives each protein its characteristics?

A

The order and composition of the side chains

“Which ones, where?”

88
Q

What are the four levels of structure in a protein?

A

Primary, Secondary, Tertiary, and Quaternary

89
Q

How many amino acids can be found in between a backbone to backbone H-bond?

A

3.6 amino acids/turn

90
Q

How do side chains contribute to protein shape and function?

A

1) side chains have different sizes
2) side chains have distinct polarities
3) some amino acids have “special properties”

91
Q

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

A

Nonpolar

Cys

Can form disulfide bonds: a covalent bond (outside cells)

92
Q

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

A

Nonpolar and aliphatic

Gly

Only a single Hydrogen as R group

93
Q

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

A

Nonpolar and aliphatic

Ala

94
Q

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

A

Nonpolar and aliphatic

Val

95
Q

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

A

Nonpolar and aliphatic

Leu

96
Q

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

A

Nonpolar and aliphatic

Met

97
Q

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

A

Nonpolar and aliphatic

Ile

98
Q

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

A

Uncharged and Polar

Ser

99
Q

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

A

Uncharged and Polar

Thr

100
Q

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

A

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
101
Q

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

A

Uncharged and Polar

Asn

102
Q

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

A

Uncharged and Polar

Gln

103
Q

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

A

Positively Charged Group

Lys

Holds a positive charge at the bottom of the linear chain in the R group

104
Q

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

A

Positively Charged Group

Arg

Has a positive charge in the second to last position of the linear chain in the R group

105
Q

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

A

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

106
Q

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)

A

Negatively Charged Group

Asp

Holds a fully ionized carboxyl group at the end (lacks hydrogen proton)

107
Q

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)

A

Negatively Charged Group

Glu

Holds full ionized carboxyl group at the end (lacks hydrogen proton)

108
Q

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

A

Nonpolar, Aromatic Group

Phe

Holds hexagon like ring at the bottom of chain

109
Q

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

A

Nonpolar, Aromatic Group

Tyr

Holds a Hydroxyl group below the hexagon like ring at the bottom of the chain

110
Q

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

A

Nonpolar, Aromatic Group

Trp

Holds a pentagon like construct sharing a side to a hexagon like ring at the bottom of the chain

111
Q

What can polar amino acids form?

A

Hydrogen Bonds

112
Q

What can fully charged side chains form?

A

Ionic Bonds

113
Q

Which three organic molecules are cell membranes composed of?

A

Lipids, Proteins, and carbohydrates

114
Q

What happens when phospholipids are placed in an aqueous environment? What is the term for this characteristic?

A

They spontaneously form structures such as micelles and bilayers

Known as being amphipathic (polar and nonpolar)

115
Q

What is membrane fluidity influenced by? (3 things)

A
  • Length of fatty acid chains
  • Presence of carbon-carbon double bonds in fatty acid chains
  • Amount of cholesterol
116
Q

The plasma membrane is a selective barrier that controls what? How does it drive work?

A

The movement of molecules between the inside and the outside of the cell

Drives work through electrochemical gradients

117
Q

What is passive transport?

A

The movement of molecules by diffusion directly through the plasma membrane (simple diffusion) or be aided by protein transports (facilitated diffusion)

118
Q

Describe membrane fluidity as temperature changes

A

Fluidity lower at low temps and higher at higher temps

119
Q

What kind of charge does phosphate carry?

A

Negative Charge

120
Q

What are phospholipids composed of?

A
  • Two hydrocarbon chains
  • A glycerol backbone
  • A phosphate group
  • A head group of some type
121
Q

What are phospholipids composed of?

A
  • Two hydrocarbon chains
  • A glycerol backbone
  • A phosphate group
  • A head group of some type
122
Q

What do phospholipids with “straight” tails make? What is the shape of their structure. Is the inside of the structure hydro-phillic or phobic?

A

Make Micelles

A structure of multiple “ice cream cones” being packed together

Outside head groups is hydrophillic, while the inside is all hydrophobic

123
Q

What is a liposome?

A

A phospholipid bilayer that surrounds a central space. “Ball with the middle space carved out”

124
Q

What is a liposome?

A

A phospholipid bilayer that surrounds a central space. “Ball with the middle space carved out”

-hydrophillic on the inside and out

125
Q

Do phospholipids in membranes contain saturated or unsaturated fatty acids?

A

Unsaturated

126
Q

What does cholesterol do?

A

Stiffens membranes

127
Q

What are the four discussed jobs of proteins in a membrane? Provide a brief description of each

A

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

128
Q

What are integral membrane proteins?

A

Transmembrane proteins that span the entire membrane (go through it)

129
Q

What are peripheral membrane proteins?

A

Temporarily associated with either the internal or the external side of the membrane (usually through covalent bonds)

130
Q

What are the three parts of a transmembrane protein?

A

Transmembrane
Extracellular
Cytoplasmic

“Pooh bear stuck in the tree”

131
Q

How to peripheral membrane proteins hold on?

A

“holding on” by hydrophobic regions

132
Q

What is an electrochemical gradient?

A

A high concentrations of protons (a “chemical”) and positive charge on one side of a membrane

133
Q

What is passive diffusion?

A

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)

134
Q

What is osmotic pressure?

A

Water pushing against gravity in order to equalize high and low concentrations generating force

135
Q

Does a more stable configuration (in terms of chemical bonds) have lower or higher potential energy?

A

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

136
Q

How might you keep a membrane fluid in colder temperatures?

A
  • 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

137
Q

How might you decrease membrane fluidity in hotter temperatures?

A

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

138
Q

Lipids are impermeable to what?

A

Polar/charged molecules

139
Q

What “calls the shots” of what gets through a membrane?

A

Membrane proteins

140
Q

List the three things a differential in molecule/ion concentration across a membrane can do.

A
  • 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)
141
Q

What is the nucleus in a cell used for?

A

Storehouse for the cell’s genetic information

Also site of RNA synthesis

142
Q

What is the mitochondria used for?

A

Site of most ATP synthesis

  • outer membrane
  • inner membrane
  • intermembrane
  • mitochondria membrane
143
Q

Describe the plasma membrane in a cell

A

Composed of phospholipids and proteins and regulates the passage of materials into and out of hte cell

144
Q

Describe chloroplasts of a plant cell

A

Help plant cells utilize sunlight as energy to synthesize sugars

145
Q

What are ribosomes used for in the cell?

A

Protein synthesis

146
Q

What is the golgi apparatus used for?

A

Modifies and sorts proteins and lipids before they head to their final destination

147
Q

What do lysosomes do in the cell?

A

Degrade macromolecules

148
Q

What does the endoplasmic recticulum do?

A

involved in protein and lipid synthesis

149
Q

What is exocytosis? What is endocytosis?

A
  • expelling things from inside cell

- bringing things into the cell