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SBI4U > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

Name the functional groups

A

Hydroxyl, carbonyl, carboxyl, amino, methyl, phosphate, sulfhydral

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2
Q

Name the functional groups associated with carbohydrates

A

Hydroxyl, carbonyl

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3
Q

Name the functional groups associated with proteins

A

Hydroxyl, carbonyl, amino, sulfhydryl

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4
Q

Name the functional groups associated with nucleic acids

A

Hydroxyl, carbonyl, amino, phosphate

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5
Q

Name the functional groups associated with lipids

A

Hydroxyl, carboxyl, phosphate

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6
Q

What is a macromolecule

A

Large, complex molecules usually composed of repeating units of smaller molecules covalently linked together

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7
Q

What is a monomer

A

One sub unit

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8
Q

What is a polymer

A

Several sub units (monomers) combined

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9
Q

What is a carbohydrate

A

A biological macromolecule that contains carbon, hydrogen and oxygen in a 1:2:1 ratio

Provide short or long term energy storage

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10
Q

What is a monosaccharide

A

A carbohydrate composed of between 3 and 7 carbon atoms

“Mono” means one, “saccharide” means sugar

Considered to be simple sugars such as glucose, fructose and galactose

Glucose, fructose and galactose are isomers

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11
Q

What is an isomer

A

One of two or more molecules with the same number and type of atoms, but different structural arrangements

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12
Q

What are the two equilibrium that sugars exist in

A

Cyclic (Haworth model) and acyclic (fisher projection)

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13
Q

What is a disaccharide

A

A carbohydrate composed of two monosaccharides joined by a glycosidic linkage

An example is sucrose, composed of glucose and fructose

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14
Q

What is a polysaccharide

A

A carbohydrate polymer composed of many monosaccharides joined together by covalent bonds

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15
Q

Explain starch

A

Responsible for energy storage in plants

Long chain of glucose subunits

Provide short term energy storage

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16
Q

Explain glycogen

A

Responsible for energy storage in animals

Animals and humans when consuming glucose break it down and convert it into glycogen where it is stored in the liver

Has a larger amount of branching than starch in order to pack more glucose units into a single cell

Too much glycogen can result in glycogen storage disease which is usually hereditary

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17
Q

Explain cellulose

A

Used by plants to build walls

Structural molecule as it protects and supports the plant

Only a few bacterial species produce the digestive chemicals to break it down, mammals and humans do not have the bacteria

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18
Q

Explain lipids

A

Lipids are hydrophobic

The presence of many energy rich C-H bonds makes lipids efficient energy storage molecules

Lipids provide long term energy storage, provide insulation, protects and cushion the organs

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19
Q

What are the four classes of lipids

A

Triglycerides, phospholipids, steroids, waxes

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20
Q

Explain triglycerides

A

Triglycerides are a lipid molecule composed of a glycerol molecule and three fatty acids linked by ester bonds

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21
Q

What is a fatty acid

A

A fatty acid is a hydrocarbon chain ending in a carboxyl group

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22
Q

What are unsaturated fatty acids

A

Fatty acids with double bonds

0 double bonds= saturated
1 double bond= monounsaturated
2+ double bonds= polyunsaturated

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23
Q

Explain saturated fats

A

No double bonds between carbon atoms

Fairly straight, pack tightly

Solid at room temperature

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24
Q

Explain unsaturated/polyunsaturated fats

A

One or more double bonds between carbon atoms

Cis double bonds cause kinks in molecules

Cannot pack tightly, trans double bonds don’t allow bending

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25
Q

Explain hydrogenation

A

Add hydrogen atoms to double bonds

For example, adding hydrogen atoms in vegetable oils to convert them to semi-solids like margarine

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26
Q

Explain trans fat

A

Trans fats are unsaturated fatty acids that are not commonly found in nature. The common unsaturated acids have a cis configuration of H’s attached to double bonds. Trans fatty acids have a trans configurations of H’s attached to double bonds

Cis- H’s go the same way
Trans- H’s go the opposite way

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27
Q

What are phospholipids

A

Lipids composed of a glycerol molecule bonded to 2 fatty acids and a phosphate groups with an R group

The head of the phospholipid molecule is polar, thus the head is hydrophilic while the tail is non-polar and hydrophobic

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28
Q

What is a phospholipid bilayer

A

A structure with hydrophilic heads of phospholipids directed towards the aqueous environment and hydrophobic tails directed toward the centre, interacting with each other

This keeps water out, allows the cell to be selective of what goes in and out

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29
Q

What is a micelle

A

A single layered barrier formed when phospholipids are added to water

Forms spheres, forms a single layer membrane with a hydrophobic interior

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30
Q

What are steroids

A

Lipids composed of four attached based rings

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31
Q

Explain cholesterol

A

A key component of cell membranes

High cholesterol can restrict blood flow. Cells convert cholesterol into compounds such as vitamin D and bile salts. Important for keeping cell membrane fluid, not rigid

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32
Q

Explain high density lipoprotein (HDL)

A

Aids in moving cholesterol through blood stream

Removes cholesterol by transporting to liver

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33
Q

Explain low density lipoprotein (LDL)

A

Deposits cholesterol onto vessel wall

Causes blockages

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34
Q

What are waxes

A

Lipids containing long chain fatty acids linked to alcohols or carbon rings

Hydrophobic, firm, pliable consistency, used as waterproof coating on plants and animals

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35
Q

What functions do proteins perform

A

Catalyze chemical reactions, provide structural support, transport substances in the body, enable organisms to move, regulate cellular processes, provide defence from disease

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36
Q

What is an amino acid

A

An amino acid is an organic molecule composed of a central carbon atom bonded to a hydrogen atom, an amino group, a carboxyl group and a R group

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37
Q

Explain the primary structure of a protein

A

The primary structure of a protein is the polypeptide chain formed by covalent peptide bonds

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38
Q

Explain the secondary structure of a protein

A

The polypeptide chain begins to fold and interact with itself due to hydrogen bonding. It has been observed to form two possible orientations: an alpha helix and a beta pleated sheet

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39
Q

Explain the tertiary structure of a protein

A

This structure forms due to hydrophobic and hydrophilic interruptions within the cellular environment. Alpha helixes and beta sheets will fold and re-orient themselves so that:
Hydrophilic groups will direct towards the water
Hydrophobic groups will be directed towards the interior of the folded protein, to avoid interaction with water

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40
Q

Explain the quaternary structure of a protein

A

When the different tertiary structure group together and interact they form a large quaternary structure.This is the functional protein stage

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41
Q

Explain denaturation

A

Understood and conditions, proteins will unfold to do breaking of bonding interactions with R groups. For example changes in temperature, change in pH of the environment, exposure to harmful chemicals, high salt concentrations)

Protein can no longer function normally at this point

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42
Q

Explain nucleic acids

A

Biological macromolecule composed of nucleotide monomers. The two types are DNA and RNA

DNA is composed of nucleotides containing sugar deoxyribose

RNA is composed of nucleotides containing the sugar ribose

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43
Q

Explain DNA

A

Composed of four different types of nitrogenous bases: adenine, thymine, guanine and cytosine

Stores genetic information of an organism

H in DNA

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44
Q

Explain RNA

A

In RNA uracil is used in place of thymine

Participates in protein synthesis

OH in RNA

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45
Q

What is a nucleic acid composed of

A

A phosphate group, a sugar, a nitrogenous base

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46
Q

What is the monomer of a carbohydrate

A

Monosaccharide

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47
Q

What is the polymer of a carbohydrate

A

Polysaccharide

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48
Q

What are the bonds between the monomers of a carbohydrate

A

Glycosidic linkage

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49
Q

What is the monomer of a lipid

A

Glycerol and 3 fatty acid chains

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50
Q

What is the polymer of a lipid

A

Triglyceride

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51
Q

What are the bonds between the monomers of a lipid

A

Ester bonds

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52
Q

What is the monomer of a protein

A

Amino acids

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53
Q

What is the polymer of a protein

A

Polypeptides

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54
Q

What are the bonds between the monomers of a proteins

A

Peptide bonds

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55
Q

What is the monomer of a nucleic acid

A

Nucleotides

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56
Q

What is the polymer of a nucleic acid

A

Strands

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57
Q

What are the bonds between the monomers of a nucleic acid

A

Phosphodiester bonds

58
Q

What is an acid

A

A substance that produces hydrogen ions when dissolved in water

59
Q

What is a base

A

A substance that produces hydroxide ions when dissolved in water

60
Q

pH scale

A 
>7 = basic 
<7 = acidic 
7 = neutral
61
Q

What is the normal pH range of human blood

A

7.35 - 7.45, slightly alkaline

62
Q

Define alkalosis

A

If the pH increases to 7.5

This could be the result of breathing too quickly at high altitudes, feeling anxious, too many antacids, the person can feel dizzy and agitated

63
Q

Define acidosis

A

The pH falls between 7.1-7.3 and symptoms include disorientation and fatigue and can result from severe vomiting, brain damage, and kidney disease

64
Q

Define buffer

A

A substance that minimizes changes in pH by donating or accepting hydrogen ions as needed

Buffers tend to exist as a pair of acids and bases

65
Q

Define oxidation

A

The process involving the loss of electrons

66
Q

Define reduction

A

The process involving the gain of electrons

67
Q

Define redox reaction

A

The chemical reaction that involves the transfer of electrons from one substance to another

68
Q

What is a condensation reaction

A

A chemical reaction that results in the formation of a covalent bond between two molecules with the production of a water molecule

69
Q

What is a hydrolysis reaction

A

A chemical reaction that results in cleavage of a covalent bind with the addition of a water molecule

70
Q

What are enzymes

A

Enzymes are catalysts- these are chemicals that speed up a chemical reaction without being used up in the process

The molecule that the enzyme acts on is called the substrate molecule

Enzymes are very specific to the substance which they bind

The site where the enzyme binds to the substrate is called the active site

When the two are attached, this creates the enzyme substrate complex

Enzymes can be inorganic (cofactors) or organic (coenzymes)

71
Q

Why are enzymes important

A

Enzymes prepare substrates for reaction by changing the substrate, its environment or both in some way

Enzymes reduce the activation energy required for a reaction to begin, thus less energy is needed for reactions to occur

72
Q

What is an inhibitor

A

Molecules that bind to the allosteric site or active site of an enzyme and causes a decrease in the activity of that enzyme

73
Q

What is an allosteric site

A

A site on an enzyme that is not the active site

74
Q

What is competitive inhibition

A

Interferes with the active site of the enzyme so substrate cannot bind

75
Q

What is non-competitive inhibition

A

Changes the shape of the enzyme so it cannot bind to substrate

76
Q

What is an activator

A

Molecules can also bind to an allosteric site

It is a molecule that keeps an enzyme active or causes an increase in the activity of that enzyme

77
Q

What are the factors that affect enzyme activity

A

Temperature, pH, substrate concentration

78
Q

Explain how temperature affect that activity of an enzyme

A

As temperature increases, so does the vibrational energy of each atom. This causes the intermolecular forces holding the protein together to break. This result in a denatured protein, thus the enzyme is non functioning

79
Q

Explain how pH affects the activity of an enzyme

A

As pH changes, the enzymes amino acids R-groups gain or lose protons, which change their shape and thus activity

80
Q

Explain how substrate concentration affects the activity of an enzyme

A

If there are more molecules present in a solution, there is a higher chance that one will interact with the enzyme. At a certain point (x), there are not enough enzyme molecules to catalyze all of the substrate molecules. The enzyme becomes the limiting factor

81
Q

Give an example of a buffer

A

In the human body, carbonic acid and hydrogen carbonate

If blood becomes to basic, carbon dioxide and water react to produce carbonic acid which dissociates into hydrogen carbonate and hydrogen ions and increases the acidity of the blood

82
Q

Describe cytoplasm

A

The region of the cell that is contained within the cell membrane; Includes the cytosol, the organelles and other life supporting materials

83
Q

Describe the nucleus

A

Contains DNA which stores and replicates the genetic information of the cell

84
Q

Describe nucleoplasm

A

A thick fluid that fills the nucleus of a cell

85
Q

Describe nuclear matrix

A

A filamentous Network of proteins that is found inside the nucleus and lines the inner nuclear membrane; serves to organize chromosomes

86
Q

Describe nuclear envelope

A

A double membrane surrounding the nucleus of a cell

87
Q

Describe nuclear pore complex

A

A group of proteins forming openings in the nuclear envelope

88
Q

Describe nucleolus

A

A non-membrane-bound structure in the nucleus, contains RNA and proteins

89
Q

Describe chromosome

A

A strand-like complex of nucleic acids and protein tightly bounded together; chromosomes contain the hereditary units known as genes

90
Q

Describe chromatin

A

The non-condensed form of genetic material that predominates for most of the eukaryotic cell cycle. Chromatin represents the unfolded state of chromosomes

91
Q

Describe rough endoplasmic reticulum

A

Studded with ribosomes, plays a key role in the initial synthesis of proteins

92
Q

Describe smooth endoplasmic reticulum

A

Synthesizes lipids and lipid containing molecules

93
Q

Describe ribosomes

A

I structure composed of RNA and proteins; and responsible for synthesis of polypeptides in the cytosol and on the surface of the rough ER

94
Q

Describe lysosome

A

A membrane-bound vesicle containing enzymes that catalyze hydrolysis reaction thereby breaking down macromolecules

95
Q

Describe Golgi apparatus

A

A stack of curved membrane sacs that packages, processes, sorts, and distributes proteins, lipids and other substances within the cell

96
Q

Describe peroxisomes

A

A membrane-bound sac containing oxidative enzymes that break down excess fatty acid and hydrogen peroxide, and participate in the synthesis of bile acids and cholesterol

97
Q

Describe vesicle

A

Small membrane bound sac that stores substances within a cell

98
Q

Describe vacuole

A

Large membrane bound sac in plant cells and some other cells that store water, ions, macromolecules, sugars, amino acids

99
Q

Describe chloroplast

A

An organelle in the cells of photosynthetic organisms, in which light energy from the sun is captured and stored in the form of high energy organic molecules such as glucose

100
Q

Describe chlorophyll

A

Photosynthetic pigment; absorbs light energy as part of the process that converts carbon dioxide and water into energy rich organic molecules

101
Q

Describe stroma

A

The fluid filled interior surrounding the grana in a chloroplast

102
Q

Describe thylakoids

A

One of many interconnected sac-like membranous disks within the chloroplast, containing the molecules that absorb energy from the sun

103
Q

Describe granum/grana

A

In a chloroplast, a structure made up of stacked thylakoids

104
Q

Describe mitochondria

A

An organelle found in eukaryotic cells that supplies most of the cells ATP

105
Q

Describe matrix

A

The fluid filled space in the inner membrane of the mitochondria

106
Q

Describe cristae

A

Folds of the inner membrane of the mitochondria

107
Q

Describe cytoskeleton

A

A network of protein fibers that extend throughout the cytosol, providing structure, shape, support and motility

108
Q

Describe microtubules

A

Proteins that form hollow tubes. Maintain cell shape, facilitate movement of organelles, assist in cell division (spindle formation)

109
Q

Describe intermediate filaments

A

Proteins coiled together into cables. Maintain cell shape, anchor some organelles, form the internal scaffolding of the nucleus

110
Q

Describe microfilaments

A

Two strands of actin wound together. Maintain cell shape, involved in muscle contraction, assist in cell division (cleavage furrow)

111
Q

Describe cilia

A

Numerous short appendages protruding from a cell; each cilium is composed of a microtubule-based shaft covered in an extension of the cell membrane; allow a cell to propel itself or to propel substances across the surface of the cell

112
Q

Describe flagella

A

Long, thin appendages that allow cells to move themselves, or to move substances over their surface

113
Q

Describe cell wall

A

A rigid layer surrounding plant, algae, fungal, bacteria and some archaea cells. Composed of proteins and/or carbohydrates; gives the cell its shape and structural support

114
Q

Describe cell membrane

A

A thin structure composed of various macromolecules, that separates the inside of the cell from extracellular environment; controls the flow of substance in and out of the cell

115
Q

Explain the surface area to volume ratio

A

The surface area to volume ratio is very important for a cell. As it grows, the cells volume becomes too large for the membrane to hold and the ratio decreases. It is fixed by cell division and folding of the organelles

116
Q

Explain fluid in regards to the fluid mosaic model

A

Varies it shape due to weak intermolecular attractive forces, not covalent bonds

It is flexible

A small tear is quickly fixed by lipids rearranging themselves

117
Q

Explain mosaic in regards to the fluid mosaic model

A

A variety of macromolecules make up the membrane inside and surface, such as proteins, glycoproteins and cholesterol’s

118
Q

What are the three factors affecting fluidity

A

Temperature: change in state

Double bonds: create kinks and affects ability to pack tightly

Fatty acid tail length: more molecules increase intermolecular attraction

119
Q

How does temperature affect fluidity

A

As temperature increases, molecules gain more energy and intermolecular forces break, fluidity increases.

Thus, as temperature increases, so does fluidity. As temperature decreases, so does fluidity

120
Q

How do double bonds affect fluidity

A

A double bond in the fatty acid tail creates bends or kinks in the chain. The more kinks a chain has, the lower its ability to pack tightly. Less tightly packed molecules have lower intermolecular interactions and therefore higher fluidity.

Thus, more double bonds, lower intermolecular forces, higher fluidity. Less double bonds, higher intermolecular forces, lower fluidity

121
Q

How does tail length affect fluidity

A

The longer a fatty acid tail is, the more C/H atoms there are compared to a shorter tail. Intermolecular forces increase as the number of atoms increase

Thus, as chain length increases, fluidity decreases. As chain length decreases, fluidity increases

122
Q

What are the two types of protein associated with the cell membrane

A

Integral and peripheral

123
Q

Explain integral proteins

A

Integral membrane proteins are embedded, with hydrophobic ends within the membrane

124
Q

Explain peripheral proteins

A

Per for a membrane proteins are loosely bound to the surface

125
Q

What is passive transport

A

The movement of ions or molecules across a cell membrane from a region of higher concentration to a region of lower concentration, without the input of energy

126
Q

What is diffusion

A

The net movement of ions or molecules from an area of higher concentration to an area of lower concentration

127
Q

What affects diffusion

A

Molecule size- larger molecules are difficult to transport

Molecule polarity- highly polar molecules have difficulty passing through

Molecule or ion charge- cannot generally pass through a lipid bilayer

128
Q

What is osmosis

A

The movement of water from an area of higher concentration to an area of lower concentration, across a semi permeable membrane

Water moves in and out of a cell, along their concentration gradient until their concentrations on both sides of the membranes are equal

129
Q

What are the three types of osmosis solutions

A

Hypertonic: solute in the solution is higher than inside the cell

Hypotonic: solute in the solution is lower than inside the cell

Isotonic: both solutions have the solute concentration

130
Q

Define lysis

A

In a hypotonic solution the osmotic pressure inside the cell is so great that it bursts

131
Q

What is facilitated diffusion

A

The transport of ions or molecules across a membrane by means of a membrane protein along the concentration gradient for that ion or molecule

132
Q

What is a channel protein

A

Forms a channel across a cell membrane, which allows specific ions or molecules to cross the membrane along the concentration gradient

133
Q

What are carrier proteins

A

Binds to specific molecules, transport them across the membrane, and then release them on the other side. Thus, the proteins carry the molecules across

134
Q

What is active transport

A

The transport of a solute across a membrane against its gradient

Occurs with the aid of ATP

With the aid of water, ATP undergoes hydrolysis to create ADP which releases energy for the cell

135
Q

Explain primary active transport

A

The sodium – potassium pump transports sodium ions out of the cell while transporting potassium ions into the cell

  1. Three sodium ions bind to the ion pump in the cell membrane and hydrolyzed
  2. Three sodium’s are released outside the cell
  3. The potassium ions bind from outside the cell
  4. Phosphate is released and the pump switched and two potassium’s ions are released into the cytosol
136
Q

Explain secondary active transport

A

Uses an electrochemical gradient as a source of energy to transport molecules or ions across a cell membrane

137
Q

What is an electrochemical gradient

A

A result of a build up of positive or negative charges

138
Q

Explain secondary active transport

A
  1. Hydrogen binds to the protein
  2. ATP undergoes hydrolysis to produce ADP
  3. Hydrogen is transported to the extracellular environment
  4. Hydrogen binds to the protein as well as sucrose
  5. Hydrogen ions provide energy to transport sucrose against its chemical gradient
139
Q

What is endocytosis

A

Process by which a cell engulfs material by folding the cell membrane around it and then pinching off to form a vesicle inside the cell

Phagocytosis- involves solid particles

Pinocytosis- involves liquid particles

140
Q

What are receptor-mediated endocytosis

A

Use of receptor proteins on a portion of a cell that bind with specific molecules outside the cell

141
Q

Explain exocytosis

A

Transport method in which you back your fuses with the cell membrane and releases its contents outside the cell

This is important in plants to construct cell walls

In animal cells provides a mechanism for secreting and releasing many hormones, neurotransmitters, digestive enzymes and other substances

142
Q

What is a concentration gradient

A

A difference in concentration between one side of a membrane and the other

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