Biochemistry Flashcards
(142 cards)
1
Q
Name the functional groups
A
Hydroxyl, carbonyl, carboxyl, amino, methyl, phosphate, sulfhydral
2
Q
Name the functional groups associated with carbohydrates
A
Hydroxyl, carbonyl
3
Q
Name the functional groups associated with proteins
A
Hydroxyl, carbonyl, amino, sulfhydryl
4
Q
Name the functional groups associated with nucleic acids
A
Hydroxyl, carbonyl, amino, phosphate
5
Q
Name the functional groups associated with lipids
A
Hydroxyl, carboxyl, phosphate
6
Q
What is a macromolecule
A
Large, complex molecules usually composed of repeating units of smaller molecules covalently linked together
7
Q
What is a monomer
A
One sub unit
8
Q
What is a polymer
A
Several sub units (monomers) combined
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
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
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
12
Q
What are the two equilibrium that sugars exist in
A
Cyclic (Haworth model) and acyclic (fisher projection)
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
14
Q
What is a polysaccharide
A
A carbohydrate polymer composed of many monosaccharides joined together by covalent bonds
15
Q
Explain starch
A
Responsible for energy storage in plants
Long chain of glucose subunits
Provide short term energy storage
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
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
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
19
Q
What are the four classes of lipids
A
Triglycerides, phospholipids, steroids, waxes
20
Q
Explain triglycerides
A
Triglycerides are a lipid molecule composed of a glycerol molecule and three fatty acids linked by ester bonds
21
Q
What is a fatty acid
A
A fatty acid is a hydrocarbon chain ending in a carboxyl group
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
23
Q
Explain saturated fats
A
No double bonds between carbon atoms
Fairly straight, pack tightly
Solid at room temperature
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
25
Explain hydrogenation
Add hydrogen atoms to double bonds
| For example, adding hydrogen atoms in vegetable oils to convert them to semi-solids like margarine
26
Explain trans fat
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
27
What are phospholipids
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
28
What is a phospholipid bilayer
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
29
What is a micelle
A single layered barrier formed when phospholipids are added to water
Forms spheres, forms a single layer membrane with a hydrophobic interior
30
What are steroids
Lipids composed of four attached based rings
31
Explain cholesterol
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
32
Explain high density lipoprotein (HDL)
Aids in moving cholesterol through blood stream
Removes cholesterol by transporting to liver
33
Explain low density lipoprotein (LDL)
Deposits cholesterol onto vessel wall
Causes blockages
34
What are waxes
Lipids containing long chain fatty acids linked to alcohols or carbon rings
Hydrophobic, firm, pliable consistency, used as waterproof coating on plants and animals
35
What functions do proteins perform
Catalyze chemical reactions, provide structural support, transport substances in the body, enable organisms to move, regulate cellular processes, provide defence from disease
36
What is an amino acid
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
37
Explain the primary structure of a protein
The primary structure of a protein is the polypeptide chain formed by covalent peptide bonds
38
Explain the secondary structure of a protein
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
39
Explain the tertiary structure of a protein
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
40
Explain the quaternary structure of a protein
When the different tertiary structure group together and interact they form a large quaternary structure.This is the functional protein stage
41
Explain denaturation
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
42
Explain nucleic acids
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
43
Explain DNA
Composed of four different types of nitrogenous bases: adenine, thymine, guanine and cytosine
Stores genetic information of an organism
H in DNA
44
Explain RNA
In RNA uracil is used in place of thymine
Participates in protein synthesis
OH in RNA
45
What is a nucleic acid composed of
A phosphate group, a sugar, a nitrogenous base
46
What is the monomer of a carbohydrate
Monosaccharide
47
What is the polymer of a carbohydrate
Polysaccharide
48
What are the bonds between the monomers of a carbohydrate
Glycosidic linkage
49
What is the monomer of a lipid
Glycerol and 3 fatty acid chains
50
What is the polymer of a lipid
Triglyceride
51
What are the bonds between the monomers of a lipid
Ester bonds
52
What is the monomer of a protein
Amino acids
53
What is the polymer of a protein
Polypeptides
54
What are the bonds between the monomers of a proteins
Peptide bonds
55
What is the monomer of a nucleic acid
Nucleotides
56
What is the polymer of a nucleic acid
Strands
57
What are the bonds between the monomers of a nucleic acid
Phosphodiester bonds
58
What is an acid
A substance that produces hydrogen ions when dissolved in water
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What is a base
A substance that produces hydroxide ions when dissolved in water
60
pH scale
```
>7 = basic
<7 = acidic
7 = neutral
```
61
What is the normal pH range of human blood
7.35 - 7.45, slightly alkaline
62
Define alkalosis
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
Define acidosis
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
Define buffer
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
Define oxidation
The process involving the loss of electrons
66
Define reduction
The process involving the gain of electrons
67
Define redox reaction
The chemical reaction that involves the transfer of electrons from one substance to another
68
What is a condensation reaction
A chemical reaction that results in the formation of a covalent bond between two molecules with the production of a water molecule
69
What is a hydrolysis reaction
A chemical reaction that results in cleavage of a covalent bind with the addition of a water molecule
70
What are enzymes
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
Why are enzymes important
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
What is an inhibitor
Molecules that bind to the allosteric site or active site of an enzyme and causes a decrease in the activity of that enzyme
73
What is an allosteric site
A site on an enzyme that is not the active site
74
What is competitive inhibition
Interferes with the active site of the enzyme so substrate cannot bind
75
What is non-competitive inhibition
Changes the shape of the enzyme so it cannot bind to substrate
76
What is an activator
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
What are the factors that affect enzyme activity
Temperature, pH, substrate concentration
78
Explain how temperature affect that activity of an enzyme
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
Explain how pH affects the activity of an enzyme
As pH changes, the enzymes amino acids R-groups gain or lose protons, which change their shape and thus activity
80
Explain how substrate concentration affects the activity of an enzyme
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
Give an example of a buffer
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
Describe cytoplasm
The region of the cell that is contained within the cell membrane; Includes the cytosol, the organelles and other life supporting materials
83
Describe the nucleus
Contains DNA which stores and replicates the genetic information of the cell
84
Describe nucleoplasm
A thick fluid that fills the nucleus of a cell
85
Describe nuclear matrix
A filamentous Network of proteins that is found inside the nucleus and lines the inner nuclear membrane; serves to organize chromosomes
86
Describe nuclear envelope
A double membrane surrounding the nucleus of a cell
87
Describe nuclear pore complex
A group of proteins forming openings in the nuclear envelope
88
Describe nucleolus
A non-membrane-bound structure in the nucleus, contains RNA and proteins
89
Describe chromosome
A strand-like complex of nucleic acids and protein tightly bounded together; chromosomes contain the hereditary units known as genes
90
Describe chromatin
The non-condensed form of genetic material that predominates for most of the eukaryotic cell cycle. Chromatin represents the unfolded state of chromosomes
91
Describe rough endoplasmic reticulum
Studded with ribosomes, plays a key role in the initial synthesis of proteins
92
Describe smooth endoplasmic reticulum
Synthesizes lipids and lipid containing molecules
93
Describe ribosomes
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
Describe lysosome
A membrane-bound vesicle containing enzymes that catalyze hydrolysis reaction thereby breaking down macromolecules
95
Describe Golgi apparatus
A stack of curved membrane sacs that packages, processes, sorts, and distributes proteins, lipids and other substances within the cell
96
Describe peroxisomes
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
Describe vesicle
Small membrane bound sac that stores substances within a cell
98
Describe vacuole
Large membrane bound sac in plant cells and some other cells that store water, ions, macromolecules, sugars, amino acids
99
Describe chloroplast
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
Describe chlorophyll
Photosynthetic pigment; absorbs light energy as part of the process that converts carbon dioxide and water into energy rich organic molecules
101
Describe stroma
The fluid filled interior surrounding the grana in a chloroplast
102
Describe thylakoids
One of many interconnected sac-like membranous disks within the chloroplast, containing the molecules that absorb energy from the sun
103
Describe granum/grana
In a chloroplast, a structure made up of stacked thylakoids
104
Describe mitochondria
An organelle found in eukaryotic cells that supplies most of the cells ATP
105
Describe matrix
The fluid filled space in the inner membrane of the mitochondria
106
Describe cristae
Folds of the inner membrane of the mitochondria
107
Describe cytoskeleton
A network of protein fibers that extend throughout the cytosol, providing structure, shape, support and motility
108
Describe microtubules
Proteins that form hollow tubes. Maintain cell shape, facilitate movement of organelles, assist in cell division (spindle formation)
109
Describe intermediate filaments
Proteins coiled together into cables. Maintain cell shape, anchor some organelles, form the internal scaffolding of the nucleus
110
Describe microfilaments
Two strands of actin wound together. Maintain cell shape, involved in muscle contraction, assist in cell division (cleavage furrow)
111
Describe cilia
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
Describe flagella
Long, thin appendages that allow cells to move themselves, or to move substances over their surface
113
Describe cell wall
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
Describe cell membrane
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
Explain the surface area to volume ratio
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
Explain fluid in regards to the fluid mosaic model
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
Explain mosaic in regards to the fluid mosaic model
A variety of macromolecules make up the membrane inside and surface, such as proteins, glycoproteins and cholesterol’s
118
What are the three factors affecting fluidity
Temperature: change in state
Double bonds: create kinks and affects ability to pack tightly
Fatty acid tail length: more molecules increase intermolecular attraction
119
How does temperature affect fluidity
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
How do double bonds affect fluidity
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
How does tail length affect fluidity
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
What are the two types of protein associated with the cell membrane
Integral and peripheral
123
Explain integral proteins
Integral membrane proteins are embedded, with hydrophobic ends within the membrane
124
Explain peripheral proteins
Per for a membrane proteins are loosely bound to the surface
125
What is passive transport
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
What is diffusion
The net movement of ions or molecules from an area of higher concentration to an area of lower concentration
127
What affects diffusion
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
What is osmosis
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
What are the three types of osmosis solutions
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
Define lysis
In a hypotonic solution the osmotic pressure inside the cell is so great that it bursts
131
What is facilitated diffusion
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
What is a channel protein
Forms a channel across a cell membrane, which allows specific ions or molecules to cross the membrane along the concentration gradient
133
What are carrier proteins
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
What is active transport
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
Explain primary active transport
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
Explain secondary active transport
Uses an electrochemical gradient as a source of energy to transport molecules or ions across a cell membrane
137
What is an electrochemical gradient
A result of a build up of positive or negative charges
138
Explain secondary active transport
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
What is endocytosis
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
What are receptor-mediated endocytosis
Use of receptor proteins on a portion of a cell that bind with specific molecules outside the cell
141
Explain exocytosis
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
What is a concentration gradient
A difference in concentration between one side of a membrane and the other
