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Flashcards > BIO TEST 1 MODULES 3 & 4 > Flashcards

BIO TEST 1 MODULES 3 & 4 Flashcards

1
Q

how does energy flow through biological systems?

A

Chloroplasts create chemical energy by harnessing light energy;
Non-photosynthetic organisms will get their energy from breaking down organic molecules (sugars) produced by chloroplasts

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2
Q

how are carbs formed?

A

Carbs are formed by the polymerization of monosaccharides through glycosidic bonds in order to form complex sugars

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3
Q

monosaccharides

A

glucose, fructose, galactose

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4
Q

disaccharides

A

Lactose, Sucrose, Maltose

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5
Q

how are cards used to make atp?

A

Reaction occurs between the OH (hydroxyl) group on carbon 1 and carbon 4 of another monosaccharide to form a glycosidic linkage

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6
Q

starch

A

polysaccharide used for energy storage in plants ;2 Alpha 1-4 glycosidic linkages between two alpha-glucose monomers

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7
Q

glycogen

A

Used for energy storage in animals
Highly-branched glycogen polysaccharides helices
This is then broken down into glucose through cell resp to produce ATP

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8
Q

cellular respiration

A

process by which cells use ATP to metabolize simple sugar molecules

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9
Q

4 steps taken for synthesis of ATP

A

glycolysis, pyruvate oxidation (oxidative decarboxylation), kreb’s cycle, oxidative phosphorylation

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10
Q

oxidative decarboxylation

A

Pyruvate is processed with a compound known as acetyl-CoA;
This enters the mitochondrial matrix and enters the krebs cycle

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10
Q

glycolysis

A

2 molecules of pyruvate produced for each molecule of glucose; occurs in cytosol of the cell;Produces 2 ATP and 2 NADH which are electron donors

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10
Q

kreb’s cycle

A

produces ATP, CO2, NADH, FADH2 in mitochondria

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11
Q

how many molecules of ATP are produced in the inner mitochondrial membrane of the electron transport chain

A

32

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12
Q

process of the electron transport chain

A

inner mitochondrial matrix through the ATP synthase, which is driven by the electron transport chain which receives electrons from NADH and FADH2;
The proton pumps will pump protons into the intermembrane space of the mitochondria where a concentration gradient is formed;
This drives protons to passively transport through ATP synthase protein channels embedded in the membrane

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13
Q

how many molecules of ATP does glucose produce in the ETC

A

36 theoretically but research has shown 30

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14
Q

how are proteins and fats used for fuel?

A

Carbs, lipids and proteins can be broken down for ATP;
Carbs are metabolized the fastest, then fats, then proteins

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15
Q

how is energy released as hydrolysis of ATP?

A

Adenosine triphosphate consists of 3 phosphate groups attached to a ribose sugar and an adenine;
3 phosphate groups have 4 negative charges which repel each other which is the energy used when a phosphate group is removed;
During a hydrolysis reaction of ATP (split using water), this forms ADP and an inorganic phosphate;
Highly exergonic reaction

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16
Q

how is ATP important for many cellular processes?

A

An athlete uses ATP hydrolysis to fuel muscle contraction;
Also useful for transport of substances across a membrane against a concentration gradient;
Used by enzymes to carry out certain functions and helps drive endergonic reactions (photosynthesis)

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17
Q

A group of organelles in eukaryotic cells that perform most lipid and protein synthesis

A

Endoplasmic reticulum (ER), golgi apparatus and lysosomes

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18
Q

What are the functions of proteins?

A

1) Transport and signaling
Integral membrane proteins move substance across membranes;
Cytoplasmically situated proteins are important amplifying cell signaling
2) Movement and Structure
Actin and myosin will slide past each other during muscle contraction
3) Enzymes
Can speed up the synthesis of carbohydrates
4) Defense
Specialized immune cells; antibodies which destroy viruses and bacteria

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19
Q

TATA box binding protein

A

interacts with DNA molecules using a groove in the protein

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20
Q

porin proteins

A

are used in transport of water across a cell membrane;
it has a hydrophilic pore which allows for this to happen

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21
Q

cellular proteins

A

Have globular shapes, hydrophobic interior and a hydrophilic exterior;
Allows it to be soluble in an aqueous environment like cytosol

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22
Q

space-filled diagram

A

Shows the actual size and location of each atom, and each atom type is a diff colour

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23
Q

overview of protein synthesis

A

DNA is encoded to produce a strand of RNA
This RNA is read by a protein complex to synthesize a polypeptide
In prokaryotic cells translation of RNA is done by free ribosomes
In eukaryotic cells the RNA is processed into mRNA and then transported through the nuclear pores and into the cytoplasm where ribosomes will translate the mRNA into proteins

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24
Q

ribbon diagram

A

Lines represent the backbone of the protein polymer
The ribbon represents the an organized structure of the alpha helix

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25
Q

protein synthesis in prokaryotic cells

A

DNA → RNA → Ribosomes will synthesize proteins

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26
Q

protein synthesis in eukaryotic cells

A

DNA → RNA → Post DNA transcription forms mRNA → Exits the nucleus through nuclear pores → Enters cytoplasm →Ribosomes will generate proteins (polypeptide)

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27
Q

how do ribosomes synthesize protein?

A

Structural components of ribosomes are made in the nucleolus and then transported out of the nucleus
Outside of the nucleolus the ribosome is made up of a small and large subunit which synthesize protein
Ribosomes remain soluble in cytoplasm as free ribosomes or the can attach to the endoplasmic reticulum and become bound ribosomes

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28
Q

how many different amino acids are there?

A

20

29
Q

what is the structure of an amino acid?

A

A central carbon atom + an amino group + carboxyl group + hydrogen atom + an R group

30
Q

what is a polypeptide?

A

a linear strand of amino acid monomers covalently bound by condensation reactions which release water

31
Q

non-polar side chains

A

hydrophobic amino aicds; amino acids will face the inside of the protein

32
Q

what does the r group of non-polar side chains consist of?

A

benzene ring, CH3, CH2 chain, hydocarbon chains

33
Q

polar side chains

A

hydrophilic amino acids; amino acids will face outside of the protein

34
Q

characteristic of non-polar side chains

A

Can clump in aqueous environments through stable hydrophobic interactions

34
Q

what does the r group of polar side chains consist of

A

Part of the r-group will be able to make hydrogen bonds
In the r-group
NH2 , NH

35
Q

characteristic of polar side chains

A

Can be charge-polarized and able to form ionic bonds;
Some can favour the formation of hydrogen bonds

36
Q

characteristic of glycine

A

R group is Has a single H bounded to the carbon can make hydrogen bonds with water
hydrophobic

37
Q

characteristic of proline

A

Hydrophobic
Will donate one of its hydrogens
Will make non-covalentl bodies

38
Q

characteristic of cysteine

A

Can make covalent bonds with other amino acids

39
Q

how does translation occur inside the ribosome?

A

mRNA binds to the small ribosomal unit and then the large ribosomal unit will attach;
The mRNA is translated and the corresponding tRNA molecules (with corresponding amino acid) will bind and move into the next position in the growing polypeptide chain

40
Q

how are primary protein structures formed?

A

when peptide bonds (C-N) forms between the carboxyl group of one amino acid and the amino group of another amino acid

41
Q

how does the R group affect an amino acid?

A

The R group can change the size, shape or chemical properties of the amino acid

42
Q

secondary structures

A

folded;Interactions between the proteins backbone are responsible for alpha and beta helices

43
Q

alpha helices

A

Amino and carboxyl group form covalent peptide bonds to form a polypeptide
The polymer is spiraled and coiled by the formation of non-covalent hydrogen bonds
The H-bonds form between carbonyl and carboxyl groups of 1 amino acid residue and the amide of an amino acid 4 positions away
Due to this the R-groups will stick out from the helix

44
Q

beta pleated sheets

A

Made up of parallel protein strands with hydrogen bonds with carboxyl and amino groups

45
Q

tertiary structure

A

shape that determines function; overall shape due to interactions between R groups which cause backbone to fold and form 3d shape;Includes H-bonds, van der waals interaction, covalent and ionic bond, disulfide bonds, hydrophobic interactions
Interactions within the protein backbone and the variable side chain (r-groups) are essential in producing folds and functional proteins

46
Q

how does protein folding occur?

A

Some are spontaneous
Others need the help of cellular mechanisms

47
Q

molecular chaperons

A

will bind to hydrophobic regions of polypeptides to prevent incorrect folding until the correct structure is formed

48
Q

chaperonins

A

isolation chambers which incase a protein in a chamber away from other proteins which might interfere with formation of the bonds

49
Q

endomembrane system

A

series of compartments that work together to package, label, and ship proteins and molecules, includes: nuclear envelope, endoplasmic reticulum, golgi apparatus, lysosomes

50
Q

endomembrane system process

A

mRNA (code for proteins needed for EM system) have special sequence and causes ribosomes to bind to ER; SRP binds to SRPR in ER membrane; polypeptide translates and enters lumen of ER (central canal); inside lumen, signal removed polypeptide matures; proteins carried by vesicles; glycosylation occurs for protein stability, cell to cell recognition; vesicle travels to golgi app and fuses; deposits contents into lumen; golgi has more protein mod where carb groups are added; some proteins go to cell membrane (porins receptors); some get secreted out of cell (enzymes, antibodies, hormones)

51
Q

why are proteins tagged as they leave the golgi

A

Lets them be packaged into a particular transport vesicle;
These transport vesicles also have their own tags which determine whether they go to the cell membrane, lysozyme or even back to the ER;
The phospholipid bilayer of the vesicle will fuse with the cell membrane or ER and releases the protein or embedded it in the target membrane

52
Q

what is aquaporin

A

Membrane embedded in the plasma membrane which transports water across the membrane

52
Q

what is cytoskeleton

A

dense network of fibers (microtubules) that maintain and change cell shape

53
Q

structure of aquaporin

A

Has a hydrophobic exterior and hydrophilic core;
Each aquaporin is made up of 4 monomer which make an aquaporin channel (quaternary structure);
Each monomer forms alpha-helices which make a central pore and independent pores for water to go in and out;
When transporting water the protein does not change shape

54
Q

what is bacterial porin

A

Forms beta sheets with a hydrophobic exterior and hydrophilic interior
This structure is seen in the membranes of mitochondria and chloroplasts

55
Q

what happens when a protein misfolds? (cystic fibrosis)

A

Cystic fibrosis is a genetic disease in which there is a mutation in a gene which encode for the cystic fibrosis transmembrane conductance regulator (CFTR) ion channel protein;
This causes the accumulation of mucus in the lungs

56
Q

STREPTOCOCCUS PNEUMONIAE

A

found in the upper respiratory tract

57
Q

what are the two strains of streptococcus pneumoniae?

A

r strain (benign and harmless; lacks a capsule and is recognized and attacked by immune system); s strain (viral;Has a polysaccharide coat which prevents the immune system from detecting it;
Can multiply and produce toxins which can pneumonia and cause death)

58
Q

what did researchers discover when mice were injected with the two strains?

A

1920s, S strain caused death, R strain was harmless

59
Q

Avery, McCarty and Macleod

A

showed that DNA carries hereditary information; isolated macromolecules one by one; mice were injected with S strain, after destroying each macromolecule, Mouse still died and live s strain were recovered, so none of them were responsible for carrying that information; but when DNA was destroyed, the mouse lives and no live S strain was recovered, meaning the DNA carried the hereditary information from the S strain

59
Q

griffith’s experiment

A

Heated viral bacteria to sterilize them and get rid of pathogenic bacteria but the macromolecules are still there;
The dead S-strain was injected into the mice and had no effect;
Using this he hypothesized that the viral cell was present but the cell carrying the information was dead;
Then Grifith tested to see what would happen if the dead virulent stain was incubated with living cells of the benign strain, and injected this into mice;
RESULTS: the mice ended up dying showing that the benign cells (R-strain) are now virulent
He hypothesized that the this information must have been passed on from the S-strain

60
Q

X-ray crystallography

A

Rosalind Franklin used x-ray diffraction to aim x-rays at DNA to create images based on the diffraction by the atoms of the DNA molecule
This showed the helical shape of DNA
Watson and crick described the double helical structure of DNA based on these findings

61
Q

what are nucleotides made of?

A

A phosphate group, a 5-C deoxyribose sugar and a nitrogenous base

62
Q

Pyrimidines

A

single ring, smaller (cytosine and thymine)

63
Q

purines

A

two rings, larger (guanine and adenine)

64
Q

how is DNA assembled?

A

Through condensation reaction where a water molecule is released;
A covalent bond known as a phosphodiester bond is formed between 2 nucleotides;
The 5’ C of the deoxyribose forms a phosphodiester bond with the 3’ C on the next deoxyribose;
This results in a sugar phosphate backbone with a 5’ to 3’ polarity, and the nitrogenous bases stick out;
There is a free (OH-) hydroxyl group at the end of a strand

65
Q

chargaff’s rule

A

ratio of purines to pyrimidines;The ratio of pyrimidine to purine bases should be 1:1 (base pair rule);
# of guanine = # of cytosine (G-C with 3 H-bonds) – more stable
# of adenine = # of thiamine (A-T with 2 H-bonds) ;
Purine + pyrimidine = formation of DNA
DNA is double helixed and runs antiparallel to each other facing inwards to provide a 2.0nm diameter;
There is a major groove and a minor groove with on turn occurring every 10 nucleotides

66
Q

RNA vs DNA

A

RNA 5-c sugar is ribose, for DNA is deoxyribose; RNA has OH at 2’, DNA has H- at 2’; RNA has uracil instead od thiamine

67
Q

messenger RNA

A

A single stranded RNA molecule contains the genes that are translated by ribosomes to produce proteins
RNA polymerase will read the template strand of the DNA in order to synthesize RNA (will be identical to the antisense strand)

68
Q

transfer RNA

A

This RNA is never translated
Has a 3-D structure which is held together by base pairing between nucleotides
FUNCTION: attaches amino acids and brings them to the ribosome complex during translation

69
Q

ribosomal RMA

A

Transcribed from ribosomal genes (there is a large proportion of total RNA in a cell)

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