Unit 1.5 & 2

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6 types of proteins

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1

6 types of proteins

structural, enzyme, hormone, contractile, immunological & transport

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2

Polypeptides

unbranched chain of amino acids

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condensation reaction (draw)

removal of water links monomers together to combine smaller organic molecules to form larger moleculeU

<p>removal of water links monomers together to combine smaller organic molecules to form larger moleculeU</p>
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Proteins

single polypeptide or more than one polypeptide of amino acids linked together

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Structure of an amino acid (draw)

an amino group, a carboxylic acid, and a R group (varies for each amino acid

<p>an amino group, a carboxylic acid, and a R group (varies for each amino acid</p>
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amino acid condensation reaction

  • linked by condensation reaction

  • new bond called peptide

  • dipeptide; 2 amino acids

  • tripeptide: 3 amino acids

<ul><li><p>linked by condensation reaction</p></li><li><p>new bond called peptide</p></li><li><p>dipeptide; 2 amino acids</p></li><li><p>tripeptide: 3 amino acids</p></li></ul>
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Number of amino acids

20

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Synthesis of polypeptides

DNA provides info, transcribed into RNA, where the synthesis takes place in the ribosomes (translation)

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Number of polypeptides in proteins

one or more

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Polypeptide structures

  • primary, secondary, tertiary, quaternary

  • folding determined by amino acid sequence

  • stabilized by intramolecular bonds between amino acids

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Determinant of shape & function of protein

Order of amino acids

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R group determines

types of bonds, interactions w/ other molecules, properties, function, structure

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Conformation

three-dimensional shape of a proteinmolecule

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Effect of gene mutation

changes protein's conformation, shape, loss of function

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Primary structure

Simple linear sequence, defines all aspects of structure & function

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Secondary structure

Folding chains on themselves (pleated sheet or alpha helix)

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teritary structure

foils & coils to form complex 3d shape

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Quarternary stucture

2 or more polypeptide chains held in a multi

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Denaturation

Permanent loss of secondary, tertiary (sometimes quaternary) due to hydrogen bond disruption between R groups & amino groups

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Cause of folding & touching of proteins

Ionic bonds between positively and negatively charged R groups

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Genome

unique DNA content in every organism

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Proteome

Unique set of proteins coded by genome

  • varies because diff cells make diff proteins and depends on cell activity

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gel electrophoresis

Process to separate proteins

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Divisions of protein

globular & fibrous

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Determinant of divisions of protein

solubility in water

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Globular proteins

Complex polypeptide chains linked to other chains, soluble in water cause hydrophobic R groups fold into the core away from surrounding water

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Role of Globular proteins

active in cell metabolism

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Fibrous proteins

Long polypeptide chains with hydrophobic R groups exposed therefore insoluble in water

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Role of fibrous proteins

structural parts: tendons, skin, collages, keratin

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Rubisco

  • globular enzyme

  • active site catalyzing photosynthesis reaction that fixes CO2 from atmosphere

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Insulin

  • globular, hormone, 2 diff polupeptide chains

  • produced by pancreas

  • carried, dissolved in blood

  • binds specifically & reversibly to insulin receptors causing absorption pf glucose to lower blood glucose conc

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Immunoglobulin

Globular, Y shaped, antibodies to fight infections by recognizing and binding to antigen molecules

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Rhodopsin

  • globular, pigment protein

  • retina rod cells become light-sensitive to serve a nerve impulse

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Collagen

Fibrous, 3 diff polypeptide chains. structural protein, in muscles, tendons, ligaments to give tensile strength. In skin & bones to prevent tearing & fractures

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Spider silk

Fibrous, structural protein, produced by spiders for webs, can be extended & resistant to breaking

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36

Ways to denature proteins

higher temperatures, extreme pH of surrounding solution

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3 properties of enzymes

substrate specific, optimum pH, optimum temperature

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Why primary structures are not affected by denatueation

peptide bonds holding adjacent amino acids do not break

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Reason for high fever danger

Some proteins start to denature, enzymes no longer function

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Effect of temperature change on amino acids

Interaction between amino acids changed, affecting quaternary, tertiary & secondary

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Effect of pH on amino acids

strong solutions can break bonds between non adjacent amino acids or between polypeptide chains

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Coagulation: Structure when denatured

Hydrophilic attracts water molecules, hydrophobic portions unstable therefore associates with other hydrophobic molecules

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Enzyme role

control metabolism of cell

  • globular protein

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Define Enzyme

biocatalyst that regulates the role of biochemical reactions without taking part

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How is enzyme a catalyst

lowers minimum activation energy needed for reactants to react

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Location of enzyme & substrate reactions

watery environment

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Active site

location where substrate binds to enzyme to react

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State of enzyme after reaction

unchanged & used again

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Enzyme structure

large polypeptides with tertiary or quaternary structure, globular with specific active site

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Induced fit

Once substrate binds to active site and during transition stage, enzyme changes slightly resulting in tighter binding

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Role of induced fit

enzyme induces bond weakening within molecules thus reducing activation energy needed

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Enzymatic reaction

1. attraction of substrate to enzyme (diff shapes)

2. conformational change reaction of substrate-enzyme complex

3. enzyme revers to original shape and products leave reaction

<p>1. attraction of substrate to enzyme (diff shapes)</p><p>2. conformational change reaction of substrate-enzyme complex</p><p>3. enzyme revers to original shape and products leave reaction</p>
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Active site structure

sequence of amino acids responsible for catalytic activity

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Activation energy

minimum energy that reacting particles should possess for a reaction to make products

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Collision theory

  1. particles must collide to react together

  2. need sufficient energy to break & form bonds

  3. orientation (opposite charge molecules)

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Exothermic or exergonic reation

product formation releases energy

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Endothermic or endergonic

product formation associated with energy absorption (usually heat)

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Causes of structural changes to active site

1. temperature

2. pH

3. Substrate concentration

4. Enzyme concentration

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Effect of temperature on collision theory

  • Low temp = slowly, collision low

  • High temp = rapid, collision high, denature

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Low Substrate concentration

  • more substrate than enzyme

  • low rate of reaction

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High substrate concentration

  • more collision chances

  • rate of enzymatic reaction rises gradually

  • increase halted when active sites occupied

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Graph structure of optimal temperature & pH

  • increases due to more collisions of heat

  • peak reached

  • drops due to denature of heat and pH

  • increase, peak and drop with pH

<ul><li><p>increases due to more collisions of heat</p></li><li><p>peak reached</p></li><li><p>drops due to denature of heat and pH</p></li><li><p>increase, peak and drop with pH</p></li></ul>
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Graph structure of substrate/enzyme concentration

  1. increases because more collisions between substrate and active site

  2. plateau phase because most active sites are occupied

<ol><li><p>increases because more collisions between substrate and active site</p></li><li><p>plateau phase because most active sites are occupied</p></li></ol>
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Immbolisation of enzyme

process of attaching enzyme to a material to restrict movement

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Permit of immboilisation of enzyme

  • not present in final product

  • doesn't restrict conc

  • avoid adverse effects to human consumption

  • higher conc of enzymes

  • faster rate of reaction

  • immediate separation from reaction mixture

  • recycled

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How to increase pH as dependent variable

  • increase rate of reaction!

  • increase enzyme conc

  • increase temp

  • longer time

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Value of V(velocity) at start of reaction

Minimum since active sites are free

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Amino acids

carbon center. monomers of proteins

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Cell theory

1. All living organisms are composed of one or more cells.

2. The cell is the basic unit of structure and organization in organisms

3. Cells arise from pre-existing cells.

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70

Louis Pasteur method & results

Heated broth with swan necks \n 1. Sealed & upright: no growth \n 2. Unsealed: microbial growth \n 3. Tilted: growth

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Louis Pasteur Conclusion

Air carries microbes but non-living conditions do not make living things

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Spontaneous generation

Living things arise from non-living aka abiogenesis

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Biogenesis

cells formed from pre-existing cells

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Miller Urey Method

Recreated early earth conditions:

  • atmosphere (low oxygen, high radiation, gasses)

  • heating of water vapor

  • electrical storm shocks

<p>Recreated early earth conditions:</p><ul><li><p>atmosphere (low oxygen, high radiation, gasses)</p></li><li><p>heating of water vapor</p></li><li><p>electrical storm shocks</p></li></ul>
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75

Miller Urey Conclusion

Solution found organic molecules including amino acids found in living organisms

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4 conditions for life to emerge & persist

1. Simple organic molecules (amino acids, fatty acids, carbohydrates)

2. Larger organic molecules must be assembled from simpler molecules (DNA, phospholipids)

3. Reproduction for replication

4. Biochemical reactions require set conditions therefore self-contained structures need membranes

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endosymbiotic theory

Mitochondria (likely anaerobes) & chloroplasts (likely cyanobacteria) were prokaryotes taken by larger prokaryotes

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evidence for endosymbiotic theory

In mitochondria & chloroplasts

  • double membrane

  • circular naked DNA like prokaryotes

  • DNA as single chromosomes

  • 70s ribosomes like prokaryotes

  • binary fission like prokaryotes

  • susceptible to some antibiotics

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How do living organisms control composition?

complex web of chemical reactions

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Metabolism

web of all enzyme

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Why is life carbon

based

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4 types of macromolecules

carbohydrates, lipids, proteins & nucleic acids

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Lipids

  • triglycerides, phospholipids, and steroids

  • carbon compounds made by living organisms

  • mostly or entirely hydrophobic

  • 2-3 hydrocarbon chains or quadruple ring structure (steroids)

  • stores energy for later use

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triglyceride

  • fatty acid tails are flexible

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fatty acids

  • carboxyl group: acidic and -COOH

  • unbranched hydrocarbon

  • type of lipid

  • 3 fatty acids form a triglyceride

<ul><li><p>carboxyl group: acidic and -COOH</p></li><li><p>unbranched hydrocarbon</p></li><li><p>type of lipid</p></li><li><p>3 fatty acids form a triglyceride</p></li></ul>
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Macromolecules

organic compound made of smaller molecules

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Role of macromolecules

build living cells & take part in biochemical reactions

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glycerides

  • lipids

  • fatty acids linked to glycerol by condensation reaction

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Composition of carbohydrates

carbon, hydrogen & oxygen

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Role of starch

energy storage in plants

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Color of iodine solution if starch present

blue

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Color of biuret test for proteins

purple

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Color of benedict solution for carbohydrates

orange or brick red

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Structure of Alpha Glucose (draw)

H top, OH down

<p>H top, OH down</p>
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Structure of Beta glucose (Draw)

OH top, H down

<p>OH top, H down</p>
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Anabolism

  • synthesis of complex molecules to simpler molecules

  • requires energy input

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Catabolism

  • breakdown of complex into simpler molecules

  • hydrolysis of macromolecules into monomers

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Hydrolysis reaction

breaking chemical bonds by adding water molecules

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Urea formula

CO(NH2)2

<p>CO(NH2)2</p>
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Use of urea

human body to excrete nitrogen because urea is non

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