Cell Biology Test One

What is a cell

smallest unit that has characteristics of life

7 Characteristics of life

1. Cellular organization

2. reproduces

3. metabolism

4. heredity

5. Responds to stimuli

6. Grow/develop

7. Adapt

Every cell has 3 things in common they areeeeee

• plasma membrane

• genetic information

• ability to produce protein

Prokaryotic cells

• smaller than eukaryotes

• many shapes

• can have external cell wall

• simple internal structure w/o membranes

• division is rapid - binary fission

• Like studio apartment - no separate rooms

• single cell

Eukaryotic cell

• 1000 X larger than prokaryotes

  • more complex

• can live as single entity or in a multicellular organism

• contain organelles which are membrane bound units

Nucleus

• Contains molecules of DNA (instructions for cell to make protein)

• surrounded by nuclear envelope

• Double membrane

Mitochondria

• muscles have a bunch of them

• inner and outer membrane

• generates chemical energy for the cell through cellular respiration

• Larger surface area in inner membrane (where proton gradient ocurs and it crosses membrane to generate atp occurs) so more ATP is generated

  • This is during oxidative phosphorylation

• contains its own DNA and ribosomes and can divide on its own (looks like binary fission)

• Mitochondria are from pre existing prokaryotic cells this is the endosymbiotic theory (but they lost the ability to be independent)

Ribosome

• No membrane which is why prokaryotes have it too

• Combo of RNA and protein that act to produce protein

• There are 2 kinds

  • Attached - in ER make protiens designed to leave the cell or delivered to other organelles

  • Free - produce proteins that act within the cytoplasm

Endoplasmic Reticulum

• Membrane channels involved in the production of materials

• Rough and smooth

Rough ER

has ribosomes and makes proteins

Smooth ER

Lacks ribosomes

makes lipids (like the plasma membrane)

detox chemicals ( converting lipid-soluble drugs and metabolic wastes into water-soluble compounds)

Golgi apparatus

• Close to the ER

• Set of membrane sacks

• Recieves information from the ER then modifies and dispatches materials to parts of the cell

• Similar to a post office - can add cellular adresses can replae and send out material

Lysosome

• Small membranous sacks w/ digestive enzymes that work at an acidic pH of 4/5

• Binds to macromolecules organelles or microbes to digest and recycle material

• It has sugar on the internal membrane to protect from the acidic pH

• garbage disposal

Proxysome

• cousin of the lysosome

• reactions that occur here use or generate hydrogen peroxide

• oxidative reaction that breaks down lipids and destroys toxic materials

Cytoskeleton

• intercellular proteins, mainteance of cell shapes and structure

Actin

• thinnest

• cell shape, muscle contraction, and motility, including cell movement and the formation of extensions like pseudopods

Intermediate filaments

• middle size

• provide mechanical strength, resist tension, and help anchor organelles and cell junctions

Microtubules

• hollow tubes

• largest

• cellular transport

• intracellular "highways" for organelle transport, serve as structural components, and are involved in chromosome movement during cell division

Chloroplast

• plants

• photosyntheis

• double membrane with increased innter SA

• Own DNA and ribosomes and can divide on its own

Vesicles

• transportation, packaging system

Endomembrane system

• subset of organelles connectd to produce transport and modify protein

• almsot every membrane in organelle is similar (phospholipid)

Transition from DNA to protein for ribosomes on ER

• DNA replication and RNA synthesis using transcription

• Protein synthesis through translation

• Proteins produced go to lumen inside of the ER

• proteins folded and modified inside of the lumen

• Material moved from the ER by vessicle to the golgi body through exoctytosis

• goes from donor compartment to vessicle and into the recipient compartment through fusion

2 faces of the golgi aparatus

• cis faces adjacent to the ER (in)

• trans is facing towards the plasma membrane (out)

Materials destined for the outside surface of the cell are released by…

exocytosis

How to describe differences in cells

• look at the ratios of the organelles

sugars

polysaccarides and oligosaccharides

fatty acids

fats and membrane lipids

amino acids

proteins

nucleotides

nucleic acids

monomers make up…

polymers

Condensation reactions

• polymeric chains grow through condensation process

• h2o released as a product

• A-H + OH-B —> A-B + H2O

• Energetically unfavourable cuz energy is needed to make bonds

Hydrolysis

• energetically favorable

• Water as a reactant

• A-B + H20 —> A-H + OH-B

saturated fats

• maximum number of hydrogens

• all single bonds

• all straight tails so they pack tightly

• Solid at room temp

• tighter pack

unsaturated fats

• they have double bonds

• lack some hydrogens between carbons

• bent tails dont stack neatly

• more liquid

• looser pack

chemistry behind life

• based on carbon compounds

• Aqueous environments

• complex

• polymeric molecules invovled

• tightly regulated

energy stored within…

bond

how are two strands of DNA held together

hydrogen bond

4 major groups of small organic mlcls

• sugars

• fatty acids

• amino acids

• nucleotides

Structure of sugars

• simple sugars - monosaccharides

• general formula is (CH2O)n

• Covalent linkage between monosaccharides produces larger carbohydrates (condensation)

• oligisaccharides/poly…

Carbohydrate functions

• Energy source

• energy storage - starch

• Mechanical support - cellulose of cell wall

• Cell surface molecules - recognition

Fatty Acids structure

• molecules with 2 distinct regions - amphipathic + and -

• differ due to amount of carbon and hydrogen in tails + double bonds/single

• unsat/sat

Fatty Acid function

• food reserve

• component of phospholipid

Nucleotides structure

• Sugar, phosphate and a base

• building blocks for nucleic acids - links btw phophates and sugars

nucleotides function

• can carry chemical energy in short term - release a phosphate from tri to di

96 % of elements in living organism

C H N O

Main difference between DNA and RNA

RNA has 2 hydroxyl groups on sugar and DNA has one

Structure of amino acid

• all of them hjave a amino group, carboxyl group and a central atom

• R group changes from amino groups ( side chain)

How are amino acids linked

• peptide bond links carboxyl group of one with the amino group of the next

How many amino acids and how many proteins in human body

20 amino acids and 30 - 40 000 proteins

What charge do amino acids have

the can be positive negative uncharged polar and nonpolar

Are peptide chains flexible?

Yes they can have rotation around peptide bonds, they are not a linear molecule

n terminus

this is the begginging group , the first amin group of the first amino acid

c terminus

this is the end group, the carboxyl group of the last amino acid

bonds in amino acids

• noncovalent bonds involve atoms in the backbone (C=O groups (carbonyl oxygens and N–H groups (amide hydrogens)) these can form hydrogen bonds with each other making secondary structures

• bonds between side chains also occur which help w/ shape of proteins

How does folding occur

• it is influenced by distribution of polar and nonpolar amino acids

• In aqueous environments, like the cytoplasm:

  • Hydrophobic amino acids avoid water → cluster inside the protein.

  • Hydrophilic amino acids interact with water → on the outside of the protein.

• In membranes (hydrophobic environment, phospholipid tails):

  • Hydrophobic amino acids are on the outside, interacting with the fatty acid tails.

  • Hydrophilic amino acids are tucked on the inside (for stability or forming channels).

what happens when you change the sequence of the amino acids

you change the protein produced and change the shape

How many shapes does a protein fold into

each protein normally folds into one stable shape

hydrogen bonds stabilize shape

Where do bonds occur that help a protein fold

between backbone - backbone

side chain - side chain

backbone - side chain

Sickle cell anemial

• Normal hemoglobin has a polar amino acid at a certain spot in the β-globin chain (one of 4 peptide chains that make up the protein since its a tetramer) a mutation changes this to a nonpolar amino acid

• Since it is hydrophobic it sticks to other hydrophobic patches on nearby hemoglobin molecules.

• This causes hemoglobin proteins to aggregate (clump together).

• Aggregation distorts the shape of red blood cells into a long, rigid “sickle” shape.

• Sickle-shaped cells are less flexible, can block blood vessels, and don’t carry oxygen as efficiently → leading to the disease symptoms.

Protein Fucntions

1. Enzyme - every chemical process is driven by an enzyme (catalyst)

2. Structure- maintain structure like a microtubule

3. Transport - motor protein and channels

4. Motor - Muscles made of actin/ myosin , sliding filaments

5. Storage

6. Signals- alert other cell that its doing smth

7. Receptor - surface of cell to receive info

8. Regulatory - control which/ how something is used

9. Special purpose - like gfp and glow

Primary Structure

The amino acid sequence- this is the first step in determining the shape of a protein

amino acid chain linked by covalent peptide bonds

Secondary Structures

regular folding patterns formed by hydrogen bonding in the polypeptide backbone (the N-H and C=O not the R groups)

2 Primary shapes of secondary structure

• alpha helices α

• Beta sheets and strands β

Helices structure

• cylindrical twisting spiral w/ side chains projecting out

• Right handed and left handed

• Majority of biological molecules are right handed

• usually shape thats part of a larger molecule

How does a alpha helix get made

when a hydrogen bond forms between the c=o and the N-H every 4th amino acid

Where are helices seen

spanning cell membranes

help insert protein in membrane cuz other protein can be connected to stick out

they make mores to get material into and out bunch of these in a circle

aquaporon

alpha helices form together in a circle to make an opening with hydrophobic on outside and hydrophilic on the inside for wahter to transport through these channels

coiled coil

multiple α-helices twisted around each other, held together by hydrophobic interactions, often for structural stability or protein-protein interaction.

they twist around each other and its very stable

karotin is an example

Beta strand

• other type of secondary structure

• when hydrogen bonds form between chains running side by side

• rigid structures at the core of protein

How do beta strands turn into sheets

• hydrogen bonds between beta strands

• can be parralel or antiparralel

• for antiparralel c terminus is close to n terminus and for parallel they are on opposide side

• have a looping domain that links the strands together in the sheet

• like a fan with paper

• they are rigid structures cuz of hydrogen bonds

Polarity of a beta sheet

• the side chains of each strand alternate above and below the plane of the sheet so polar and nonpolar are on opposite sides

• can have chemistry on top completely different to on the bottom

β-barrel

• The β-strands form a β-sheet, which then curves and connects to make a barre

• In membrane proteins, like porins in bacteria, mitochondria, or chloroplasts.

• Forms pores or channels for selective transport across membranes.

Secondary breakers

amino acids that interrupt α-helices or β-sheets, often causing kinks or flexible regions.

say when the secondary structure is over

Motif

patterns of secondary structures for example a beta sheet or helices

Tertiary structure

the overall total 3d shape of the protein

can include a domain

Domain

part of a protein that can fold seperetaly and usually has a function w/ that part of a protein. protein can have 2 functions

Binding Domain

type of protein domain that is specifically structured to recognize and attach to another molecule (ligand)

Quaternary structure

all polypeptide chains and their interaction

the diff proteins fom chains with each otjher

more than 2 proteins togther

forms a complex

4 proteins - a tetromer

Advantages of quaternary structures

• repeating subunits require less genetic info

• assembly and disassembly controlled

• Errors detected during assembly

Types of shapes formed by protein subunits

• at the quaternary level

• Filaments / Fibrous proteins

  • provide structural support (hair)

• Globular

  • Often enzymes, transport proteins, or regulatory proteins

• Sheets/tubes/shell

  • Can form β-sheets that roll into barrels (β-barrels) or tubular structures.

Capsid

protective protein coat of a virus, made of repeating subunits

What are disulfide bonds and what role do they play in proteins

Stabilizes tertiary or quaternary structure

Helps protein maintain 3D shape under stress

Chaperone proteins

guide the folding of a polypeptide chain

not part of the final structure

has a chamber cap at the top

Antibody model of binding

• protein function depends on binding with specificity

• item that binds a protein is called a ligand

• portion of protein that associates with ligand is the binding site

• depends upon weak non covalent bonds

• change the y ends and change the specificity of the binding site

• y ends are looped domains that change in size lettings different ligands bind to it

Lysozymeenzyme model

• enzyme and substrate complementary in shape

• enzyme funciton begins at binding. material that binds to an enzyme is a substrate

Enzyme characteristics

• increases the rate of a reaction (but cant make a reaction occur of it normally wouldnt)

• substrates orient differently, electrons rearrange to favor a reaction, substrates are strained

• enzymes end in -ase

• lysozome severs peptidoglycan in bacterial cell walls

Free energy

• G

• extractable energy content in a molecule

• reactions that occur spontaneously result in a decrease of G

• High g are peptide chains

• low g is the individual amino acids

Transitional state

• the positional change

• for example sugar neeeds to reach a transitional state and the amount of E needed to bend it is the activation energy

how lysozyme works

• this enzyme works to decrease the activation energy (transitional) needed by changing the shape of the mlcl

• First it enters the active site

• then it bends the bonds within the substrate

• then the amino acids interact with the carbons in the backbone

• then the bonds between sugar subunits are broken

Control of proteins

• maze of metabolic procceses that occur in the cell and uses enzymes

• each pathway requires many different enzymes for each step and relies on many different substrates

• enzyme production location and activity an be regulated

Ways to alter the rate of enzyme conversion

1. negative regulation: prevents an enzyme from acting

2. Positive regulation:one item stimulates activity of an enzyme

both these occur with the changing of shape

Feedback inhibition

• type of negative feedback - an early acting enzyme is altered by a product later in the pathway

• Prevents the cell from making too much of a product

allosteric regulation

• Feedback inhibition often uses allosteric inhibition

• The end product of a pathway binds to an allosteric site on an early enzyme

• regulatory mlcl has diff shape than normal substrate and binds on alternate site (allosteric site)

Reversible phosphorylation

• A way to regulate proteins

• Addition of a negatively charged phosphate group

• adding this negative charge makes a + charge attracted so the shape changes and function change

How does reversible phosphorylation work

• protein kinase adds a phosphate

• protein phosphatase removes a phosphate

1. reversible phosphorylation is triggered by cell signals

2. adds a phosphate to serine theorine or tyrosine

some are turned on with the additon of the phosphate or off and vise versa with the removal too

GTP binding proteins

• these act as switches

• uses a larger molecule as a switch instead of ATP

• Guanine nucleotide normally bound to the protein it is active if GTP is bound and inactive if GDP is bound

• GTP to GDP through hydrolysis

Motor Protein Regulation

• conformational change requires hydrolysis of ATP to ADP

• unidirectional movement - cant go backwards so it has another motor protein that goes the other way

• On the microtubule

• Movement thorugh ATP binding and removal

Nucleotide Hydrolysis

• responsible for movement and function of protein machines

• can use it where there are multiple parts - more than one protein

• Add something that changes the shape as usual

• Protein machines only assembled when required

How do you know how important a process is

• how many different ways to be able to do it

• More backup and regulation it will take

Covalent modification

A chemical group is covalently attached to a protein, altering its properties