UMKC Cell Biology 202 Exam 1

What elements make up 0.9% of the cell?

Na, Mg, P, S, Cl, K, and Ca

What element is the "backbone of life"

Carbon

What are the four main classes of macromolecules?

1. Polysaccharides (Carbohydrates)

2. Nucleic Acids

3. Proteins

4. Lipids

What are structural types of polysaccharides?

branched and linear

How many structure types do nucleic acids have?

two

How many structures do proteins have?

1

How many structures do polysaccharides have?

2

What is a polymer?

chain of same or similar molecules

what is an oligopeptide?

a relatively small peptide, up to about twenty residues, di-tri-and tetrapeptide cell to cell signals

ex: substance P

What is a polypeptide?

long chain of amino acids, 30 or more amino acids

Proteins synthesized in the ____ specifically the ____

cytoplasm, ribosome

Protein synthesized must be _____ when newly synthesized and must be _______ to be functional

unfolded, folded

How many traits do proteins have?

3

what are the protein traits?

Trait 1. all proteins must adopt at least two stable 3-D shapes or conformations

Trait 2. all proteins must bind to at least one molecular target

Trait 3. all proteins perform at least one cellular function

Every amino acid has a ___ and ___ ____

Every amino acid also has a _________ and a ______

N and C terminus

Also has a core alpha carbon and a side group (R2)

Amino acids are NOT _____

symmetrical

What elements make up 99% of the cell?

C,N,H,O

Protein backbone, like all biopolymers has a _______

polarity

Which terminus is on the left? Which is on the right?

N terminus on the left, C on the right

N->->->->->->->-> C

what are the 5 classes of amino acids based on chemistry of side group? Give examples of each.

Nonpolar side group- Methionine

Aromatic side group- Phenylalanine

Polar side group- Threonine

Pos charged side group- Lysine

Neg charged side group- Glutamate

What are the 4 levels of protein structure?

primary, secondary, tertiary, quaternary

primary structure of protein

the amino acid sequence of the polypeptide chain ex: mythyonine, lysine, threonine

secondary structures of protein

Alpha helix= coil shape

Beta pleated sheet= angled plane

Random= not specified shape

Protein function comes down to two things:

1. Which side chains are next to other side chains

2. Overall shape of protein and folding of protein

What holds proteins together?

Van der Waals forces and hydrogen bonds

Tertiary structure of proteins and examples

Two ways:

3A(local)- arrangements of 2nd structure pieces that come together ex: helix-loop-helix motif

3B(overall)- how shape of protein looks ex: hairpin turn (2 head-to-tail beta sheets) motif

2 types of overall tertiary structure proteins

1. globular: not necessarily spheres

2. fibrous- long rod-shaped proteins. Made from parallel cross-linked polypeptide chains

Types of globular and fibrous proteins

Globular: catalase, myoglobin, porin, lysozyme, aspartate transcarbamoylase

Fibrous: Collagen

quaternary structure of protein

The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.

have 2 light chains held together with 2 heavy chains that form a Y shape

5 quaternary structure protein assemblies

1. dimer

2. helix

3. ring

4. spherical

5. tubular

5 types of chemical bonds fold and stabilize 2, 3, and 4 structure

Covalent:

Disulfide = strong and stable, rare

Noncovalent:

Hydrogen- ex: alpha helix and beta sheet

Electrostatic- neutralize charged residues keeping interior hydrophobic

Hydrophobic- occur in the interior protein leaving polar/ionic residues at surface to interact with water

Van der Waals forces- only act at short distances

in-vitro

Cellular components isolated outside of the cell, usually within a glass, observable within a test tube

How protein folding in-vitro works

By adding harsh chemicals like urea and mercaptoethanol, the protein is denatured, the bonds break and the protein unfolds. Remove the harsh chemicals and the protein will return to its original state, or as close as it can get.

in-vivo

occurring in the cell

Protein folding in-vivo

2 types of chaperone proteins

1st type- help make sure bond is efficient and guide it to how its supposed to be folded

2nd type- prevent protein misfolding by isolating the protein from other proteins and folding it there.

To be functional proteins must be able to be ___________ and ________, which are called ________

Activated and inactivated, called conformations

4 mechanisms for controlling protein activity

chemical modification of amino acids

binding of small molecules to allosteric sites

binding of regulatory proteins

protein degradation

chemical modification of amino acids

in a protein, can cause switch between states

7 types of covalent modifications of amino acids

Disulfide bonds

Ubiquitin

Sugars

Lipids

Phosphate groups

Methyl groups

Acetyl groups

OR

CYS, LYS, ASN, SER, THR, TYR, ARG

_________ is important for initial folding of proteins

Glycosilation

binding of small molecules to allosteric sites

can switch states

binding of regulatory proteins to a protein

can cause switch between states

protein degradation

controls how much protein in a cell, how much activity

Disulfide bonds example

CYS

ubitiquin example

LYS

Sugars example

Glycosylation (ASN,SER,THR)

Lipids example

Farbesyl, CYS

Phosphate groups example

(TYR, SER, THR)

Methyl groups example

(LYS,ARG)

Acetyl example

LYS

How many nucleic acids are there

2, DNA and RNA

What direction does dsDNA run?

5'3

What is the backbone of DNA?

sugar-phosphate backbone

ssDNA is ____

Polar, antiparallel

dsDNA is ______

Nonpolar and symmetrical

A=T has how many hydrogen bonds

2

G=C has how many hydrogen bonds

3

DNA helicase

An enzyme that unwinds the DNA double helix during DNA replication

Uses ATP hydrolysis to break the h bonds of double helix along short region to separate strands

RNA

single-stranded nucleic acid that contains the sugar ribose, uracil substituted for thymine, has more single stranded regions than DNA

RNA is _____ and ____ than DNA

More reactive and unstable

DNA/Chromosomes

They contain genes along their length; these genes are hereditary information and serve as instructions on how to build proteins.

Gene

A segment of DNA on a chromosome that codes for a specific trait, contains exons and introns

Intergenic DNA

noncoding DNA found between genes

Ex: centeimeres, telomeres, replication origin, repetitive DNA

What is a germ cell?

sex cell (egg and sperm)

DNA can be replicated or ______ and ______

Transcribed (nucleus) into RNA and translated (cytoplasm) to make a protein

mechanism 2: small molecules bind to allosteric sites

binding regulates the activity of enzymes, costs a lot of energy

allosteric site

A site on an enzyme other than the active site, to which a specific substance binds, thereby changing the shape and activity of the enzyme.

mechanism 3: binding regulatory proteins

binding of alpha i protein to Adenylate cyclase (AC) inhibites AC activity

binding of alpha s protein to AC activates AC activity

mechanism 4: protein expression levels

includes how much protein is in the cell

uses protein degradation to regulate protein stability and recycle amino acid subunits for new proteins

3 degradation mechanisms

1. proteasomes (nucleus and cytosol)

2. lysosomes (plasma membrane and Golgi apparatus)

3. Soluble proteases (extracellular matrix, ECM)

Proteasome

A giant protein complex that recognizes and destroys proteins tagged for elimination by the small protein ubiquitin.

Made of core and caps, targeted proteins are unfolded by cap and degraded in the core

Enzymes

Proteins that speed up chemical reactions

motor proteins

generate force to move cells or cellular components within cells

response proteins

detect signals inside or outside of cell, translate signals to activate cellular changes

structural proteins

provide scaffolds for the cell or for structures within the scaffold

transport proteins

move material in and out and within the cell

proteins work in _____

complexes

how are proteins studied

What do you need in order to go from 2nd level dna packaging to 3rd level

H1 linker histone

In the Avery mcloyd McCarthy experiment they obtained a sample that contained no DNA by adding what

Deoxyribonucleus

What makes single stranded DNA polar?

The sugars run 5'3 direction and the carbon is on the outside so it is asymmetrical and polar

Griffith's discovery of bacterial transformation

Smooth mixes with rough and even after heat killed smooth still viable so mouse dies

Conclusion of McCarthy experiment

Compartment of S strain transforms R strain in DNA thus virulence information during transformation is carried by DNA

5 levels of DNA packaging lvl 1

1st: double stranded DNA

5 levels DNA Packaging lvl 2

2nd: double stranded DNA wrapped twice around each core nucleosome

Core nucleosome 2x (H2A, H2B, H3, H4) + DNA

Structure formed by long DNA molecule wrapped into multiple nucleosome sort of like beads on string called 10 nm filament

DNA packaging 5 levels level 3

using moderate extraction (detergent+ hi salt) core nucleosome + H1

H1 linker histone used

Nucleosomes coiled together

Transmission Electron Microscope (TEM)

A microscope that uses an electron beam to study the internal structure of thinly sectioned specimens.

DNA packaging five levels: level 4

30 nm filament attached to protein scaffold in long loops

The basic form of most chromatin for most euchromatin during interphase

Scaffold attachment regions (SARS) are linked to the scaffold my MARS

Alternative extraction (dextran sulfate polysaccharide) histone removed scaffold stays

5 levels of protein packaging: 5A

Heterochromatin are fully condensed and super packed throughout the entirety cell cycle

Heterochromatin shows up as super dark stains

Genome= heterochromatin + euchromatin

Euchromatin is less dense and stains lighter

5 levels of protein packaging level 5B

Chromatin loops condensed into short blobs during mitosis and form fully condensed chromosomes

Very mild extraction- chromosomes released from cell with most protein still associates

Mars proteins only bind to ____ protein and cause _____

SAR proteins and cause loops to form

scanning electron microscope

-An electron microscope used to study the fine details of cell surfaces

-NOT measuring how much is getting thru but secondary electrons where atoms incorporates an electron and emits electron chemicals

- can tell you composition of material on amount of backscattering

-only SEM uses 2ndary electrons

extraction

process of removing proteins from sample

Alternative structures

Enzyme uses ATP to remove DNA

Alternative packaging: histone modification

Justine's are globular except for n-terminal "histone tails" which project out from the core.

Chemical modification of histone tails changes affinity of nucleosomes for other proteins

nuclear pores

holes in the nuclear envelope that allow materials to pass in and out of the nucleus

The fluorescent in situ hybridization (FISH)

probes are applied to intact cells and observed microscopically for the presence and location of

semiconservative replication

Method of DNA replication in which parental strands separate, act as templates, and produce molecules of DNA with one parental DNA strand and one new DNA strand

This one is right

dispersive replication

replication results in both original and new DNA dispersed among the two daughter strands

conservative replication

A disproved model of DNA synthesis suggesting that one-half of the daughter DNA molecules should have both strands composed of newly polymerized nucleotides.