bmb 210 exam 1

what are the 4 basic types of macromolecules

• nucleic acid

• protein

• carbohydrate

• lipid

polymers are built from

monomers

what do you have to have to build a polymer?

energy

what must happen to monomers before they can join with other monomers

they must be activated

what energy is used to activate monomers

ATP or other equivalent nucleoside triphosphate (CTP, GTP, or UTP)

why can macromolecules self assemble?

• they can do this because the information needed to form complex 3d shapes and supramolecular structures is inherently encoded in sequence of monomers it contains

• they are at their lowest energy state in the more complex folded form (thermodynamics drives this)

name the 4 non covalent interactions that drive polymer folding

• hydrophobic interactions

• hydrogen bonds

• ionic bonds

• Van Der Walls forces onomersm

what 2 things will activate a monomer?

must be attached to a carrier group

energy from ATP or equivalent

when 2 monomers join what leaves via a condensation rxn?

• a carrier molecule

• water

polymers have distinct ends! what are 3 examples of this?

DNA/RNA: 5’-3’

Proteins: N terminus → C terminus

Carbs: non-reducing → reducing end

name the 7 types of proteins

1) enzymes

2) transport protein | ex: hemoglobin

3) nutrient / storage protein

4) contractile / motile protein

5) structural protein

6) defense proteins | ex: antibody

7) regulatory protein

draw out the basic structure of an amino acid

yes

which type of amino acid is mostly found in nature

L-amino acid (means the amino group is on the left)

what 4 amino acids do we need to know? draw and name!

• glycine

• alanine

• serine

• cysteine

what kind of bonds/ interactions do proteins have

peptide bonds (all proteins), disulfide bonds (some)

non-covalent interactions

• hydrophobic interactions

• van Der walls forces

• hydrogen bonding

• ionic bonds

what kind of function group are peptide bonds?

amide

how many atoms are actually involved in a peptide bond? draw one! note what relationship the carbonyl oxygen and amino hydrogen have

4! okay

the oxygen and hydrogen are trans to each other (on opposite sides)

characteristics of a peptide bond

planar, has resonance, trans positioning of oxygen and hydrogen

native conformation

the most stable three dimensional structure for that particular sequence of amino acids

broadly speaking, proteins can be divided into what two categories

fibrous and globular

fibrous protein, definition and examples

• long and strand like molecules

• secondary structure is much more important than tertiary interactions in determining shape

examples:

• silk (B sheet)

• keratin (alpha helix)

• collagen (triple helix)

globular proteins

• compact structure, secondary structures folded on one another to give globular shape due to irregularly structured regions (random coils)

• most proteins are globular proteins

describe primary structure

• amino acid sequence and gives location of disulfide bonds (they aren’t formed until tertiary structure though)

describe secondary structure and give examples

local folding of polypeptide backbone, held together by hydrogen bonds

examples:

• alpha helix

• beta pleated sheet

what is an alpha helix, give characteristics

a type of secondary structure that is a right handed spiral

• has 3.6 amino acids per turn

• every 4th aa lines up

• series of linked planes (peptide bonds)

• H bonds run the length of the helix

• R-groups stick out

when and who published papers about alpha helixes and beta pleated sheets

both were published in 1951

The paper on alpha helixes was published by Pauling, Corey and Branson

The paper of beta pleated sheets was published by Pauling and Corey only

describe a beta pleated sheet

type of secondary structure that involves 2 peptide backbones that are connected by a loop

• formed from stretched out segments of polypeptide called beta strands

• can be parallel or antiparallel

• peptide-carbon backbone follows a zig-zag pattern

• H bonds occur between the 2 peptide backbones

what is protein “motif” and give 3 examples and draw them

motif: small recurring patterns of secondary stricture

a: B-A-B motif

b: hairpin loop motif

c: helix turn helix motif

describe tertiary structure and what is it held together by? what can it include? what can it be determined by?

• overall/final 3-d shape of a single protein chain

• thermodynamically the most stable (low energy)

• disulfide bonds, non-covalent interactions

• can include non proteins (prosthetic groups or co-enzymes)(helpers)

• can be determined by x ray crystallography and cryo-electron microscopy

2 types of tertiary structures (protein types)? which type are most proteins?

fibrous and globular

most are globular

what is a protein domain?

structurally distinct parts of protein chain

a single protein can be divided into different domains

describe quaternary structure and

• highest level of protein organization

• occurs when two or more protein subunits assemble into a single cohesive functional complex

ex: hemoglobin (has 4 subunits)

which 3 fields’ developments influenced the creation of and Molecular Biology (or cell biology)

cytology, biochemistry, and genetics

what field did Robert Hooke contribute to? what did he do and when did he do it

Robert Hooke contributed to: cytology

• published “Micrographia” in 1665 where he used the word “cell” to describe what he saw

what field did Leeuwenhoek contribute to? what did he do and when did he do it

Leeuwenhoek contributed to cytology.

• In the 1670’s he coined the term “animalcules”

• made his own microscopes

what field did Robert Brown contribute to? what did he do and when did he do it

He contributed to cytology

• In 1831, he described nuclei

What did Schleiden and Schwann propose? when? What were the 2 tenants? contributed to which field?

Schleiden and Schwann proposed the cell theory in 1838 contributing to cytology

2 tenants:

• 1) all organisms contain 1 or more cells

• 2) the cell is the basic unit of structure for all organisms

what field did Virchow contribute to? when?

he contributed to cytology by adding a 3rd tenant to the cell theory in 1855, addressing spontaneous generation

• 3) all cells arise from pre-existing cells

what contribution did Louis Pasteur make to cytology? when?

• in 1859, he disproved spontaneous generation through the swan neck flask experiment

limitations to microscopy

• sometimes you may need to stain things, "fix” them with chemicals

• limited resolution

resolution def

ability to distinguish between 2 objects

best resolution we have using light microscopy is 200nm

with this, you can see big features of plant and animal cells but molecules are too small

what field did Wohler contribute to? when?

Wohler contributed to biochemistry

• published rxn of urea in 1828

• this showed biological processes were chemical reactions

how did Louis Pasteur contribute to biochemistry? when?

In 1857, he proved yeast to be responsible for fermentation (links the cell to a chemical reaction)

what field did Buchner contribute to? how and when?

in 1897, Buchner broke yeast cells apart and found that fermentation still took place due to a chemical entity.. enzymes!

when was the golden age of biochemistry

20’s-60’s

what field did embden, Meyerhof, and parnes contribute to? how and when?

in 1940, they explained glycolysis

contributed to biochemistry field

what field di sir Hans Krebs contribute to? how and when?

in 1937, he discovered TCA cycle or “Krebs Cycle”

contributed to biochemistry field

what field did Melvin Calvin contribute to? how and when?

in 1950, he explained the “Calvin Cycle” (second stage of photosynthesis)hat fiew

what field did Mendel contribute to? how and when?

in 1866, Mendel publishes work on “hereditary factors” (genes)

this publication is regarded as the basis for modern genetics

what field did Fleming contribute to? how and when?

In 1878, he published his work on chromosomes and mitosis but did not link his work to mendels “hereditary factors”

contributed to genetic field

what field did roux and weissman contribute to? how and when?

in 1883, they suggested the role of chromosomes

• contributed to genetics

what field did Sutton contribute to? how and when?

In 1902, Sutton linked Fleming’s chromosomes to Mendel’s “hereditary factors”

what field did Thomas Hunt Morgan contribute to? how and when?

in 1910, Thomas hunt morganatic introduced drosophila as model organism and explained sex-linked traits

what field did Meischer contribute to? how and when?

meischer contributed to genetics, more specifically answering the question is protein or dna the genetic material

in 1869 he isolated a material from nucleus and called it “nuclein” = dna

what field did Avery, Macleod and McCarty contribute to? how and when?

they contributed to genetics, more specifically answering the question is protein or dna the genetic material

in 1944, they said DNA is the genetic materials through an experiment of bacterial transformations

what field did Hershey and chase contribute to? how and when?

they contributed to genetics, more specifically answering the question is protein or dna the genetic material

in 1952, they showed definitive proof that DNA was genetic material using radioactively labeled bacteriophages

what field did Watson and crick contribute to?

genetics

in 1953, they proposed the structure of DNA

monosaccharide def

polyhydroxy aldehydes or ketones

the two types of monosaccharides? what makes them different

aldoses: aldehyde at carbon 1 (terminal aldehyde)

ketoses: ketone at carbon 2 (usually)

monosaccharides are named by…

number of carbons

for ex:

monosaccharide with 3 carbons = triose

with 4 carbons = tetrose

with 5 carbons = pentose

draw the alpha form of glucose (Haworth structure)

okay

draw the beta form of glucose (Haworth structure)

okay

draw alpha form of mannose (remember which carbon is different from glucose)

okay. carbon 2 is different

draw beta form of mannose (remember which carbon is different from glucose)

okay. carbon 2 is diff.

draw alpha form of galactose. remember what carbon is different

okay. carbon 4 is different

draw beta form of galactose. remember what carbon is different

okay

draw ribose.

okay

draw deoxyribose

okay

sugars are in either D or L configuration based on which side the last hydroxyl group is on. we will only look at:

D configuration where the last hydroxyl group is on the right

what is a Fischer projection

linear structure (drawn in hydrogens)

anomers def

the alpha and beta forms of a monosaccharide

anomeric carbon

the carbonyl carbon which is not chiral in the linear form but becomes chiral in the ring form

its the carbonyl carbon that gets attached by the OH

having functional groups in which position on a chair configuration is the most thermodynamically favorable

equatorial.

B-D-glucose has this and its the most thermodynamically favorable aldohexose

if a monosaccharide is alpha that means..

the hydroxyl on the 1st carbon will be pointing down

if a monosaccharide is beta that means..

the hydroxyl on the 1st carbon will be pointing up

the deoxyribose sugar is exactly like ribose except..

the O on the 2nd carbon is not there

fructose is..

the only ketohexose we will have to recognize

has two CH2OH groups on 1st and 4th carbon

polysaccharides function can be either storage or structure, or even cellular communication. give examples of polysaccharides that do these functions

structural:

• cellulose (plant)

• chitin (fungi)

storage of energy:

• starch (plants)

• glycogen (animals)

cellular communications:

• glycoproteins/glycolipids

what type of monosaccharide is glucose

an aldohexose

what is this sugar? note differences from ribose

fructose

what are glycosidic bonds

links 2 carbs (monosaccharides) together

what happens when a glycosidic bond is made versus what happens when it is destroyed

• when it is made, you lose H2O (condensation)

• when it is broken, you gain H2O (hydrolysis)

difference between reducing and non reducing end of a carb

reducing end: has a “free” anomeric carbon

• drawn on the right by convention

non-reducing: “locked” anomeric carbon

• involved in a. glycosidic linkage

• drawn on the left by convention

what is maltose made of? what kind of linkage occurs between components?

two glucose monosaccharides linked together makes maltose

glucose (a) (1→4) glucose

what is lactose made of? what kind of linkage occurs between components?

one galactose and one glucose

galactose B (1→4) glucose

what is sucrose made of? what kind of linkage occurs between components?

glucose and fructose

glucose (a) (1→2) fructose

which carbon on the fructose is the anomeric?

the one bonded to two oxygens

two types of polysaccharides

• storage

• structure

name storage polysaccharides

• starch (plants) (amylose and amylopectin)

• glycogen (animals)

name structural glycans

peptidoglycan

extracellular matrix glycans (glycosaminoglycans (GAG) and proteoglycans)

chitin

cellulose

name the two forms of starch in plants

amylose

amylopectin

which type of starch in plants is more abundant

amylopectin is the more present starch in plants

• 70-90% of starch is amylopectin

how many monomers does it take for amylopectin to branch? what is the linkage for the branch?

every 12-25 monomers, amylopectin will branch

linkage for the branch is (a) 1→6 branch links)

what is the lesser abundant starch in plants? how many times does it branch?

the lesser abundant starch in plants is amylose

10-30% of starches are these

amylose is unbranched

what is the main storage polysaccharide in animals? does it branch? if so how often? what is the linkage?

glycogen

branches every 8-12 monomers

(a) 1→6 branch linkages (similar to amylopectin)

major similarity between glycogen and amylopectin

both contain glucose in (a) 1→ 4 links with occasional (a) 1→6 branches

draw an (a) 1→6 branch point that could be found in amylopectin or glycogen

y

starches and glyocgen are both

insoluble granules

name 2 types of glycans we learned about

• peptidoglycan

• extracellular matrix glycans

what are two types of extracellular matrix glycans

• glycosaminoglycans (GAGs)

• proteoglycans