Chapter 4-7 Biology Flashcards
Nucleic acid monomers
Nucleic acids are made up of nucleotides
DNA has deoxyribonucleotides
RNA has ribonucleotides
Nucleic acid polymers?
DNA and RNA are both nucleic acid polymers
DNA= deoxyribonucleic acid
RNA= ribonucleic acid
Primary structure of DNA
Linear sequence of nucleotides/nitrogenous bases (ATGC) linked together via phosphodiester bonds
Secondary structure of DNA
Double- helix, hydrogen bonding between the bases, antiparallel strands
Tertiary structure of DNA
Supercoils, wrapping around histones
What are all the bases of DNA and how do they pair?
Adenine - Thymine
Guanine - Cytosine
What are all the bases of RNA and how do they pair?
Adenine - Uracil
Guanine - Cytosine
Which bases are pyrimidines and which ones are purines? (Remember shorter name longer structure)
Pyrimidines: cytosine, uracil, and thymine
Purines: guanine, adenine
4 differences between DNA and RNA
- The sugar-phosphate backbone in DNA is deoxyribose and RNA’s sugar is ribose (Primary structure diff.)
- RNA has uracil instead of thymine (Primary structure diff.)
- RNA is single-stranded and DNA is double-stranded (Secondary structure), therefore making RNA less stable
- The OH group on ribose is much more reactive than the H in deoxyribose
Primary structure of RNA
Linear structure of bases, extending from a sugar-phosphate backbone
Secondary structure of RNA
Double helical stem and unpaired loop
Tertiary Structure of RNA
Pseudoknots and more complex, weird loops
Three components of nucleotides
- Phosphate group
- Five carbon sugar
- Nitrogenous base
Between RNA and DNA which has the sugar with a hydroxyl group (OH) on the 2’?
RNA has the OH, DNA just has an H (hence the DEOXY…)
The relation between amino acid and polypeptide is similar to the relationship between
a) phospholipid and plasma membrane
b) nucleotide and nucleic acid
c) glycogen and glucose
d) triglycerides and steroids
b
How do nucleotides polymerize to form nucleic acids? What bonds form between nucleotides?
Condensation reaction; phosphodiester bond, a covalent bond between the sugar of one nucleotide and the phosphate of a second
How is the double helix stabilized?
- Hydrogen bonding between the base pairs
- Hydrophobic interactions (what causes the DNA to twist)
- Van der Waals interactions (what forms base stacking)
Which bases pairs have three hydrogen bonds? (Hint: think about how which base pairs are have a faithful marriage when in DNA and RNA)
Guanine and Cytosine.
Adenine (the cheater) has two bonds with both thymine and uracil.
Which RNA structure will form spontaneously?
Secondary
In RNA’s secondary and tertiary structures, the bases participating in hydrogen bonding are ___.
antiparallel
Carbohydrate monomers
monosaccharides
Oligosaccharides = __ sugars
Few
Polysaccharides = __ sugars
Many
4 ways carbohydrates differ
- Aldose or ketone placement of the carbonyl group
- Number of carbon
- Different arrangement of hydroxyl groups in space
- Linear and alternative ring forms
What is the carbohydrate molecular formula?
(CH2O)n
n= # carbon hydrates
ranges 3=1000+
Where is the carbonyl group located on an aldose?
The end of a carbon chain
Where is the carbonyl on a ketose?
Within the carbon chain
___ can be used as a source of carbon atoms or energy. ___ must be converted to (first blank) first.
Glucose, Galactose, Glucose
Phosphodiester is between __’ phosphate group and __’ hydroxyl group
5, 3
N-terminus vs C-terminus
N has amino
C has carboxyl
Purines will always bind to ___
pyrimidines
Steps in DNA replication
- Strand separation (breaking of hydrogen bonds)
- Complementary base pairing
- Polymerization
True or False: RNA is more diverse in size and shape compared to DNA
True
What is the function of a ribozyme
To catalyze reactions (have active sites like proteins)
Carbohydrates would be considered
a) polar
b) nonpolar
c) hydrophobic
d) hydrophilic
a and d
5 types of carbohydrates
- Starch
- Cellulose
- Glycogen
- Chitin
- Peptidoglycan
OH placement on glucose and galactose
glucose: behind plane
galactose: above plane
The predominant form of glucose dissolved in an aqueous solution is __.
the ring configuration
Aldose and ketone are both __
carbonyls
Pentose is in ___.
DNA
What are two things you can look at to distinguish carbohydrates?
- # of carbon atoms
- OH orientation
Monosaccharides polymerize via ___ reaction and form ___ linkages
condensation, glycosidic
2 most common glycosidic linkages
- alpha 1-4
- beta 1-4
1 and 4 refers to the C-1 and c-4
A glycosidic linkage is analogous to __ in proteins and ___ in nucleic acids
Peptide, phosphodiester
5 types of polysaccharides
- Starch
- Glycogen
- Cellulose
- Chitin
- Peptidoglycan
Starch is energy storage in ___ cells. and has __ glucose monomers, forming an ___ helix
plant, alpha, alpha
Amylose has an alpha-_ glycosidic linkage and amylopectin has an alpha 1-_ glycosidic linkage. Which one has a branching structure?
4, 6, amylopectin
Glycogen is energy storage in __ and it’s stored in the __ and __.
animals, liver, muscle
Glycogen can be broken into __ monomers for energy and has a ___ alpha glucose polymer (1-6).
glucose, branched
Cellulose is a ___ polymer and has a __ 1-4 glycosidic linkage. It has __ bonds between adjacent parallel strands.
structural, beta, hydrogen
Cellulose is a major component of the __ __ in plant cells.
cell wall
True or false: Cellulose is not a linear molecule
False, it is linear and looks like a ladder (hydrogen bonds are the rungs)
Similar to cellulose, chitin is a ___ polymer.
structural
Chitin is a major component of the cell wall of __ and the exoskeleton for __ and __.
fungi, insects, crustaceans
Chitin has a beta __ glycosidic linkage and it has hydrogen bonds between ___ parallel strands.
1-4, adjacent
Peptidoglycan is found in __ cell walls.
bacterial
All of the structural carbohydrates have __ structures.
linear
Peptidoglycan has a __ 1-4 glycosidic linkage and ___ bonds between adjacent strands (make it a bit stronger).
beta, peptide
Glycosidic bonds form between what groups?
hydroxyl
Why can animals easily degrade starch, but not cellulose?
Animals can degrade alpha 1-4 but not beta 1-4
Cellulose, chitin, and peptidoglycan form short/long strands.
long
4 functions of carbohydrates
- Precursors for many different types of molecules
- Structural support
- Cell identity
- Storage of chemical energy
Two reasons why beta 1-4 glycosidic linkages do NOT hydrolyze easily
- Most organisms lack the enzymes to hydrolyze them
- Fibers exclude water, making hydrolysis difficult
2 structures important for cell identity function
- Glycoproteins- protein+carb
- Glycolipids- lipid+carb
What is cell-to-cell recognition?
When cells can identify themselves
Cell-cell signaling
communication b/w cells
C-O bonds are held tightly and have high/low potential energy.
C-H/C-C bonds are weaker and have high/low potential energy.
low, high
3 types of lipids
- Fats
- Steroids
- Phospholipids
All three types of lipids found in cells are insoluble in water because they all possess __
a) fatty acids
b) many ester linkages
c) lots of hydrocarbons
c
Why is a plasma membrane necessary?
- keeps all organelles inside the cell
- facilitates what goes in and out the cell
- important in chemical reactions
- creates different concentration gradients
What are key parts of lipid structure?
- Carbon containing compounds
- HYDROCARBONS
- Nonpolar C-C and C-H
VERY hydrophobic
Fatty acids are a hydrocarbon chain with around __ to __ carbon atoms and a ___ functional group.
14, 20, carboxyl
What are the two types of fatty acids, which one has the double bond?
- Unsaturated, has the double bond
- Saturated
What can the double bond create in unsaturated fatty acids?
Kinks, meaning unsaturated fatty acids can be polyunsaturated
Three S’s: Saturated, ___, and ___
single (bonds), solid (because long tails are stiff)
Which ones has the max amount of Hydrogens, unsaturated or saturated?
Saturated
Unsaturated bonds have long or short bonds?
short
Steroids have a bulky __ __ structure.
four-ring
How do steroids differ?
By functional groups attached to the C’s in the ring
Lipids always have a ___ and ___ section.
polar (head), nonpolar (tail)
Fats, or triglycerides, have three fatty acids linked to a ___. Fats are useful for storing ___.
glycerol, energy
Do fats or carbs store more energy? Why?
Fats, because they have high energy bonds (equal sharing, non covalent)
When a dehydration reaction takes place to form a triglyceride, what sort of linkage is formed? How many are in a triglyceride?
Ester linkage, three
An ester linkage forms between a hydroxyl group of a ___ and a carboxyl group of a ___ ___ ___.
glycerol, free fatty acid
Phospholipids are a glycerol linked to a ___ group and two ___ chains. They form cell membranes in ___ environment.
phosphate, hydrocarbon, aqueous
Bacteria and Eukarya have __ __ tails and Archaea have ___ tails
fatty acid, isoprenoid
What type of chemical interaction do phospholipid have with their environment?
a) only hydrophobic
b) amphipathic
c) covalent
d) only hydrophilic
b
Amphipathic is a quality ALL lipids share, meaning they have a hydrophilic ___ and hydrophobic ___.
head, tail
Parts of a lipid head
- glycerol
- phosphate (negative charge)
- charged polar group
Parts of a lipid tail
- nonpolar
- no hydrogen bonds
What does the lipid head and tail form together?
Phospholipid bilayer
Hormones and ligands are part of what lipid function?
Cell signaling
5 main lipid functions
- Store chemical energy
- Act as pigments that capture sunlight (chlorophyll)
- Serve as signals between cells
- Form waterproof coating on skin and cells
- Act as vitamins in cellular processes
Lipid bilayers show ___ permeability
selective
What passes through lipid bilayer the easiest?
Small, nonpolar molecules
ex: O2, CO2, N2
What passes the lipid bilayer from easiest to hardest?
- Small, non polar/uncharged
- Small, charged (ex:H2O)
- Large, uncharged, polar (ex: glucose)
- Small ions
4 factors that affect permeability
- Length of hydrocarbon tails
- Saturation state of hydrocarbon tails
- Presence of cholesterol
- Temperature
Permeability =
Fluidity
Which is MORE fluid, short or long tails?
Short, because there are less van der Waals and less packing
Which is LESS fluid, saturated or unsaturated?
Unsaturated, because the double bonds can lead to kinks
Does cholesterol reduce or increase membrane permeability?
Reduce, because it increase packing density
Fluidity increase as the temperature goes ___
up.
Diffusion or Osmosis
-spontaneous
-molecules and ions
-based on concentration gradient
-high to low concentration
Diffusion
What is the end goal of osmosis AND diffusion?
Equilibrium
After diffusion reaches equilibrium, will molecules still move around?
Yes, but there will be no more net movement
Is diffusion active or passive transport?
Passive, not energy required
What are the two conditions for osmosis to occur?
- there has to be a concentration gradient
- membrane only allows water to pass through
Hypertonic
Solution OUTSIDE concentration is HIGHER than concentration inside than the cell
Hypotonic
Solution OUTSIDE the cell is LOWER than concentration outside the cell.
For a hypertonic solution, water will move__ the cell, resulting in __ of the cell
out, shrinking
For a hypotonic solution, water will move __ the cell, resulting in __ of the cell
into, swelling/bursting
How does the cell change in an isotonic solution?
It doesn’t
Isotonic
Inside cell and solution concentration are equal, no net water movement
Integral membrane proteins, also known as ___ proteins, are proteins that span the ___ and have segments facing both interior and exterior surfaces.
transmembrane, membrane
___ membrane proteins bind to the membrane lipid without passing through.
Peripheral
True or False:
Peripheral membrane proteins are only found on the exterior of the cell.
False, they can be found on the exterior and the interior
Fluid mosaic model
A dynamic structure with proteins floating in or on the fluid lipid bilayer.
___ can be use to isolate proteins from membranes.
Detergents
Detergents are/are not water soluble, unlike other amphipathic molecules
are
What is the function of membrane proteins?
They assist in cell signaling and transport of substances
Receptors are ___ proteins.
signaling
3 types of integral proteins
- Channels
- Carrier
- Pump
Channel proteins help facilitate ___.
Diffusion
Ion channels form __ in the membrane allowing for ions to pass through the membrane.
Pores
Ion channels are involved in ___ and ___ diffusion, going ___ the concentration gradient.
passive, facilitated, with
____ gradient establishes both concentration gradient AND charge gradient.
Electrochemical gradient (key idea is CHARGE)
Gated channels regulate ___.
Movement
ex: voltage and ligand
How do gated channels open and close?
In response to a signal
-binding of a certain molecule
-change in voltage
Molecules that move down a concentration gradient and require transport proteins to cross a membrane use __ __.
facilitated diffusion
Carrier proteins move substances via ___ changes.
structural
(the whole protein changes shape)
Carrier proteins selectively pick up ___ on one side of the membrane and drop it on the other side.
solute
Passive transports moves __ the gradient, does/doesn’t need the input of energy, and includes channels or __.
with, doesn’t, carriers
Active Transport three A’s
Active
Against (gradient)
ATP
The Sodium-Potassium pump is ___ transport and uses __+/ __= ATPase.
active, sodium, potassium
Pumps are ___ the concentration gradient
against
Protein functions
- speed up reactions
- structures
- defense
Eukaryotes v.s Prokaryotes main difference
-Prokaryotes do NOT have a membrane-bound nucleus
Are the following eukaryotes or prokaryotes?
Eukarya
Archaea
Bacteria
Eukaryote, prokaryote, prokaryote
4 parts of a prokaryote
- At least one chromosome
- Protein-synthesizing ribosomes
- Phospholipid membrane
- Cytoplasm
Prokaryotes have chromosomes that are organized into a ___.
nucleoid
___ are circular, supercoiled DNA molecules.
Plasmids
Ribosomes manufacture ___ in a process known as translation.
proteins
Photosynthetic membranes are in ___, and they contain multiple membrane layers.
bacteria
What is the benefit of having organelles?
- separation of incompatible chemical reactions
- increases efficiency
Nucleus is surrounded by a _____ with pores and has a distinct region named, ___, which is where rRNA is synthesized
double membrane/nuclear envelope, nucleolus
Nucleus stores __
chromosomes
Nuclear lamina function
structural support
Ribosomes are either free in the ___ or attached to the ___
cytosol, ER
The ER is continuous with the ____ ____
nuclear envelope
3 main functions of rough ER
synthsized proteins that will be
- shipped to another organelle
- inserted into plasma membrane
- secreted to cell exterior
Smooth ER lacks ___ and is a reserve for ____ ions
ribosomes, Ca2+
The ___ ER is what synthesizes lipids/ breaks down poisonous lipids.
smooth
Golgi apparatus is a series of flat membrane sacs called ___. Has two sides, ___ and ___.
cisternae, cis and trans
Golgi apparatus processes, sorts, and ships ___ synthesized in the rough ER.
proteins
___ side of Golgi receives rough ER products and the ___ ships them out.
Cis, trans
Lysosomes contain around ___ different enzymes and have acid ___.
40, hydrolase
3 functions of lysosomes
- Recycling (in animal cells)
- Hydrolyzing macromolecules
- Acid hydrolases=digestive enzymes
Cell wall forms a protective ___.
exoskeleton
Which two structures of bacterial surfaces enable movement and attachment?
- flagella (long to propel)
- fimbrae (needles to attach)
Which structure is common to plant and animal cell?
mitochondria
Eukaryotes are about __X bigger than prokaryotes.
10
Ribosomes are not considered organelles because they lack a ___.
membrane
If the smooth ER breaks down proteins, would liver cells have more or less smooth ER.
more
What pH do lysosomes work best at?
around 5
Vacuole structure
- prominent
- found in plants, fungi, and other eukaryotes
Vacuoles can digest but their main function is to store:
1.
2.
3.
4.
- Water
- Ions
- Proteins
- Pigments or noxious compounds
Peroxisome structure
- globular organelles (all eukaryotes)
Peroxisomes are the site of what reactions?
Redox
___ is to recycle and degrade as ___ is to detox.
Lysosome, peroxisome
Why would a double membrane be useful in mitochondria?
For cellular respiration reactions
Chloroplasts have a lot a membranes (like mitochondria) for photosynthesis and they are called ___.
thylakoid
Endosymbiosis Theory
Mitochondria and chloroplasts were one free-living bacteria. Evidence is:
- they have their own DNA
- they have their own ribosomes
- they can self replicate
Thylakoids, DNA and ribosomes are all components found in ___.
chloroplasts
Cytoskeleton 3 structures
- Actin filaments/ microfilaments
- Intermediate filaments
- Microtubules
Cytoskeleton 4 functions
- system of protein fibers
- gives cell shape and stability
- transports materials within cell
- organizes organelles
3 organisms that have a cell wall
- plant
- algae
- fungi
Animal cells don’t have a cell wall, they have an ___ ___.
extracellular matrix
Things that are allow to pass the nuclear pore will have a ___.
tag/signal (coded in)
What can enter the nucleus?
Anything involved in DNA and RNA synthesis.
If one adds the nuclear localization signal to a cytosolic protein, what will happen?
Rather than going to the cytosol, it can enter the nucleus
What is the endomembrane system function?
Shuttle proteins to the right destinations in the cell
A protein lacking a signal sequence will likely reside in the ___.
cytoplasm
Parts of the Endomembrane System/Secretory Pathway
- Protein is made by ribosomes and is sent to
Rough ER - Enter the ER and protein is folded
- A vesicle buds off ER, fusing with the cis- side of Golgi
3 processes lysosomes go through for protein recycling
- Receptor-mediated endocytosis
- Phagocytosis
- Autophagy
Endocytosis is when materials ___ the cell and bind to ____, forming endocytic vesicles and developing into a ___.
enter, receptors, lysosome
Phagocytosis forms ___ , which fuses with lysosomes
phagosomes
Autophagy (same eating) has to with ___ organelles.
damaged
Many cell movements are based on ____ - ____ interactions.
actin-myosin
Actin is important in ____ and cytokinesis.
muscles
Nuclear lamina is made up of ____ ____.
intermediate filaments
Intermediate filaments help ___ the nucleus and anchor ____.
shape, chromosomes
____ serve as tracks for vesicle transport.
Microtubules
Flagella and cilia are made up of ___.
microtubules
Which is NOT a function of actin?
a) maintain cell shape
b) move chromosomes
c) move cells and organelles
d) divide animal cells in two
b, microtubules move chromosomes
NLS stands for:
nuclear localization signal
Structure =
Function
___ are highly organized and regulated
Cells
